ARIDFLO Scientific Report

Environmental Flow Requirements of

Arid Zone Rivers with Particular Reference to the Lake Eyre Drainage

Basin

Authors: Justin F. Costelloe1,2, Peter J. Hudson2, Janet C. Pritchard3,2,

Jim T. Puckridge2, Julian R.W. Reid4,2 (listed alphabetically)

With significant contributions by: Vanessa Bailey5, Roger Jaensch7, Joan Powling8, Russell Shiel2

(listed alphabetically)

Preferred report citation: Costelloe J.F., Hudson P.J., Pritchard J.C., Puckridge J.T., Reid J.R.W. (2004). ARIDFLO Scientific Report: Environmental Flow Requirements of Arid Zone Rivers with Particular Reference to the Lake Eyre Drainage Basin. School of Earth and Environmental Sciences, University of Adelaide, Adelaide. Final Report to South Australian Department of Water, Land and Biodiversity Conservation and Commonwealth Department of Environment and Heritage.

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ARIDFLO

Preferred report citation:

Costelloe1,2 J.F., Hudson2 P.J., Pritchard3,2 J.C., Puckridge2 J.T., Reid4,2 J.R.W.

(2004).

ARIDFLO Scientific Report: Environmental Flow Requirements of Arid Zone Rivers with Particular Reference to the Lake Eyre Drainage Basin. Final Report to South Australian Department of Water, Land and Biodiversity Conservation and Commonwealth Department of Environment and Heritage. School of Earth and Environmental Sciences, University of Adelaide, Adelaide.

With significant contributions by: Vanessa Bailey5, Roger Jaensch7, Joan Powling8, Russell Shiel2

Further contributions by:

Phil Bourke5, Scotte Wedderburn6, Melissa White9

Institutional Affiliations of Authors and Contributors

1Department of Civil and Environmental Engineering, University of Melbourne 2School of Earth and Environmental Sciences, University of Adelaide 3Department of Botany and Zoology, Australian National University, Canberra 4CSIRO Sustainable Ecosystems, Canberra

5Environmental Protection Agency, Queensland 6Department of Water, Land and Biodiversity Conservation, South Australia 7Wetlands International Oceania, c/- Queensland Herbarium, Brisbane 8Department of Microbiology and Immunology, University of Melbourne 9Applied Ecology Research Group, University of Canberra

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Acknowledgments ARIDFLO was a collaborative project between the University of Adelaide, the University of Melbourne, CSIRO Division of Sustainable Ecosystems, the CRC for Freshwater Ecology, the CRC for Catchment Hydrology, the South Australian Department of Water, Land and Biodiversity Conservation, the Queensland Environmental Protection Agency/Parks and Wildlife Service and the Queensland Department of Natural Resources and Mines. The project has been funded through the Natural Heritage Trust as part of the Environmental Flows Initiative of Environment Australia. The success of the ARIDFLO project could not have been achieved without the enthusiasm, support, help and advice of a large number of people. In particular the contribution to data collection under difficult field conditions and the positive experiences shared with the army of field volunteers will leave many warm memories for the project scientists. Special mention is also made of the level of involvement and enthusiasm of the community without whose local knowledge, generous help and advice, ARIDFLO scientists would have missed important areas to sample, would not have gained as many essential insights into the ecology and hydrology of Lake Eyre Basin rivers and would have got lost on more than one occasion. The authors would like to acknowledge the assistance during the ARIDFLO project of the following people. Community Members Thanks to landholders assistance with access & information for survey planning: QLD: Frank, Joyce, Mary, Neil & Glen Rogers “Toobrack”, James & Susie Milson “Bogewong”, Bob & Linda Young “Brighton Downs”, Wattie & Chrissie Campbell “Verdon Valley”, Kirrendirri Indigenous group; SA: Tony & Patsie Williams, Paul Williams “Mt Barry” & “Nilpinna”, Normi Sims “The Peake”, Andrew & Donna Clarke “Allandale”, Digby Giles “Wintinna”, Peter & Danielle Weston “Clifton Hills”, David & Jane Morton “Pandie Pandie”, David & Nell Brook “Alton Downs”, Graham & Maree Morton, “Innamincka”; and, additionally to the foregoing for aerial surveys: Garth Tully “Cluny”, Sharon Oldfield and John Germain “Cowarie”, Mary Oldfield “Mugerannie”, Darryl & Sharon Bell “Dulkaninna”, John & Jasaleen Fergusson “Durham Downs”, Derek & Maxine Trapp “Durrie”, Mike Brazel “Gidgealpa”, Jon Cobb & Michelle Reay “Glengyle”, Craig Lasker, Nicki Smith, Ian Holstead “Morney Plains” & “Mooraberree”, Rob McAuliffe and the Darleys “Mt Leonard”, Gary & Margie Overton “Mulka”, Peter Hill “Nappa Merrie”, Rodney Betts “Orientos”, Ted & Dale Brown “Naryilco”, George & Bill Scott “Tanbar”, John & Helen Rickertts “South Galway”, Sandy Kidd “Mayfield”, Bruce Scott “Moothandella”, Bob Morrish “Springfield”, Geoff & Bev Morton “Roseberth”, Greg Campbell (CEO, S. Kidman Co.), Jim Crombie of Birdsville.

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Scientific Advice Assoc. Prof. Andrew Boulton, Dr Holger Maeier, Dr Megan Lewis, Prof. Tom McMahon and Dr David Roshier provided critical advice and encouragement as members of the Peer Review Panel. Dr Fran Sheldon played an instrumental role in designing the study, particularly macroinvertebrate aspects. Mr Ross Cunningham and Drs Keith Walker, Richard Kingsford, Stephen Morton, Sue Briggs, Mike Austin and Nick Nicholls are thanked for their expert advice when needed. Professors Peter Cullen, Stuart Bunn and Peter Davies provided valuable insights into river function. Ms Mel White provided a brief report on turtle ecology, with supervisory assistance from Dr Arthur Georges. The University of Adelaide, School of Earth and Environmental Sciences (Environmental Biology) Staff Russ Baudinette, Bob Hill, Gail Edwards, Piers Brissendon, Annie Richards, Tricia Catford, Julie Francis, David Ladd, and Marilyn Saxon are thanked for their excellent administrative and other support. Vladamir Tsymbal, Simon Westergaard, Adrienne Frears, Michael Hammer, Ben Goode, Kirrily Blaylock, Renee Fielke, Nick Whiterod, Rachael Skinner, Richard Saunders and Rudi Regel are thanked for their many careful hours of fish and macroinvertebrate sorting and identification work. Ditto to Michelle Hall and Mel White for faultless bird data entry. The University of Melbourne Rodger Grayson and Rodger Young for tireless efforts in setting up hydrological monitoring equipment and field assistance; Rodger Grayson, Tom McMahon and Rob Argent for intellectual input to hydrological modelling and data analyses; Geoff Duke, Tony Lowe and Barry Wilson for preparation of equipment for field trips; Jacqui Wise for administrative support. South Australian Department of Environment and Heritage Staff Christine Crafter, Senior Ranger at Innamincka Regional Reserve, for much local information, access approvals, resupplies and generous field assistance. Peter Canty for permits. Geoff Axford (and Santos Ltd) for helicopter flying time. South Australian Department of Water, Land and Biodiversity Conservation Staff Michael Good for project management, field assistance and report production. Scotte Wedderburn for assistance with preparation of spreadsheets for analysis and graphics. Commonwealth Department for Environment and HeritageStaff Gayle Stewart for project management and field assistance. Queensland Government Staff Lochern NP – Graeme and Helen Cross Diamantina NP - Alex Whitehead & Natalie Eves QPWS Mt Isa – boat loaned for QLD surveys NR&M Rockhampton - boat loaned for QLD survey

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Aerial Waterbird Survey Pilots Robin Young (SANPWS), and Alan (Cracker) McDonald of Charleville for safe and intrepid flying. Assistance with ground truthing in QLD reaches: Phil Bourke (QPWS), Jason Chavasse (NR&M); also Bruce Wilson, Arnon Accad, Rosemary Niehus & Troy Honeman, all of the Queensland Herbarium, Qld EPA, provided RPJ with assistance related to the waterbird studies. Field Team Members All volunteers are thanked for their enthusiasm, dedication and good humour. We would especially like to thank the volunteers who returned for more adventures over several trips; Graeme ‘GT’ Tomlinson, Peter ‘Leopard’ Richards, Melissa ‘Queen of the Desert’ Castleman, Alison ‘Cookies’ Dedman, Rodger ‘Cyclone’ Grayson, Gayle ‘Keeping an eye on us’ Stewart, Russ ‘mixed grill’ Shiel, Brian ‘Fairy Shrimp’ Timms, David ‘Rosh’ Roshier. A list of participants involved in the field surveys is included below: Trip 1 - April 2000 SA: Jim Puckridge, Julian Reid, Peter Hudson, Justin Costelloe, Michael Good, Janet Pritchard, Rodger Grayson, Rodger Young, David Roshier, Heather McGuiness, Roger Jaensch, Russ Shiel, Graeme Tomlinson, Frank Mangeruca, Ali Ben Kahn, Alison Dedman, Kirrily Blaylock, Matthew Ward, Melissa Castleman, QLD: Vanessa Bailey, Phil Bourke, Chris Mitchell, Alun Hoggett. Trip 2 - August 2000 SA: Jim Puckridge, Julian Reid, Peter Hudson, Justin Costelloe, Graeme Tomlinson, Janet Pritchard, Erika Calder, Melissa Castleman, David Ladd, Peter Richards, James Van Daele, David Woodgate, Michael Good. QLD: Vanessa Bailey, Phil Bourke, Chris Mitchell, Pascal Seyer, Nicolas Arnaldi Martin, Peter Bullen, Maree Mostert, John Targett, Billi-Jo Harbour. Trip 3 - November 2000 SA: Jim Puckridge, Julian Reid, Peter Hudson, Justin Costelloe, Graeme Tomlinson, Alison Dedman, Brian Timms, Lunette Puckridge, Lys Muirhead, Manfred Meidert, Maxie Ashton, Peter Richards, Philippa Kneebone, Rodger Grayson, Alison Dedman. QLD: Vanessa Bailey, Phil Bourke, Chris Mitchell, Ruth Anderson, John Targett, Jason Chavasse, Peter Bullen, Ruth Anderson. Trip 4 - April 2001 SA: Julian Reid, Peter Hudson, Janet Pritchard, Anna Brooks, Brian Johnston, Dave Roshier, David Wilson, Gayle Stewart, Graeme Tomlinson, Heather Atkin, Krista Chin, Melissa Castleman, Michelle Hall, Scott Poulton. QLD: Vanessa Bailey, Phil Bourke, Justin Costelloe, Brian Timms, Todd Kelly, Mike Chuk. Trip 5 - November 2001 SA: Julian Reid, Peter Hudson, Janet Pritchard, Justin Costelloe, Graham Blair, Gayle Stewart, Graeme Tomlinson, Jarrod Eaton, John Wischusen, JulieAnne Taylor, Lydia Cetin, Sophia Dimitriadis, Ulrike Bedziecha. QLD: Vanessa Bailey, Mike Chuk, Ruth Anderson, Nora Brandli, Dave Akers, Kath Brennan, Peter Bullen, Craig Magnussen, Phil Bourke, Leanne Bowen, Maree Mostert, Bill Haddrill. Trip 6 - April 2002 SA: Julian Reid, Peter Hudson, Janet Pritchard, Justin Costelloe, Alison Dedman, Brydie Hill, Graeme Tomlinson, Graham Blair, Joan Powling, Karina Mercer, Mark Walter, Maxie

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Ashton, Meredith Smith, Michael Hammer, Peter Richards, Rodger Grayson, Russ Shiel, Sally Gartelmann. QLD: Vanessa Bailey, Phil Bourke, Leanne Bowen, Maria Peter, Ian Hoggett, Helen & Graeme Cross, Don Cook, Rod Hobson, John Augusteyn. Trip 7 - February 2003 SA: Julian Reid, Peter Hudson, Janet Pritchard, Justin Costelloe, Gayle Stewart, Graeme Tomlinson, Glen Scholz, Jason van Laarhoven, Kirsten Meredith, Mark Walter, Mel White, Melinda Brouwer, Nicole Cranston, Pascal Geraghty, Susan Watkins, Vanessa Gorecki. QLD: Vanessa Bailey, Phil Bourke, Sam Pegg, Julia Harris, Claire Harris, Jess Walters, Shannon Schloss, Alun Hoggett, Dave Akers, Joslin Eatts, Mark Dancey. Publicans and Roadhouse Proprietors For advice and putting up with a thirsty mob of scruffy scientists descending upon their establishments with flat tyres and broken items needing fixing at short notice and doing it all with good humour: John and Genevieve Hammond, Mungerannie Roadhouse; Kym Fort, Jo Laurie and Theo of Birdsville Hotel & Store; Ruth and Ian Doyle, Birdsville Caravan Park; Linney and Adam Plate, Pink Roadhouse, Oodnadatta; Des, Dylan, Dave, Anne, Scott and Barbie at Innamincka; Ian and Marilyn Simpson, Western Star Hotel, Windorah; Marree Post Office & General Store. Also thanks to the Constabulary at Marree and Oodnadatta for advice and assistance.

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Table of Contents

Table of Contents....................................................................................................................................7

Appendices (separate volume on CD) .................................................................................................12

Table of Figures ....................................................................................................................................13

Table of Tables .....................................................................................................................................18

Summary...............................................................................................................................................24

Chapter 1 Introduction .................................................................................................................57

1.1 Aims and objectives.............................................................................................................57

1.2 Approaches..........................................................................................................................58

1.3 Scope...................................................................................................................................59 1.3.1 Spatial .........................................................................................................................59 1.3.2 Temporal .....................................................................................................................61 1.3.3 Biotic ...........................................................................................................................62 1.3.4 Hydrologic and geomorphic ........................................................................................62

1.4 Previous work in the Lake Eyre Basin .................................................................................63 1.4.1 Hydrological ................................................................................................................63 1.4.2 Biological.....................................................................................................................66

1.5 Similar projects outside the LEB..........................................................................................68

1.6 Background on the LEB.......................................................................................................68 1.6.1 Hydrology ....................................................................................................................68 1.6.2 Aquatic Biology of the LEB .........................................................................................70

1.7 Key Research Questions and Hypotheses..........................................................................76 1.7.1 Hydrological Hypotheses ............................................................................................76 1.7.2 Biological Hypotheses.................................................................................................77

Chapter 2 Methods ......................................................................................................................90

2.1 Introduction and Overall Approach ......................................................................................90

2.2 Field Sampling Program and Design...................................................................................90 2.2.1 Spatial extent ..............................................................................................................90 2.2.2 Temporal extent ..........................................................................................................95 2.2.3 Biotic assemblage data collected................................................................................96

2.3 Hydrology - Field Data Collection ........................................................................................98 2.3.1 Water level and flow data............................................................................................99 2.3.2 Geomorphological data.............................................................................................101 2.3.3 Water quality data .....................................................................................................101 2.3.4 Spatial mapping of flood patterns using satellite images..........................................101

2.4 Hydrology - Development of Hydrological Models ............................................................110 2.4.1 Model requirements and extents...............................................................................110 2.4.2 Model Shell and Inputs .............................................................................................112 2.4.3 Neales Model Structure ............................................................................................114 2.4.4 Model structure – other reaches ...............................................................................115 2.4.5 Model Calibration ......................................................................................................120

2.5 Hydrology - Derivation of Hydrological Parameters ..........................................................121

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2.5.1 Hydrological Parameter Types..................................................................................121 2.5.2 Event Parameters .....................................................................................................122 2.5.3 Regime Parameters ..................................................................................................127 2.5.4 Categorical Parameters ............................................................................................128

2.6 Algae..................................................................................................................................129 2.6.1 Field Sampling ..........................................................................................................129 2.6.2 Laboratory Analysis...................................................................................................129

2.7 Zooplankton .......................................................................................................................130 2.7.1 Field sampling ...........................................................................................................130 2.7.2 Laboratory methods ..................................................................................................131

2.8 Macroinvertebrates ............................................................................................................133 2.8.1 Taxonomy .................................................................................................................133 2.8.2 Selection of sampling sites within waterbodies.........................................................134 2.8.3 Sampling methodology .............................................................................................135 2.8.4 Sample processing and data preparation .................................................................136 2.8.5 Calculation of biological measures ...........................................................................136

2.9 Fish ....................................................................................................................................142 2.9.1 Introduction ...............................................................................................................142 2.9.2 Taxonomy .................................................................................................................143 2.9.3 Selection of sampling sites within waterbodies.........................................................143 2.9.4 Sampling methods ....................................................................................................143 2.9.5 Gear selectivity..........................................................................................................148 2.9.6 Habitat assessment...................................................................................................149 2.9.7 Data entry and verification ........................................................................................150 2.9.8 Calculation of biological measures ...........................................................................150

2.10 Biology – Waterbirds..........................................................................................................151 2.10.1 Field Methods, Ground Surveys ...............................................................................152 2.10.2 Field Methods, Aerial Surveys ..................................................................................157

2.11 Biology – Vegetation..........................................................................................................162

2.12 Hydrology – Biology Modelling ..........................................................................................163 2.12.1 Approaches ...............................................................................................................163 2.12.2 Appropriateness of Methodologies ...........................................................................164 2.12.3 Univariate Modelling..................................................................................................164 2.12.4 Multivariate Analysis .................................................................................................166 2.12.5 Neural Networks........................................................................................................168 2.12.6 Interrelationships and redundancy analysis of hydrological parameters ..................172

Chapter 3 Hydrological Results .................................................................................................175

3.1 Introduction ........................................................................................................................175

3.2 Waterhole Loss Processes................................................................................................177 3.2.1 Introduction ...............................................................................................................177 3.2.2 Water Level Data ......................................................................................................180 3.2.3 Shallow Groundwater Observations .........................................................................181 3.2.4 Results and Discussion of Waterhole Loss Rates ....................................................181 3.2.5 Conclusions from waterbody loss rates ....................................................................185

3.3 Waterhole Morphology.......................................................................................................186 3.3.1 Geomorphological Measures ....................................................................................186 3.3.2 Waterbody Morphology - Riparian Vegetation Patterns ...........................................191

3.4 Surface Water Salinity Variations ......................................................................................193 3.4.1 Spatial Patterns.........................................................................................................193 3.4.2 Temporal Patterns of Salinity....................................................................................200 3.4.3 Discussion on Salinity Processes .............................................................................204

3.5 Upper Diamantina Reach - Hydrology...............................................................................204 3.5.1 Hydrological Summary..............................................................................................204

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3.5.2 Waterbody Characteristics........................................................................................206 3.5.3 Recent Flood Events.................................................................................................206 3.5.4 Model Inputs and Calibration ....................................................................................207

3.6 Lower Diamantina Reach – Hydrology ..............................................................................211 3.6.1 Hydrological Summary..............................................................................................211 3.6.2 Flow Paths ................................................................................................................212 3.6.3 Waterbody Characteristics........................................................................................214 3.6.4 Recent Flood Events.................................................................................................215 3.6.5 Model Inputs and Calibration ....................................................................................216 3.6.6 Model Performance...................................................................................................217 3.6.7 Flood Extents ............................................................................................................218 3.6.8 Other Features ..........................................................................................................221

3.7 Upper Cooper Reach – Hydrology ....................................................................................221 3.7.1 Hydrological Summary..............................................................................................221 3.7.2 Waterbody Characteristics........................................................................................223 3.7.3 Recent Flood Events.................................................................................................224 3.7.4 Model Inputs and Calibration ....................................................................................225 3.7.5 Flood Extents ............................................................................................................228

3.8 Lower Cooper Reach - Hydrology .....................................................................................229 3.8.1 Hydrological Summary..............................................................................................229 3.8.2 Geomorphology.........................................................................................................229 3.8.3 Recent Flood Events.................................................................................................231 3.8.4 Model Inputs and Calibration ....................................................................................232 3.8.5 Flood Extents ............................................................................................................235

3.9 Neales Reach – Hydrology ................................................................................................238 3.9.1 Hydrological Summary..............................................................................................238 3.9.2 Waterbody Characteristics........................................................................................238 3.9.3 Recent Flood Events.................................................................................................239 3.9.4 Model Inputs and Calibration ....................................................................................240 3.9.5 Model Results ...........................................................................................................241 3.9.6 Flood Extents ............................................................................................................245 3.9.7 Model Summary ........................................................................................................245

3.10 Comparison between reach models ..................................................................................246 3.10.1 Modelling Arid Zone Floodplain Rivers .....................................................................246 3.10.2 Influence of channel and floodplain land types.........................................................248 3.10.3 Comparison of upper reach model parameters ........................................................250 3.10.4 Conclusion ................................................................................................................251

3.11 Transmission Loss and Flow Timing Analysis...................................................................252 3.11.1 Methodology..............................................................................................................252 3.11.2 Transmission Losses ................................................................................................253 3.11.3 Flow Timing...............................................................................................................255 3.11.4 Antecedent Conditions..............................................................................................258 3.11.5 Model Performance in Simulating Transmission Losses..........................................259

Chapter 4 General Biological Results........................................................................................260

4.1 Introduction ........................................................................................................................260

4.2 Algae..................................................................................................................................260 4.2.1 Summary of taxa collected........................................................................................260 4.2.2 Systematics/Functional Groups ................................................................................262 4.2.3 Potential Biases in Sampling ....................................................................................262 4.2.4 Taxon Richness ........................................................................................................266 4.2.5 Rank Abundance.......................................................................................................268 4.2.6 Community Composition...........................................................................................271 4.2.7 Hypotheses ...............................................................................................................283 4.2.8 Summary...................................................................................................................284

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4.3 Zooplankton and Littoral Microfauna .................................................................................285 4.3.1 Summary of taxa collected........................................................................................285 4.3.2 Systematics/Functional Groups ................................................................................288 4.3.3 Potential Biases in Sampling ....................................................................................289 4.3.4 Taxon Richness ........................................................................................................289 4.3.5 Zooplankton Abundance ...........................................................................................293 4.3.6 Community Composition...........................................................................................296 4.3.7 Hypotheses ...............................................................................................................309 4.3.8 Summary...................................................................................................................309

4.4 Macroinvertebrates ............................................................................................................310 4.4.1 Summary of taxa caught ...........................................................................................310 4.4.2 Taxonomic/Functional Groups ..................................................................................310 4.4.3 Potential Biases in Sampling ....................................................................................311 4.4.4 Taxon Richness ........................................................................................................312 4.4.5 MacroinvertebrateTaxon Abundance........................................................................323 4.4.6 Community Composition...........................................................................................325 4.4.7 Hypotheses ...............................................................................................................342 4.4.8 Summary...................................................................................................................343

4.5 Fish ....................................................................................................................................344 4.5.1 Overview and Summary of Major Findings...............................................................344 4.5.2 Summary of Species Caught ....................................................................................352 4.5.3 Potential Biases in Fish Catch Data..........................................................................368 4.5.4 Species Richness......................................................................................................384 4.5.5 Species Abundance ..................................................................................................404 4.5.6 Fish Disease Outbreaks and Fish Kills Associated with Flooding ............................425 4.5.7 Hypotheses ...............................................................................................................430

4.6 Ground Waterbird Survey Results.....................................................................................432 4.6.1 Summary of Species and Breeding ..........................................................................432 4.6.2 Trends in Functional Feeding Group Richness and Abundance ..............................446 4.6.3 Species Richness......................................................................................................453 4.6.4 Assemblage Abundance ...........................................................................................456 4.6.5 Assemblage Composition .........................................................................................459 4.6.6 Hypotheses ...............................................................................................................470 4.6.7 Summary...................................................................................................................471

4.7 Aerial Waterbird Survey Results........................................................................................472 4.7.1 Raw Counts and Estimates.......................................................................................473 4.7.2 Calibration with Ground Surveys ..............................................................................480 4.7.3 Estimates of Population Sizes in the Channel Country, 2000-2003 .........................483 4.7.4 Breeding Results and Trends ...................................................................................491 4.7.5 Hypotheses ...............................................................................................................493

4.8 Vegetation..........................................................................................................................493 4.8.1 Summary of Species and Ordination ........................................................................493

4.9 Turtles in Arid Australia......................................................................................................496

Chapter 5 Analytical and Modelling Results ..............................................................................498

5.1 Summary............................................................................................................................498

5.2 Introduction ........................................................................................................................502

5.3 Artificial Neural Network Modelling....................................................................................504

5.4 PCA Analysis of Hydrological Variables ............................................................................508 5.4.1 Introduction ...............................................................................................................508 5.4.2 Event 1 PCA variables ..............................................................................................511 5.4.3 Event 2 PCA variables ..............................................................................................513 5.4.4 Regime PCA Variables .............................................................................................519

5.5 Modelling and Analytical Results by Biotic Group .............................................................521

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5.5.1 Algae .........................................................................................................................521 5.5.2 Zooplankton ..............................................................................................................528 5.5.3 Macroinvertebrates ...................................................................................................540 5.5.4 Fish ...........................................................................................................................570 5.5.5 Waterbirds.................................................................................................................583 5.5.6 Hypotheses ...............................................................................................................596

5.6 Inter-biota modelling results...............................................................................................599 5.6.1 Introduction to inter-biota modelling..........................................................................599 5.6.2 Methods ....................................................................................................................600 5.6.3 Simple Mantel results................................................................................................602 5.6.4 Partial Mantel results.................................................................................................607

5.7 Discussion of modelling results and identification of the principal environmental drivers of LEB river ecosystems .....................................................................................................................619

5.7.1 Statistical considerations when interpreting the modelling results ...........................619 5.7.2 Identification of the major environmental drivers of LEB river ecosystems ..............621 5.7.3 Inter-biota relationships.............................................................................................638 5.7.4 Timescale of response of different biotic groups to environmental drivers...............640 5.7.5 Timeframe over which extreme hydrological events continue to influence biotic groups ..................................................................................................................................642

Chapter 6 Interpretation and Discussion ...................................................................................644

6.1 Summary............................................................................................................................644 6.1.1 Sampling program design and limitations to prediction ............................................644 6.1.2 Observed biological patterns over the 2000-2003 sampling period .........................645 6.1.3 Environmental (Abiotic) Drivers ................................................................................645 6.1.4 Biotic Drivers .............................................................................................................649 6.1.5 Suppression of Exotic Fish Species..........................................................................652

6.2 Introduction ........................................................................................................................654 6.2.1 Survey Design...........................................................................................................654 6.2.2 Data Structure ...........................................................................................................655

6.3 Limitations to Prediction.....................................................................................................655 6.3.1 Variability...................................................................................................................656

6.4 Modelled Biological Parameters and Assemblages ..........................................................657

6.5 Observed Biological Patterns ............................................................................................658 6.5.1 Overall Patterns ........................................................................................................658 6.5.2 Flood Patterns...........................................................................................................663 6.5.3 Drought Patterns .......................................................................................................665

6.6 Environmental (Abiotic) Drivers .........................................................................................667 6.6.1 Season ......................................................................................................................667 6.6.2 Hydrology – the variable overprint. ...........................................................................670 6.6.3 Geomorphology.........................................................................................................677 6.6.4 Salinity.......................................................................................................................678

6.7 Biotic Drivers......................................................................................................................684 6.7.1 Inter-biota relationships.............................................................................................684 6.7.2 Role of algae in primary production ..........................................................................688 6.7.3 Predation...................................................................................................................690 6.7.4 Dispersal ...................................................................................................................694 6.7.5 Disconnection............................................................................................................695

6.8 Suppression of Exotic Fish Species ..................................................................................696 6.8.1 Introduction ...............................................................................................................696 6.8.2 Exotic versus native fish species abundance patterns .............................................696 6.8.3 Discussion of controls on exotic fish abundance ......................................................699

6.9 Suggested Areas of Further Research ..............................................................................700 6.9.1 Algae .........................................................................................................................701

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6.9.2 Zooplankton ..............................................................................................................702 6.9.3 Macroinvertebrates ...................................................................................................702 6.9.4 Fish ...........................................................................................................................703 6.9.5 Waterbirds.................................................................................................................705 6.9.6 Hydrology ..................................................................................................................706 6.9.7 Modelling...................................................................................................................708

6.10 Graphical Conceptual Models ................................................................................................709

Chapter 7 Monitoring and River Health Assessment.................................................................727

7.1 Introduction ........................................................................................................................727

7.2 Monitoring – General Discussion.......................................................................................727 7.2.1 Basis for monitoring ..................................................................................................727 7.2.2 Monitoring objectives ................................................................................................731 7.2.3 Biotic assemblages that could be monitored ............................................................731 7.2.4 Rationale for the approach to monitoring..................................................................745 7.2.5 Issues........................................................................................................................745 7.2.6 Key Sites to Monitor ..................................................................................................747 7.2.7 Statistical considerations ..........................................................................................747

7.3 Hydrological Monitoring .....................................................................................................750

7.4 Preliminary Assessment of LEB River Health using an Index of Biotic Integrity ...............754 7.4.1 Summary...................................................................................................................754 7.4.2 Introduction ...............................................................................................................758 7.4.3 Methods ....................................................................................................................768 7.4.4 Results ......................................................................................................................770

7.5 Fish Kill Monitoring Network ..............................................................................................794

7.6 Draft Waterbird Monitoring Protocols ................................................................................795

7.7 ARIDFLO Recommendations ............................................................................................796

Chapter 8 References................................................................................................................799

Appendices (separate volume on CD)

Appendix 1 Field data sheets Appendix 2 Auxillary biological data Appendix 3 ARIDFLO publications Appendix 4 Peer review reports Appendix 5 Statisticians advice

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Table of Figures

Figure 1-1 ARIDFLO Sampling Sites ....................................................................................................60 Figure 1-2. Annual discharges for Lower Diamantina and Lower Cooper reaches ..............................61 Figure 2-1. Map of sampled waterbodies in all reaches surveyed by ARIDFLO project. .....................92 Figure 2-2. Flow paths for different sized flood events - downstream half of the Diamantina Lakes to

Birdsville reach of the Diamantina River ....................................................................................105 Figure 2-3. Lower Diamantina reach incorporating Goyder Lagoon- NOAA-AVHRR greyscale NDVI

image ..........................................................................................................................................106 Figure 2-4. Illustration of flow patterns in lower Diamantina for different peak discharge thresholds 109 Figure 2-5. Location of modelled reaches within the LEB. .................................................................112 Figure 2-6. Conceptual model for rainfall-runoff processes in Neales catchment ..............................114 Figure 2-7. Flow paths for different sized flood events shown in Landsat MSS images of the lower half

of the Diamantina Lakes to Birdsville reach of the Diamantina River. .......................................116 Figure 2-8. Flow diagram of conceptual water balance model for each grid cell................................119 Figure 2-9. Curve of function relating grid cell storage to the percentage of cell inundated. .............119 Figure 2-10. Hydrograph showing “flow envelope” for flow events in Lower Diamantina reach during

2000............................................................................................................................................122 Figure 2-11. A - Frey net [37 μm-mesh], on extendable handle, for sampling in shallow or vegetated

sites (qualitative); B - Perspex trap (4-litre); C - Trap drained into ‘bucket net’. ........................131 Figure 2-12. Examples of video imagery used for zooplankton..........................................................132 Figure 2-13. Map of sampling locations in lower Cooper reach, DRY/WET and ARIDFLO ...............169 Figure 3-1. Location of waterholes with water level loggers installed:................................................178 Figure 3-2. Relationship between salinity coefficient (see Equation 1) and waterbody salinity. ........180 Figure 3-3. Monthly losses measured by twelve depth loggers installed across ten waterbodies. ....183 Figure 3-4. Bankfull width to depth relationship for the four classes of a priori defined waterbodies. 187 Figure 3-5. Cease-to-flow depth differences among waterbodies on all ARIDFLO reaches, including

average evaporation losses for a one and two year period. ......................................................188 Figure 3-6. Typical waterhole profile showing the positions of major vegetation types (CHOS, lower

Diamantina). ...............................................................................................................................192 Figure 3-7. Relationships between surveyed, riparian vegetation levels and geomorphological

measures....................................................................................................................................193 Figure 3-8. Waterbodies sampled by ARIDFLO project. ....................................................................194 Figure 3-9. Location of Neales-Peake river system showing distribution of sampled waterholes (green

circles) and artesian springs (brown triangles)...........................................................................195 Figure 3-10. Spatial pattern of mound springs and surface salt deposits around Mt Dutton and

Algebuckina Waterhole using a Landsat 7 image as background. ............................................196 Figure 3-11. Typical channel section of the Warburton River.............................................................198 Figure 3-12. Salinity variations measured in surface waterbodies on a stretch of the Warburton River,

12th November, 2001. ................................................................................................................198 Figure 3-13. Salinity variations measured in surface waterbodies on a stretch of the Warburton River,

9th April, 2002. ...........................................................................................................................199 Figure 3-14. Variations in salinity of surface waters in Coongie Lakes wetlands, April 2002.............200 Figure 3-15. Variation in salinity of Algebuckina Waterhole during flow events, May 2000 – March

2002............................................................................................................................................201 Figure 3-16. Relationships between discharge and salinity of flow during flow events at Algebuckina

Waterhole (A) and Hookey Waterhole (B), Neales River, November 2000. ..............................202 Figure 3-17. Position of salinity samples in tributaries of Neales River, 26 Nov 2000. ......................202 Figure 3-18. Salinity and depth variations at Ultoomurra section of Warburton River........................203 Figure 3-19. Upper Diamantina catchment showing hydrological model extent (area of grid cells) and

sampled waterbodies. ................................................................................................................205 Figure 3-20. Modelled discharge at Diamantina Lakes, upper Diamantina River, for period October

1999 to March 2003. ..................................................................................................................207 Figure 3-21. Comparison between original and rerated discharge records for Diamantina Lakes

gauging station. ..........................................................................................................................208 Figure 3-22. Modelled versus observed flow at Diamantina Lakes for flood years (October –

September) 1975-1976. .............................................................................................................210

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Figure 3-23. Modelled versus observed flow at Diamantina Lakes for flood years (October – September) 1968-1970. .............................................................................................................210

Figure 3-24. Modelled discharge at Diamantina Lakes and observed stage height for period 1999-2001............................................................................................................................................211

Figure 3-25. Lower Diamantina catchment showing hydrological model extent (area of grid cells) and sampled waterbodies (circles)....................................................................................................212

Figure 3-26. Lower Diamantina region on 1st February, 2000. ..........................................................213 Figure 3-27. Flow measured at Birdsville for period 1999-2003, as hydrograph of daily flow volumes

and as annual volume totals.......................................................................................................215 Figure 3-28. Detailed section of depth logger data from Warburton River. ........................................216 Figure 3-29. Modelled flow and measured depth variations for the Ultoomurra stretch of the Warburton

River. ..........................................................................................................................................217 Figure 3-30. Timing of modelled versus measured flow peaks at KUNC and GOYD. .......................218 Figure 3-31. Modelled versus satellite-observed flood extent from 1st February, 2000.....................219 Figure 3-32. Modelled versus satellite-observed flood extent from 3rd April, 2000............................220 Figure 3-33. Thomson River catchment showing hydrological model extent (area of grid cells),

sampled waterbodies (red circles) and gauging station locations (brown triangles)..................222 Figure 3-34. Comparison of annual flow volumes through Longreach (upstream) and Stonehenge

(downstream) gauging stations on the Thomson River, 1969-1991. .........................................223 Figure 3-35. Flow measured at Longreach and Stonehenge for period October 1999- February 2002.

....................................................................................................................................................224 Figure 3-36. Modelled versus observed flow at Stonehenge for the period 1970-1977. ....................226 Figure 3-37. Modelled versus observed flow at Stonehenge for period 1984-1990. ..........................227 Figure 3-38. Modelled and observed flow at Stonehenge, Thomson River for period October 1999 to

April 2003. ..................................................................................................................................227 Figure 3-39. Modelled versus satellite observed extent of flooding for Thomson River on 28th

February 2000. ...........................................................................................................................228 Figure 3-40. Lower Cooper sites showing sampling sites (red dots) and depth logger locations (green

squares)......................................................................................................................................230 Figure 3-41. Flow measured at Innamincka (Cullyamurra WH) for period 1998-2002, as hydrograph of

daily flow volumes and as annual volume totals. .......................................................................231 Figure 3-42. Model extent over lower Cooper, showing sampled waterbodies in the Coongie Lakes

wetlands and outflow cells from model (red arrows). .................................................................232 Figure 3-43. Modelled discharge and lake volume versus measured water level changes for Browne

Creek/Lake Toontoowaranie and Ellar Creek/Lake Goolangirie. ...............................................234 Figure 3-44. Modelled lake volume (Lake Goolangirie group of lakes) and measured depth variations

for Ellar Creek (joining Lakes Toontoowaranie and Goolangirie). .............................................235 Figure 3-45. Modelled versus satellite-observed flood extent from 7th May, 2000. ...........................236 Figure 3-46. Modelled versus satellite-observed flood extent from 17th March, 2001. ......................237 Figure 3-47. Modelled discharge for period 1999-2003, Algebuckina Waterhole, Neales River........239 Figure 3-48. Rated flow (solid line) and depth logger data (dashed line) from Algebuckina Waterhole

for period April 2000 to March 2002. ..........................................................................................240 Figure 3-49. Modelled (dashed black line) versus rated (solid grey line) discharge at Algebuckina

waterhole, Neales River using two different parameter sets (Sets 1 and 2, see Table 3-16)....243 Figure 3-50. Modelled (dashed black line) versus rated (solid grey line) discharge at Algebuckina

waterhole, Neales River using three land-types.........................................................................244 Figure 3-51. Modelled discharge (dashed black line) versus measured stage height (solid grey).....245 Figure 3-52. Location map of Diamantina River catchment (outlined). ..............................................253 Figure 3-53. Transmission losses of Diamantina Lakes to Birdsville reach of the Diamantina River.254 Figure 3-54. Comparison of annual flow volumes through Longreach (upstream) and Stonehenge

(downstream) gauging stations on the Thomson River, 1969-1991. .........................................255 Figure 3-55. Travel time for Diamantina Lakes-Birdsville and Monkira-Birdsville reaches. ...............256 Figure 3-56. Wave speed–discharge relation for Diamantina River (Diamantina Lakes to Birdsville)

and Darling River (Bourke to Wilcannia). ...................................................................................257 Figure 3-57. Relationship between transmission ratio of a flood pulse in mid-Diamantina reach and the

number of days since the end of the preceding flow at Birdsville. .............................................258 Figure 4-1. Cumulative general count for all three South Australian reaches. ...................................261 Figure 4-2. Differences in diversity between littoral/benthic and mid-water/benthic samples in lower

Cooper, April 2002......................................................................................................................264 Figure 4-3. Generic richness of algae for each reach per trip. ...........................................................266

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Figure 4-4. Mean relative total abundance differences among reaches (a) and trips (b), with standard errors shown...............................................................................................................................269

Figure 4-5. Percentage abundances of taxonomic groups for each reach.........................................270 Figure 4-6. Percentage abundances of taxonomic groups for each trip. ............................................271 Figure 4-7. 2D ordination plot of mean reach value for each trip using first two axes of Principal

Components Analysis.................................................................................................................272 Figure 4-8. Cumulative taxa count for zooplankton and littoral microfauna assemblage for trips 1-6

(April 2000 - April 2002). ............................................................................................................286 Figure 4-9. Percentage composition of total taxon count for major taxonomic groups of zooplankton

and littoral microfauna assemblage............................................................................................287 Figure 4-10. Comparison of microfaunal taxa richness between basins and LEB reaches (standard

deviation bars shown). ...............................................................................................................290 Figure 4-11. Mean reach microfaunal taxon richness for all trips. ......................................................291 Figure 4-12. Zooplankton and littoral microfauna relative percentage abundance data for each reach.

....................................................................................................................................................294 Figure 4-13. Zooplankton and littoral microfauna relative percentage abundance data for each trip.295 Figure 4-14. Dendrogram of 12 groups recognised by flexible UPGMA classification of 173 samples

from the three South Australian reaches for Trips 1-6. ..............................................................301 Figure 4-15. Salinity variations during flow events at Algebuckina Waterhole, Neales River, are shown

in left panel. ................................................................................................................................308 Figure 4-16. Trip cumulative taxon richness, pooling all ARIDFLO reaches. .....................................312 Figure 4-17. Mean taxon richness for the ARIDFLO reaches (based on waterbody richness) compared

with data compiled on the Murray, Darling, Diamantina and Cooper (Sheldon, unpublished). (Error bars = 1 S.E.) ...................................................................................................................313

Figure 4-18. Cumulative taxon richness for each reach sampled for macroinvertebrates during ARIDFLO. ...................................................................................................................................314

Figure 4-19. Mean sample macroinvertebrate taxon richness for each of the reaches per ARIDFLO trip. (Error bars = 1 S.E.) ............................................................................................................314

Figure 4-20. Microhabitat representation in samples analysed on a reach basis during ARIDFLO. Note the different scales on the Y axis. ..............................................................................................319

Figure 4-21. Mean sample taxon richness for each of the microhabitats. ..........................................320 Figure 4-22. Mean sample abundance of macroinvertebrates by reach and trip during ARIDFLO. ..323 Figure 4-23. Dendrogram of 23 subgroups recognised by flexible UPGMA classification of 626

samples from all reaches for Trips 1-7. ......................................................................................330 Figure 4-24. Relative Mean sample abundances with respect to Functional Feeding Groups ..........340 Figure 4-25. Mean sample taxon richness of Functional Feeding Groups. ........................................341 Figure 4-26. Photographs of several LEB grunter species, small juveniles (100-200mm) on the left

and large juveniles/adults on the right........................................................................................355 Figure 4-27. Mean number of native fish species caught per waterbody during the ARIDFLO survey of

LEB rivers and the NSW Rivers survey of MDB rivers...............................................................385 Figure 4-28. Mean number of NATIVE fish species caught per waterbody by reach and survey. .....389 Figure 4-29. Mean number of EXOTIC fish species caught per waterbody by reach and survey......390 Figure 4-30. Mean number of fish species caught per waterbody by reach and macrohabitat..........396 Figure 4-31. Mean number of native and exotic fish species caught per waterbody using the 2m

SEINE in the Coongie Lakes Reach over two different survey periods (Dry/Wet 1986-1992 and ARIDFLO 2000-2003). ...............................................................................................................401

Figure 4-32. Mean number of native and exotic fish species caught per waterbody using FYKE nets in the Coongie Lakes Reach over two different survey periods (Dry/Wet 1986-1992 and ARIDFLO 2000-2003). ................................................................................................................................403

Figure 4-33. Mean number of NATIVE fish caught per waterbody during the ARIDFLO survey. Mean abundance per waterbody plotted A) by river and B) by reach. (Note the significantly larger y-axis than the exotic fish graphs in Figure 4.34)..........................................................................407

Figure 4-34. Mean number of EXOTIC fish caught per waterbody during the ARIDFLO survey. Mean abundance per waterbody plotted A) by river and B) by reach. (Note the significantly smaller y-axis than Figure 4.33).................................................................................................................408

Figure 4-35. Mean abundance of NATIVE fish caught per waterbody by reach and survey..............410 Figure 4-36. Mean abundance of EXOTIC fish caught per waterbody by reach and survey. ............411 Figure 4-37. Mean native fish abundance for waterbodies sampled in April 2001 on the Lower

Diamantina reach. ......................................................................................................................414

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Figure 4-38. Least squares means of log transformed number of fish caught in different macrohabitat categories (± 1SE)......................................................................................................................417

Figure 4-39. Log transformed mean number of fish caught per waterbody, plotted by reach and macrohabitat...............................................................................................................................418

Figure 4-40. Log of the mean number of native and exotic fish individuals caught per waterbody in the Coongie Lakes Reach. Catch data taken from the 2m SEINE over two different survey periods (DRY/WET 1986-1992 and ARIDFLO 2000-2003). ...................................................................420

Figure 4-41. Mean number of native and exotic fish individuals caught per waterbody in the Coongie Lakes Reach over two different survey periods (DRY/WET 1986-1992 and ARIDFLO 2000-2003). Using catch data from the FYKE nets standardised to 60 minutes of net wet time........424

Figure 4-42. Average percentage of fish individuals that are diseased per waterbody. Means are plotted for each field trip along with the hydrograph for each reach. .........................................426

Figure 4-43. Example of diseased spangled grunter (Leiopotherapon unicolour) captured at Bobbiemoonga on the Lower Diamantiana, November 2001. ...................................................427

Figure 4-44. Example of diseased golden perch juvenile (Macquaria sp.B) captured at Kunchera waterhole on the Lower Diamantiana, April 2002. .....................................................................427

Figure 4-45. Percent diseased individuals on the lower Diamantina in April 2001 for each waterbody sampled. .....................................................................................................................................429

Figure 4-46. Richness by Waterbird Functional Feeding Group on upper Diamantina. .....................447 Figure 4-47. Richness by Waterbird Functional Feeding Group on lower Diamantina. .....................448 Figure 4-48. Richness by Waterbird Functional Feeding Group on upper Cooper. ...........................449 Figure 4-49. Richness by Waterbird Functional Feeding Group on lower Cooper. ............................449 Figure 4-50. Richness by Waterbird Functional Feeding Group on Neales. ......................................450 Figure 4-51. Abundance by Waterbird Functional Feeding Group on upper Diamantina. .................451 Figure 4-52. Abundance by Waterbird Functional Feeding Group on lower Diamantina. ..................451 Figure 4-53. Abundance by Waterbird Functional Feeding Group on upper Cooper. ........................452 Figure 4-54. Abundance by Waterbird Functional Feeding Group on lower Cooper..........................452 Figure 4-55. Abundance by Waterbird Functional Feeding Group on Neales....................................453 Figure 4-56. Mean waterbody species richness of waterbirds on Diamantina reaches, with standard

errors. .........................................................................................................................................455 Figure 4-57. Mean waterbody species richness of waterbirds on Cooper reaches, with standard

errors. .........................................................................................................................................455 Figure 4-58. Mean waterbody species richness of waterbirds on Neales reach, with standard errors.

Waterbodies upstream of Algebuckina on the Neales River and the Peake crossing on the Peake Creek were classified as upstream. ................................................................................456

Figure 4-59. Mean waterbody abundance of waterbirds on Diamantina reaches, with standard errors.....................................................................................................................................................458

Figure 4-60. Mean waterbody abundance of waterbirds on Cooper reaches, with standard errors...458 Figure 4-61. Mean waterbody abundance of waterbirds on Neales reach, with standard errors. ......459 Figure 4-62. Dendrogram showing major clustering of 217 waterbird observations into 14 groups, and

their amalgamation into 5 higher groups indicated by thick vertical arrow. Scale shows Bray-Curtis distance with β = -0.1 dilation. .........................................................................................460

Figure 4-63. Semi-strong hybrid, two-dimensional ordination showing position of 217 waterbird observations averaged across reaches and trips; Bray-Curtis distance used. ..........................463

Figure 4-64. Modelled (Cfits) and actual (BrS) plot of breeding waterbird species richness against log10 of conductivity, assuming negative binomial distribution or errors (generalised linear model).........................................................................................................................................470

Figure 4-65. Channel Country study region of aerial waterbird surveys (green rectangle), covering Eyre Creek in the west, lower Diamantina River to upper Warburton River, and upper to middle Cooper Creek. ............................................................................................................................473

Figure 4-66. Ordination (2D, SSH multidimensional scaling) of woody vegetation at 54 ARIDFLO waterbodies. ...............................................................................................................................495

Figure 5-1. Plot of the first two axes of the macroinvertebrate ordination and indicating the taxon richness of samples....................................................................................................................541

Figure 5-2. Plot of the first two axes of the macroinvertebrate ordination and indicating sample abundance [LN(sample abundance + 1)]. ..................................................................................542

Figure 5-3. Plot of the first two axes of the macroinvertebrate ordination and indicating water conductivity (µScm-1). ................................................................................................................542

Figure 5-4. Plot of the first two axes of the macroinvertebrate ordination and indicating the reach which samples were collected from............................................................................................543

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Figure 5-5. Plot of the first two axes of the macroinvertebrate ordination and indicating the type of microhabitat which samples were collected from.......................................................................544

Figure 5-6. Plot of the first two axes of the macroinvertebrate ordination and indicating the type of macrohabitat which samples were collected from......................................................................544

Figure 6-1. Variations in relative taxon richness for all biotic groups and reaches.............................660 Figure 6-2. Variations in abundance (natural log transformed) for all biotic groups (excluding algae

and zooplankton) and reaches. ..................................................................................................662 Figure 6-3. Daily mean water temperature at approximately one metre depth in Algebuckina

Waterhole, Neales River, September 2000 to May 2002...........................................................668 Figure 6-4. Mean (left panels) and median (right panels) monthly discharges for Birdsville (Diamantina

River) and Algebuckina (Neales River). .....................................................................................669 Figure 6-5. Seven conceptual stages of the spatial distribution of available aquatic habitat in an

intermittent river..........................................................................................................................675 Figure 6-6. Change in algal assemblage from fresh flow-structured sites (Major Group III) to saline

sites (Major Group I)...................................................................................................................678 Figure 6-7. Standardised abundances of larval and juvenile fish, algae and rotifer and

microcrustacean percentage abundances (top panel) and monthly discharge (bottom panel) for Cootanoorina (COOT) Waterhole...............................................................................................693

Figure 6-8. Natural log transformed mean abundances of plague minnow (GAMH) and gudgeons (HYPS) with standard errors, for the lower Cooper reach..........................................................697

Figure 6-9. Natural log transformed mean abundances of plague minnow (GAMH) and gudgeons (HYPS) with standard errors, for the upper Cooper (Thomson River) reach. ............................697

Figure 6-10. Conceptual models of eight stages of river function.......................................................710 Figure 7-1. The science of monitoring in an adaptive management framework.................................730 Figure 7-2. Relationship between peak amplitude and total volume of flood pulses at Stonehenge

gauging station, Thomson River.................................................................................................752 Figure 7-3. Number of native species by reach and catchment area. ................................................771 Figure 7-4. IBI scores for waterbodies on the Thomson reach by sampling trip. ...............................779 Figure 7-5. IBI scores for waterbodies on the Coongie Lakes reach by sampling trip. ......................780 Figure 7-6. IBI scores for waterbodies on the Upper Diamantina reach by sampling trip. .................780 Figure 7-7. IBI scores for waterbodies on the Lower Diamantina reach by sampling trip. .................781 Figure 7-8. IBI scores for waterbodies on the Neales reach by sampling trip. ...................................781 Figure 7-9. Mean biotic integrity scores by ARIDFLO reach. .............................................................782 Figure 7-10. Correlations of IBI scores for waterbodies on subsequent early summer and late summer

surveys (A – C) and absence of correlation in IBI score as the time lag between late summer surveys increases (D).................................................................................................................784

Figure 7-11. Mean coefficients of variation in IBI score within individual waterbodies (site level) and for individual waterbodies through time (wbody level).....................................................................787

Figure 7-12. Mean IBI score grouped by various environmental quality factors.................................790 Figure 7-13. Qualitative IBI scoring bands taking into account distance from the nearest refuge. ....793 Figure 7-14. Qualitative IBI scoring bands taking into account distance from the nearest refuge and

time and size of last flow. ...........................................................................................................794

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Table of Tables

Table 1-1. Groups of hydrological and geomorphological predictive variables used in hydrology-

biology modelling..........................................................................................................................62 Table 2-1. List of waterbodies sampled during the ARIDFLO surveys. ................................................93 Table 2-2. ARIDFLO sampling occasions.............................................................................................95 Table 2-3. Biotic assemblages and parameters measured for each group ..........................................97 Table 2-4. Position of water level loggers ...........................................................................................100 Table 2-5. Description of event parameters........................................................................................123 Table 2-6. Description of regime parameters......................................................................................127 Table 2-7. Types of means used in analysis.......................................................................................137 Table 2-8. Statistical measures used in analysis of biotic groups ......................................................137 Table 2-9. Macroinvertebrate Functional Feeding Groups . ...............................................................138 Table 2-10. Taxa recognised in each Functional Feeding Group.......................................................139 Table 2-11. Dimensions and application of fish sampling gear. .........................................................144 Table 2-12. Faunal attributes measured per gear type.......................................................................151 Table 2-13. Functional Group classification of waterbirds occurring in the LEB (after Roshier et al.

2002 * .........................................................................................................................................155 Table 2-14. Wetland complexes covered by aerial surveys ...............................................................158 Table 2-15. Performance of regression and ANN models and ANN model details. ...........................171 Table 2-16. Comparison of different association matrices, q-mode. As a measure of increasing

distance, Pearson R and Spearman R can range from 1 to –1, Gower D from 0 to 1...............173 Table 2-17. Percent variance (%var) explained by first ten components of PCA, r-mode, for Event 2

and Regime hydrological parameter datasets............................................................................174 Table 3-1. Inter-reach comparison of catchment characteristics for ARIDFLO sampled reaches of the

LEB. ............................................................................................................................................175 Table 3-2. Discharge data available for model calibration and summary of reliability of gauging station

discharge at high stage. .............................................................................................................177 Table 3-3. Morphological and salinity characteristics of the sampled waterholes. .............................179 Table 3-4. Hydrological and geomorphological parameters of ARIDFLO waterbodies. .....................189 Table 3-5. Linear models for relationship between riparian vegetation zones and geomorphological

parameters. ................................................................................................................................192 Table 3-6. Salinity and discharge of recession inflow to Algebuckina and Peake Crossing waterholes,

2000-2002. .................................................................................................................................201 Table 3-7. Calibration performance measures for upper Diamantina reach model............................209 Table 3-8. Performance of modelled versus gauged flood events. ....................................................209 Table 3-9. Description of waterbodies sampled on lower Diamantina reach......................................214 Table 3-10. Gauged versus modelled discharges at NULT, Warburton River. ..................................217 Table 3-11. Calibration performance measures for the Thomson reach model. ................................226 Table 3-12. Performance of modelled versus gauged flood events. ..................................................226 Table 3-13. Gauged versus modelled discharges ..............................................................................233 Table 3-14. Logged and modelled flow timing in Coongie Lakes wetlands. .......................................233 Table 3-15. Parameter sets following initial calibration.......................................................................241 Table 3-16. Parameter sets following calibration using three landtype classes. ................................242 Table 3-17. Number of cells of each land-type in the three models. Note that the ‘channel’ category

includes the channels of major tributaries. .................................................................................247 Table 3-18. Parameter values for three catchment models using only hillslope and channel land-types.

....................................................................................................................................................248 Table 3-19. Parameter values and statistical measures of fit for models using channel only and

channel and floodplain to describe the channel system of the mid-Diamantina model. ............249 Table 3-20. Parameter values and statistical measures of fit for models using channel only and

channel and floodplain to describe the channel system of the upper Diamantina model. .........250 Table 3-21. Model performance for upper Diamantina and Thomson reaches using parameter sets

from other model. .......................................................................................................................251 Table 4-1.Total genus richness at reach scale, number of genera unique to each reach and number of

samples per reach per trip..........................................................................................................261 Table 4-2. Differences in genus richness between littoral/benthic and mid-water/benthic samples in

lower Cooper, April 2002. ...........................................................................................................263

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Table 4-3. Relative abundance and diversity among littoral/benthic and mid-water/benthic samples in lower Cooper, April 2002. ...........................................................................................................265

Table 4-4. Two-way ANOVA of algal taxon richness by trip and reach. .............................................267 Table 4-5. Genera significantly correlated to cluster-defined groups at Pearson R>0.25. .................273 Table 4-6. Groups defined by cluster analysis – breakdown by reach, generic richness and

conductivity range.......................................................................................................................276 Table 4-7. Groups defined by cluster analysis – breakdown by trip. ..................................................276 Table 4-8. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated reaches. ...................................................................................................................279 Table 4-9. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated macrohabitats. .........................................................................................................280 Table 4-10. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated trips. .........................................................................................................................280 Table 4-11. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated seasons. ..................................................................................................................281 Table 4-12. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated salinity groups. .........................................................................................................281 Table 4-13. Correlation between waterbody salinity and both reach-scale and divisions diversity....282 Table 4-14. Total taxon richness of zooplankton and littoral microfauna for all reaches and trips.....286 Table 4-15. Taxa numbers unique to each reach. ..............................................................................286 Table 4-16. Number of samples collected within each reach per trip. ................................................292 Table 4-17. Two-way ANOVA of zooplankton taxon richness by trip and reach. ...............................292 Table 4-18. Relative zooplankton and littoral microfauna percentage abundance data at the reach

scale and for each trip. ...............................................................................................................296 Table 4-19. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the designated

major groups defined by cluster analysis. ..................................................................................299 Table 4-20(a). Groups defined by cluster analysis. ............................................................................299 Table 4-21. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated reaches. ...................................................................................................................304 Table 4-22. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated macrohabitats. .........................................................................................................304 Table 4-23. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated trips. .........................................................................................................................305 Table 4-24. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated salinity groups. .........................................................................................................306 Table 4-25. Indicator taxa (Dufrene and Legendre 1997) generated using PC-ORD for the a-priori

designated seasons. ..................................................................................................................306 Table 4-26. Correlation between waterbody salinity and both reach-scale taxon richness and

abundance..................................................................................................................................307 Table 4-27. Number of macroinvertebrate samples analysed from each microhabitat per trip. .........317 Table 4-28. Trips when maximum sample taxon richness was recorded for each of the microhabitats

per reach. ...................................................................................................................................321 Table 4-29. Analysis of variance of mean waterbody sample taxon richness against Trip and Reach.

....................................................................................................................................................322 Table 4-30. Analysis of variance of mean waterbody sample abundance against Reach. ................324 Table 4-31. Relative abundance of the Hemipteran families, Corixidae and Notonectidae, in ARIDFLO

samples. .....................................................................................................................................325 Table 4-32. Summary of Groups defined by cluster analysis. ............................................................331 Table 4-33. Indicator taxa (Dufrene & Legendre, 1997) generated using PC-ORD for the cluster

analysis Main-Groups (MG I-V)..................................................................................................332 Table 4-34. Indicator taxa (Dufrene & Legendre, 1997) generated using PC-ORD for the cluster

analysis groups (G1-13). ............................................................................................................333 Table 4-35. Indicator taxa (Dufrene & Legendre, 1997) generated using PC-ORD for the cluster

analysis subgroups (SG1A-13C)................................................................................................334 Table 4-36. Indicator taxa using PC-Ord for all a-priori designated variables. ..................................337 Table 4-37. Correlation between waterbody conductivity and Taxon Richness and Abundance.......342 Table 4-38. Fish species encountered on ARIDFLO surveys including scientific and common names.

....................................................................................................................................................352 Table 4-39. Regional representation of fishes in the LEB. .................................................................353

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Table 4-40. Comparison of numbers of native and exotic species known from available information and numbers caught over the seven ARIDFLO surveys............................................................359

Table 4-41. Total number of individuals of NATIVE fish species caught during ARIDFLO sampling by reach and survey trip (all gears summed). .................................................................................360

Table 4-42. Total Number of individuals of EXOTIC fish species caught during ARIDFLO sampling by reach and survey trip (all gears summed). .................................................................................360

Table 4-43. ARIDFLO fish catch by species and reach. .....................................................................362 Table 4-44. ARIDFLO fish catch by species and trip. .........................................................................363 Table 4-45. Provisional classification of trophic groups for fishes in the LEB rivers...........................365 Table 4-46. Number of LEB fish species by reach and trophic group. ...............................................365 Table 4-47. Classification of native and exotic fish species into tentative habitat groups by life-history

stage and catchability under the ARIDFLO sampling regime. ...................................................366 Table 4-48. Number of LEB fish species by reach and habitat group. ..............................................366 Table 4-49. Classification of native and exotic fish species into tentative tolerance, reproductive, flood-

response and colonising-ability groups. .....................................................................................367 Table 4-50. Number of individuals of each species caught by fishing gear type................................369 Table 4-51. Capture efficiency of different species and life history stages by standard ARIDFLO

fishing gears. ..............................................................................................................................377 Table 4-52. Rare species that constitute less than one percent of the catch by reach. .....................379 Table 4-53. Frequency of detection of different fish species by reach and fishing gear. ...................380 Table 4-54. Rare native species by reach at the 1% abundance threshold, and/or with restricted

distributions and/or catchability issues. ......................................................................................381 Table 4-55. Waterbodies deleted from the balanced gear effort database (2m seine and fyke net catch

data combined) due to insufficient gear replication....................................................................383 Table 4-56. Least Squares Means for the number of native species across the three LEB rivers

sampled by ARIDFLO. ...............................................................................................................386 Table 4-57. Catchment areas and numbers of native species in rivers of the LEB and Murray-Darling

Basin...........................................................................................................................................387 Table 4-58. Least Squares Means for the number of native species across ARIDFLO river reaches.

....................................................................................................................................................388 Table 4-59. Least Squares Means for the number of native species by Trip. ....................................391 Table 4-60. Least squares means of native richness for each reach and trip. ...................................392 Table 4-61. Summary of analyses of variance for different models incorporating the effects of reach,

macrohabitat and trip on native species richness. .....................................................................397 Table 4-62. Summary of analyses of variance for different models incorporating the effects of

ARIDFLO vs. Dry/Wet dataset, season and individual waterbody on native species richness. 401 Table 4-63. Summary of analyses of variance for different models incorporating the effects of

waterbody, season and dataset (ARIDFLO vs. Dry/Wet) on 2m seine exotic species richness.....................................................................................................................................................402

Table 4-64. Least Squares Means for the number of native fish individuals (natural logged) across LEB rivers and ARIDFLO reaches. ............................................................................................407

Table 4-65. Least Squares Means for the number of exotic fish individuals (natural logged) across LEB rivers and ARIDFLO reaches. ............................................................................................409

Table 4-66. Least Squares Means for the logged abundance of native species by Trip....................411 Table 4-67. Least squares means of logged native abundance for each reach and trip....................412 Table 4-68. Least Squares Means for the logged abundance of G.holbrooki by Trip on the Coongie

Lakes reach. ...............................................................................................................................416 Table 4-69. Summary of analyses of variance for different models incorporating the effects of reach,

macrohabitat and trip on native fish abundance. .......................................................................419 Table 4-70. Summary of analyses of variation for different models incorporating the effects of

ARIDFLO vs. Dry/Wet dataset, season and individual waterbody on native fish abundance for 2m SEINES. ...............................................................................................................................421

Table 4-71. Changes in the mean number of individuals caught per waterbody over two different survey periods (DRY/WET 1986-1992 and ARIDFLO 2000-2003). Data calculated for the most abundant species caught with the 2m SEINE in the Coongie Lakes Reach..............................422

Table 4-72. Changes in the mean number of individuals caught in summer versus non-summer seasons over two different survey periods (DRY/WET 1986-1992 and ARIDFLO 2000-2003).423

Table 4-73. Summary of analyses of variation for different models incorporating the effects of ARIDFLO vs. Dry/Wet dataset, season and individual waterbody on native fish abundance from FYKE NETS................................................................................................................................424

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Table 4-74. List of 71 waterbird species recorded during 217 systematic waterbody visits on ARIDFLO ground surveys. ..........................................................................................................................436

Table 4-75. Reach summary of waterbird species abundance from 217 systematic waterbody visits during ARIDFLO ground surveys. ..............................................................................................439

Table 4-76. Trip summary of waterbird species abundance recorded during 217 systematic waterbody visits on ARIDFLO ground surveys. Species are listed in taxonomic order...............................442

Table 4-77. Two-way anova of waterbody waterbird species richness by trip and reach. .................454 Table 4-78. Two-way anova of waterbody waterbird abundance by trip and reach. ..........................457 Table 4-79. Indicator waterbird taxa (Dufrene & Legendre 1997) generated using PC-ORD for the a-

priori designated trips. ................................................................................................................464 Table 4-80. Indicator waterbird taxa (Dufrene & Legendre 1997) generated using PC-ORD for the a-

priori designated reaches. ..........................................................................................................465 Table 4-81. Indicator waterbird taxa (Dufrene & Legendre 1997) generated using PC-ORD for a-priori

designated macrohabitats. .........................................................................................................467 Table 4-82. Indicator waterbird taxa (Dufrene & Legendre 1997) generated using PC-ORD for a-priori

designated rivers. .......................................................................................................................468 Table 4-83. Indicator waterbird taxa (Dufrene & Legendre 1997) generated using PC-ORD for a-priori

designated seasons. ..................................................................................................................469 Table 4-84. Indicator waterbird taxa (Dufrene & Legendre 1997) generated using PC-ORD for the a-

priori designated salinity groups.................................................................................................469 Table 4-85. Dates and Locations of seven aerial surveys. .................................................................472 Table 4-86. Composition of aerial survey segments by type of count procedure...............................474 Table 4-87. Summary statistics for all waterbirds counted on seven aerial surveys. .........................475 Table 4-88. Breeding waterbirds counted on aerial surveys by segment. ..........................................477 Table 4-89. Summary statistics for numbers of waterbird species and total waterbird abundance

counted on aerial surveys by segment.......................................................................................478 Table 4-90. Percentage abundance of waterbirds by functional feeding group across the seven

surveys. ......................................................................................................................................479 Table 4-91. Calibration data across the seven surveys comparing aerial and ground survey total

waterbird abundance estimates for designated waterbodies and wetlands identified by Segment reference. ...................................................................................................................................481

Table 4-92. Ratios of ground to aerial survey results for 41 Segments..............................................483 Table 4-93. Scaling up results for 21 floodplain transect segments from aerial survey 1, April 2000 485 Table 4-94. Scaling up results for 11 floodplain complexes on Eyre Creek from aerial survey 4, March

2001............................................................................................................................................487 Table 4-95. List of 21 species of woody vegetation and shoreline plant group ‘sedge’ surveyed in

quadrats at 54 ARIDFLO waterbodies. ......................................................................................494 Table 5-1. Model inputs determined using Partial Mutual Information (PMI)......................................505 Table 5-2. Performance of regression and ANN models. ...................................................................507 Table 5-3. Description of event parameters........................................................................................508 Table 5-4. Description of regime parameters......................................................................................510 Table 5-5. Loading of environmental parameters on Event 1 Principal components. ........................511 Table 5-6. Loading of environmental parameters on Event 2 Principal components. ........................513 Table 5-7. Loading of environmental parameters on Regime Principal components. ........................519 Table 5-8. Algal generic richness (square root transformed) – PCA variables fitted..........................523 Table 5-9. Algal generic richness (square root transformed) – raw hydrological parameters fitted. ..524 Table 5-10. Cyanobacteriae generic richness (square root transformed) – PCA variables fitted. .....526 Table 5-11. Cyanobacteria generic richness (square root transformed) – raw hydrological parameters

fitted. ...........................................................................................................................................526 Table 5-12. Zooplankton taxon richness (square root transformed) – PCA variables fitted. ..............529 Table 5-13. Zooplankton taxon richness (square root transformed) – raw hydrological parameters

fitted. ...........................................................................................................................................530 Table 5-14. Rotifer taxon richness (square root transformed) – PCA variables fitted. .......................532 Table 5-15. Rotifer taxon richness (square root transformed) – raw hydrological parameters fitted..533 Table 5-16. Microcrustacean taxon richness (square root transformed) – PCA variables fitted. .......536 Table 5-17. Microcrustacean taxon richness (square root transformed) – raw hydrological parameters

fitted. ...........................................................................................................................................537 Table 5-18. Relative abundance of microcrustacean taxa – PCA variables fitted..............................538 Table 5-19. Relative abundance of microcrustacean taxa – raw hydrological parameters fitted. ......538

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Table 5-20. Summary of models fitting hydrological event and regime PCAs as significant predictors (+ and - indicate the direction of the correlation)........................................................................546

Table 5-21. Summary of models fitting season, microhabitat and macrohabitat as significant predictors (+ and - indicate the direction of the correlation)........................................................................547

Table 5-22. Summary of models fitting conductivity, pH, Secchi depth, Temperature and hydrological categorical parameters as significant predictors (+ and - indicate the direction of the correlation).....................................................................................................................................................548

Table 5-23. Summary of models fitting hydrological categorical parameters as significant predictors (+ / - direction of the correlation).....................................................................................................549

Table 5-24. Macroinvertebrate taxon richness (square root transformed) – PCA variables fitted......553 Table 5-25. Macroinvertebrate taxon richness (square root transformed) – Raw hydrological

parameters fitted.........................................................................................................................554 Table 5-26. Macroinvertebrate abundance (natural log transformed) – PCA variables fitted. ...........556 Table 5-27. Macroinvertebrate abundance (natural log transformed) – raw hydrological parameters

fitted. ...........................................................................................................................................557 Table 5-28. First axis of macroinvertebrate PCA analysis (PSSH1) – PCA scores fitted. .................559 Table 5-29. Second axis of macroinvertebrate PCA analysis (PSSH2) – PCA scores fitted. ............560 Table 5-30. Third axis of macroinvertebrate PCA analysis (PSSH3) – PCA scores fitted. ................562 Table 5-31. Fourth axis of macroinvertebrate PCA analysis (PSSH4) – PCA scores fitted. ..............564 Table 5-32. Macroinvertebrate predator functional feeding group abundance (natural log transformed)

– PCA variables fitted. ................................................................................................................566 Table 5-33. Macroinvertebrate predator functional feeding group abundance (natural log transformed)

– raw hydrological parameters fitted. .........................................................................................566 Table 5-34. Macroinvertebrate gatherer-collector functional feeding group abundance (natural log

transformed) – PCA variables fitted. ..........................................................................................568 Table 5-35. Macroinvertebrate Scraper functional feeding group abundance (natural log transformed)

– PCA variables fitted. ................................................................................................................569 Table 5-36. Fish species richness (square root transformed )– PCA variables fitted.........................572 Table 5-37. Fish species richness (square root transformed and reach standardised to account for

differences in the regional species pool)– PCA variables fitted. ................................................572 Table 5-38. Fish abundance (natural log transformed) – PCA variables fitted. ..................................574 Table 5-39. Percentage of sites per reach containing golden perch. .................................................575 Table 5-40. Golden Perch abundance (natural log transformed) – PCA variables fitted. ..................577 Table 5-41. Golden Perch abundance (natural log transformed) – Raw hydrological parameters fitted.

....................................................................................................................................................577 Table 5-42. Bony Herring abundance (natural log transformed) – PCA variables fitted. ...................580 Table 5-43. Bony Herring abundance (natural log transformed) – Raw hydrological parameters fitted.

Model 1. ......................................................................................................................................580 Table 5-44. Bony Herring abundance (natural log transformed) – Raw hydrological parameters fitted.

Model 2. ......................................................................................................................................580 Table 5-45. Waterbird species richness (square root transformed) – PCA scores fitted. ..................584 Table 5-46. Waterbird species richness (square root transformed) – Raw variables fitted. ...............584 Table 5-47. Waterbird abundance (natural log transformed) – PCA scores fitted..............................586 Table 5-48. Waterbird abundance (natural log transformed) – Raw variables fitted. .........................586 Table 5-49. Relative percentage abundance of dabbler guild to total waterbird abundance. ............587 Table 5-50. Relative percentage abundance of diving duck guild to total waterbird abundance. ......588 Table 5-51. Relative percentage abundance of fish-eater guild to total waterbird abundance. .........589 Table 5-52. Fish-eater Waterbird species richness (square root transformed) – PCA scores fitted. .590 Table 5-53. Fish-eater Waterbird species richness (square root transformed) – Raw variables fitted.

....................................................................................................................................................590 Table 5-54. Ratio of Fish-eater Guild to Dabbler Guild Ratio – PCA scores fitted. ............................591 Table 5-55. Ratio of Fish-eater Guild to Dabbler Guild Ratio – Raw variables fitted..........................592 Table 5-56. First axis of PCA analysis (BSSH1) – PCA scores fitted.................................................593 Table 5-57. First axis of PCA analysis (BSSH1) – Raw variables fitted. ............................................593 Table 5-58. Second axis of PCA analysis (BSSH2) – PCA scores fitted. ..........................................595 Table 5-59. Second axis of PCA analysis (BSSH2) – Raw variables fitted. .......................................595 Table 5-60. Simple Mantel correlations between different assemblages for all biotic groups, T6SA3

(six trips, three SA reaches). ......................................................................................................603 Table 5-61. Simple Mantel correlations between different assemblage over seven surveys in the three

SA reaches (T7SA3)...................................................................................................................603

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Table 5-62. Simple Mantel correlations between different assemblages over seven surveys in all five reaches (T7R5)...........................................................................................................................603

Table 5-63. Simple Mantel correlations between assemblages and environment over seven surveys in all five reaches (T6SA3). ............................................................................................................606

Table 5-64. Simple Mantel correlations between assemblages and environment over seven surveys in the three SA reaches (T7SA3). ..................................................................................................606

Table 5-65. Simple Mantel correlations between assemblages and environment over seven surveys in all five reaches (T7R5). ..............................................................................................................606

Table 5-66. Partial Mantel correlations between assemblages and environment for all biotic groups over six trips, three SA reaches (T6SA3). ..................................................................................608

Table 5-67. Partial Mantel correlations between assemblages and environment over seven surveys in the three SA reaches (T7SA3). ..................................................................................................613

Table 5-68. Partial Mantel correlations between assemblages and environment over seven surveys in all five reaches (T7R5). ..............................................................................................................617

Table 5-69. Summary of models fitting season, macrohabitat and water quality parameters as significant predictors (+ and - indicate the direction of the correlation)......................................623

Table 5-70. Summary of models fitting event 1 and 2 principal components (+ and - indicate the direction of the correlation).........................................................................................................629

Table 5-71. Summary of models fitting regime principal components as significant predictors (+ and - indicate the direction of the correlation). ....................................................................................630

Table 5-72. Summary of models fitting season, macrohabitat and water quality parameters as significant predictors (+ and - indicate the direction of the correlation)......................................633

Table 5-73. Summary of models fitting season and water quality parameters as significant predictors (+ and - indicate the direction of the correlation)........................................................................636

Table 6-1. Comparison of estimates of relative abundance of two fish species in Coongie Lakes between 1986-1992 (DRY/WET) and 2000-2003 (ARIDFLO). ..................................................656

Table 6-2. Modelled parameters for each biotic assemblage .............................................................657 Table 6-3. Analysis of variance of mean abundance between trips for larval and juvenile carp gudgeon

and plague minnow in the two ARIDFLO Cooper reaches (2000-2003) and the DRY/WET lower Cooper reach (1986-1992). ........................................................................................................698

Table 6-4. Differences among trips for larval and juvenile carp gudgeon and plague minnow in the lower Cooper, 2000-2003. Significantly different trips identified using Tukey’s post-hoc HSD probability matrix. .......................................................................................................................698

Table 7-1. Summary of the main spatio-temporal coverages and advantages/disadvantages of each biotic group for monitoring as well as the threatening processes they are most likely to be sensitive to..................................................................................................................................737

Table 7-2. Statistical characteristics of peak amplitude / total volume ratio for flow pulses at Stonehenge gauging station, Thomson River. ...........................................................................751

Table 7-3. Details of the eleven metrics used to calculate the IBI for the LEB fish assemblage........761 Table 7-4. Current and potential human actions relevant to LEB rivers and identification of which IBI

metrics are likely to identify them. ..............................................................................................762 Table 7-5. Assumptions underlying the behaviour of the Index of Biotic Integrity in response to

declining environmental condition ..............................................................................................765 Table 7-6. Qualitative IBI categories by IBI score, based upon an 11 metric IBI. (Karr 1986, Harris &

Silveira, 1999).............................................................................................................................765 Table 7-7. Maximum threshold values estimated for the scale dependent metrics 1-5 and 11, by

reach. (Threshold value encloses 95% of the data)...................................................................771 Table 7-8. Scoring criteria for each of the three categories of environmental quality for the scale

dependent metrics 1-5 and 11, by reach....................................................................................772 Table 7-9. Correlations between each metric and the final IBI score for ARIDFLO and the NSW-River

Survey (Harris and Gehrke, 1997). ............................................................................................773 Table 7-10. Correlations between each metric and the final IBI score for each ARIDFLO reach and

overall. ........................................................................................................................................774 Table 7-11. IBI scores for ARIDFLO waterbodies using data from 3 randomly selected 2m seine hauls

and effort-corrected fyke nets over the 7 surveys. .....................................................................778 Table 7-12. Sites where no fish were captured during ARIDFLO sampling and reasons why this might

be so. ..........................................................................................................................................782 Table 7-13. Table of mean coefficients of variation of IBI scores, grouped by reach, macrohabitat type,

and by season/trip. .....................................................................................................................786

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Summary Preamble to summary:

The following project summary documents the principal results, conclusions and recommendations of the ARIDFLO study. It is intended to be accessible to a broad audience, and so is deliberately lightly referenced – extensive referencing of the scientific literature is presented in the full version of the Scientific Report, and full citations are presented therein. Even without appendices, the main text of the Scientific Report is a very lengthy document (>600 pages), and so a concise and readable summary of the project’s findings was considered essential. It is not possible to simplify all scientific concepts to lay English without losing valuable information and precision, and so this document inevitably had to strike a balance between accessibility to all potential readers and those with some technical training or experience. Summary The rivers of the Lake Eyre Basin (LEB) are among the world’s last large rivers to remain unregulated and minimally human-impacted and include such Australian folklore icons as the Cooper and Diamantina. They are characterised by catchments that are almost entirely within the arid zone, having low gradients throughout their course, endorheic drainage (internally draining rather than reaching the sea), wide floodplains in the mid-lower reaches, large transmission losses, and extremely high flow variability. This extreme flow variability means that rivers naturally fluctuate between an inland sea of floodwaters and a handful of isolated wetlands or waterholes. Thus at any given time there is a mosaic of different aquatic habitats in the LEB, and over time there is many a healthy ecological dynamism. This contrasts strongly with the ecological stagnation and decline of regulated rivers. Although LEB aquatic ecosystems are currently in good health, an improved understanding of the ecological functioning of these rivers is critical to balance their environmental needs against current and future demands on their waters. However, little is currently known of the basic biology and hydrology, let alone the complex hydrology-ecology relationships in these remote rivers. Some rivers are minimally gauged but most remain ungauged, and very little biological work has been carried out over a broad scale. The ARIDFLO project was devised to help address this paucity of knowledge and to allow qualitative prediction of the impacts that upstream water resource proposals would likely have on fundamental ecosystem processes. The results of this project should also be useful in the management, planning and monitoring of existing or future water use projects in arid and other remote parts of Australia, and in the restoration of dryland rivers already affected by excessive water resource use.

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ARIDFLO objectives

• Develop hydrological models for the study reaches of the LEB rivers using a consistent methodology (IMAGHYD).

• Use existing ecological data to predict environmental responses to flows in the Cooper, Diamantina and Neales-Peake river systems.

• Collect a comprehensive suite of new ecological and hydrological data for the above rivers, and evaluate the predicted environmental responses against these data.

• Develop a generic model (ARIDFLO) of relationships between flow regime, ecological processes and biodiversity for the LEB rivers.

• Establish the basis for an environmental monitoring program on these rivers. Project Design The ARIDFLO field program covered five river reaches in three major river systems of the LEB. Upstream and downstream reaches were chosen in each of the two larger eastern LEB rivers, the Cooper and Diamantina, but the much smaller Neales River to the west of Lake Eyre was treated as a single reach. Reaches in this context typically spanned about 100 km. This spatial sampling structure allowed for comparisons between upstream and downstream reaches within a river catchment, between catchments and also between major river systems and smaller systems. The inclusion of the Neales River also allowed for the methodology to be tested on an ungauged river system with no previously recorded hydrological data, a common situation for many Australian arid zone rivers. A range of waterbodies was selected in each reach to represent the different hydrological regimes and geomorphological conditions aquatic biota typically experience. Waterbodies sampled included deep waterhole refuges, main channels, outer channels, lakes and floodplains. These five macrohabitat types are a continuum of morphologies shaped by the flow regime, their position on main versus secondary/floodplain channels, and their position within the catchment. Not all macrohabitats were represented in each reach. The major elements of the aquatic food web (viz. riparian and littoral vegetation, algae, zooplankton and littoral microfauna, littoral and benthic macroinvertebrates, fish and waterbirds) were surveyed within discrete periods (1-2 months) across the five reaches. Organisms within these six biotic groups were identified to the lowest taxonomic resolution practical: generally to species for fish, waterbirds, zooplankton and woody riparian vegetation, various for algae and for different groups of macroinvertebrates. Within assemblages a consistent level of taxonomic resolution was applied throughout the study. The biotic measures recorded depended on the biotic group but included at the assemblage level: abundance, taxon richness, evenness, exotic/native ratio, functional group membership, breeding incidence, and for fish, disease incidence and movement direction. Abundance data were collected on individual species of fish and waterbirds and on macroinvertebrate taxa, while relative abundance data for zooplankton taxa were recorded.

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Overall fifty-six waterbodies were sampled, some on single occasions, but most over multiple surveys. Systematic repeated surveys were confined to the four main instream aquatic groups (algae, zooplankton, macroinvertebrates, fish) and waterbirds, and these five biotic groups are the subject of most of the report that follows. The project spanned almost four years (commencing in January 2000), and seven surveys were completed between March 2000 and April 2003 incorporating two early summer, four late summer/autumn, and one winter fieldtrip. The sampling program of ARIDFLO was designed to maximize replication at the annual scale (encompassing four flood years) across a broad geographic area. This sampling strategy of large spatial and temporal extent allowed coverage of an extreme range of hydrological events, but to a certain degree sacrificed coverage of inter-seasonal and intra-annual variation.

Conditions encountered during the ARIDFLO sampling program The ARIDFLO project coincided with an extreme hydrological cycle driven by pronounced La Nina and El Nino episodes of the ENSO climatic phenomenon. The study was able to document the major hydrological and ecological changes that take place in LEB rivers and wetlands associated with the occurrence of a large, approximately one in ten year flood event (February-April 2000), followed by small to moderate flow events, through to an extended and extreme drought (April 2002-February 2003). During this period although the annual floods across the LEB generally became progressively smaller, there was significant variation within the three rivers (such as the catchment-wide flood of June 2001 in the Neales). The large regional floods of 2000 inundated thousands of square kilometres of floodplain and produced significant longitudinal (upstream-downstream) and lateral (main channel-floodplain) connectivity over hundreds of kilometres of river. Many of the waterbodies on the primary flow channels remained connected for months, particularly in the lower reaches, and inundated areas on the floodplain persisted for weeks to months after the flood passage. Significant dispersal and breeding responses for all biota were recorded during April 2000. Sampling trips in November 2000, April 2001 and April 2002 covered a wide range of conditions including during, or soon after, moderate to small flood events as well as periods of disconnection and falling water levels (November 2000 and November 2001). The final South Australian survey in February 2003 covered a severe drought whereas the March 2003 Queensland survey sampled just after drought-breaking flows. Although the area of available aquatic habitat was greatly reduced during the extended 2002/2003 drought, biota were still found to be thriving in refuge waterholes. However, this reduction of the rivers to a handful of waterholes during drought highlights the vulnerability of these refuges.

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Critical Refuges Drought refuges are important for the maintenance of biodiversity across a range of spatial and temporal scales. Refuge waterbodies are defined to be those that persist for at least 18-24 months in the event that they do not receive inflow during a flood season. To retain water for two years, such waterbodies need cease-to-flow depths of 3-6m depending on their location within the LEB so that they are capable of withstanding large annual losses due to evapotranspiration (1.3–3.0m per annum). Long-term refuges also require approximately annual frequencies of inundation so that the lack of inflow for an entire flood season would be a rare occurrence. Prior to ARIDFLO, information concerning LEB waterhole permanency and water loss rates were rare because of the remoteness and difficulties in detection or measurement of flow events (such as local thunderstorms which are brief and unpredictable). ARIDFLO addressed this deficiency in a number of ways: through the installation of depth loggers, sourcing information from local land managers, estimating the relative importance of different waterhole loss processes, investigating the presence and relative contribution of shallow groundwater aquifers, measuring the cease-to-flow depth (a major determinant of waterhole permanence), and estimating the frequency of inundation through extensive hydrological modelling. All refuge waterbodies identified within the five reaches were deep waterholes that were rare and sparsely distributed. Typically, they are larger, deeper and have more microhabitat complexity than the other waterbody types sampled (main channels, lakes, outer channels and floodplains). Populations of aquatic organisms which lack desiccation-resistant life-stages are reliant on refuges during drought. Also, some other wetland-dependent organisms which do not readily disperse or which cannot move long distances between isolated habitat fragments are also reliant on the maintenance of suitable refuge habitats. Such fauna includes all fish, some macroinvertebrates (such as the shrimp Macrobrachium), the Cooper Creek turtle (Emydura emmoti) and the water rat (Hydromys chrysogaster). Thus it is essential that the refuge waterholes identified by ARIDFLO, and others outside the study reaches, be monitored and protected. Of course, intermittently flooded areas such as floodplains are also critically important habitats and should not be under-valued. Ephemeral habitats provide the pulses of production and food which are essential for reproduction, not only for much of the Basin’s aquatic life but also for many terrestrial organisms. For instance, the relatively shallow Coongie Lakes wetlands are outstanding habitat for waterbirds.

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Modelling hydrological regimes (IMAGHYD) ARIDFLO has successfully produced catchment models for six river reaches when only three of these reaches had downstream gauging station data for model calibration. The principal challenges faced when producing the catchment models were the lack of gauging station data (both numbers of stations and length of record), complex flow paths and the varying importance of rainfall-runoff processes in each catchment. IMAGHYD used an innovative grid-based approach coupled with a conceptual water balance model to allow the representation of spatial diversity in rainfall, land-types and streamflow patterns while maintaining a parsimonious model structure for such a data-poor environment. The model divides each reach into a grid of cells (each approximately 5km by 5km) and routes rainfall and streamflow from cell to cell to mimic hydrological patterns in space and time. To ensure historically realistic output for these grid cells, the predictions from IMAGHYD models were constrained and calibrated against gauging station data, satellite imagery, field data and local landholders’ records. Particular attention was paid to identifying the flow paths used by different sized floods in these complex river systems and incorporating this information into the model in order to achieve realistic flow patterns. This was necessary because modelled discharge data had to be generated for a range of waterbodies spread across each reach. In addition, analysis of gauging station data found that accurate flow patterns were required to simulate the highly variable transmission losses and flow timing of flood events. For the reaches which lack pre-existing discharge data (Neales, lower Diamantina and lower Cooper), the calibration of the models using such non-traditional data sources as water level logger data and satellite images is relatively imprecise, such that results are unlikely to be reliable outside of the calibration period. However, in the context of the purpose of IMAGHYD, to produce discharge data primarily for the period of the field study, such calibration procedures are the only feasible method of producing modelled hydrological output in these remote catchments. The hydrological characteristics for each reach, their catchment models and flows over 2000-2003 are briefly detailed below: Upper Cooper Reach (QLD) The Thomson River has an anastomosing channel morphology and a relatively constricted floodplain/channel width of around 2-10km, lying upstream of the Channel Country proper. During floods, net inflow to the upper portion of this reach occurs from large sub-catchments. However below Windorah, where the Cooper spreads out over an extensive floodplain, flow volumes decrease downstream as fewer tributaries contribute and transmission losses are higher. The hydrological model gave good fits in timing, magnitude, total volume and shape to the observed large floods, but more variable performance for the smaller flows. The peak discharge of the February 2000 flood at Longreach exceeded that of the exceptional 1974 flood, but the total volume was less. The 2000-01 floods had an annual volume above the median for Longreach, but the 2001-02 annual volume was only around the first quartile. The flood year 2002-03 was a drought period broken by flow in late February 2003.

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Lower Cooper (Coongie Lakes) Reach (SA) The Coongie Lakes reach differs from the other ARIDFLO reaches in the occurrence of sequentially filling lakes on the main flow path. The geomorphology is largely a product of the interactions of the river and the dunefields of the Strzelecki Desert, and this reach is immediately downstream of the Channel Country. The lakes have similar shallow saucer-shaped forms and depths between 2-2.5m at the cease-to-flow stage. The lakes fill sequentially through connecting channels so the frequency of flooding decreases downstream and the lakes are the terminus for small to medium floods. The lower Cooper has complex flow paths for different sized floods and has disjunctions with outflowing rivers viz. Strzelecki Creek, the Main Branch and the Northwest Branch of Cooper Creek. Satellite data, local observations, hydrological data collected during field trips and previous research (Dry/Wet, Puckridge et al. 1999) were used for model calibration. The final model simulated well the flow patterns and timings, while modelled discharges corresponded well with the gauged ones. In March 2000 a large flood filled most lakes but it was below the 1989 level at the Cullyamurra gauge. Small to moderate sized floods occurred in December 2000 to March 2001, and in January to March 2002. Drought conditions prevailed for the remainder of 2002 until a series of small flows during February and March 2003 reached Coongie Lake. Coongie Lake has received flow from Cooper Creek every year since 1973 and has completely dried only once in that period. However, it again effectively dried prior to the arrival of flow in February 2003. During droughts the major waterholes along the Northwest Branch and in Cooper Creek itself generally remain inundated due to their large cease-to-flow depths. Upper Diamantina Reach (QLD) ARIDFLO sampling covered the upper Diamantina upstream of the Channel country, and including the Diamantina Lakes National Park. This reach has the highest mean annual discharge of all the reaches studied. The upper Diamantina anastomoses across a floodplain 2-10km wide, with fewer variations in flow path and width than in the lower reach. Waterholes on the major channels are, with the exception of Cullyamurra on the lower Cooper, the deepest sampled in ARIDFLO. As there is no upstream gauging station, the only input into the hydrological model for the upper Diamantina reach was rainfall data provided by QNRM. The modelled data tended to overestimate the peak magnitude and total volume of the larger flood events and there was considerable variation in the model performance for the smaller flood events (total volumes of <600,000ML). Very large floods occurred in December 1999 and February 2000. The February 2000 event was the largest in total volume since 1991, and in annual discharge 2000 was second only to 1974. The 2001 total annual discharge was above the median, but the 2002 annual discharge was below the 10th percentile. The February 2003 flood followed the drought of 2002-03 and had a similar peak to that of summer 2000-01 but a smaller volume.

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Lower Diamantina Reach (SA) The lower Diamantina reach sampled in ARIDFLO comprises the Diamantina downstream of Birdsville through Goyder’s Lagoon to the upper Warburton, and represents the tail end of the Diamantina portion of the Channel Country. The geomorphology of the lower Diamantina varies between the deeply channelised section immediately downstream of Birdsville, the shallow waterholes and broad floodplain of Goyder’s Lagoon and the channelised Warburton River. Only two waterbodies on the lower Diamantina are deep enough to be refuges, but the Birdsville gauging station has recorded flows every year since 1950, so even one flood year without flow into these waterholes is rare. Goyder’s Lagoon is the terminus for small flows, whereas large flows continue into the Warburton. The Lagoon lies at the junction of the Diamantina and Georgina Rivers, so large Georgina floods occasionally (as in 2001) directly contribute to the ecosystems of this part of the Diamantina via the Eyre Creek. Flow paths in the lower Diamantina differ according to flood size, and identifying the threshold discharges which initiate flow into the different flow paths was necessary to estimate total transmission losses, and to generate hydrological data. The lower Diamantina model was successful in matching the timing of peak flow to within four days for the large 2000 flood and to within 1-2 days for the smaller flows from local rainfall. However, the modelled timing of the 2001 peak was nine days late, because there are no gauged or modelled data available for the Georgina catchment, so the timing of the Eyre Creek inflow could only be estimated. Events during ARIDFLO ranged in size from the 2000 flood, which was exceeded in annual volume only by the 1950 and 1974 records, to the 2001 floods which reached the 60th percentile at Birdsville, to the 2002 event which was the smallest since 1993. In 2001 the Georgina, via Eyre Creek, contributed floodwaters to Goyder’s Lagoon for the first time since 1997 and this connection has only occurred 8-10 times in the last 36 years. Whilst the volume of flows from local rainfall is small relative to regional events, such flows are ecologically important in maintaining water levels. By January-February 2003 many waterbodies had dried on this reach, and flow did not resume until late February 2003. Neales Reach (SA) The Neales is the smallest, most ephemeral and unpredictable of the reaches studied, and lies in the south west of the LEB. In-channel waterholes range from shallow (<1.0-2.5m), ephemeral waterholes only containing water for some months following a flow event, to rare deeper waterholes (2.5-4.5m) that are near permanent (most notably, Algebuckina). Although the flow paths for the Neales are not as complex as in the Channel Country, there was a complete lack of previous hydrological data for this catchment. Thus ARIDFLO water level logger data and local observations were crucial in the successful production of the catchment model, particularly as satellite images could not reliably resolve in-channel flows. The spatial variability of the rainfall and sparse rain-gauge network of the catchment limited the accuracy of the rainfall-runoff model of the Neales catchment in matching the absolute magnitudes and volumes of streamflow events. In particular, small but ecologically important flow events were poorly modelled. However, model performance was improved by the application of catchment-wide processes replicating quick runoff from high intensity rainfall and improving the area inundated versus discharge relationship in the channel sections of the model.

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Representing areas of high and low soil moisture storage depths in the hill-slope areas of the catchment also improved the model performance. Even so, the best model was unable to simulate all flow events accurately - it overestimated the June 2001 flood and underestimated the other flows. So to produce the data required for the hydrology-biology analyses, groups of flow events were modelled using the parameter values which best simulated those flows. The ARIDFLO project was fortunate to study the Neales-Peake catchment during a particularly wet period resulting in a number of substantial flow events in the river system. The February 2000 flood occurred throughout the Neales catchment and was the largest since 1989. The June 2001 flood was smaller but still substantial and catchment-wide, while the February 2003 flood, although smaller again was also catchment-wide and flowed into Lake Eyre North. A number of other smaller floods and flows occurred during the 2000-2003 period associated with storms in various parts of the catchment. ARIDFLO: General model of biotic response to natural flow variability Having established that the complex patterns of river flow across the LEB could be faithfully captured by the hydrological modelling, IMAGHYD, a range of biological responses were then related to hydrology using a range of analytic and modelling techniques (Chapter 5). This approach built on the DRY/WET model (Puckridge et al. 1999), which related hydrological patterns in the lower Cooper to biological responses in the Coongie Lakes wetlands. However, ARIDFLO tested the predictions of the DRY/WET model over a larger geographic area for a greater range of biotic assemblages. It also extended the range of biology-hydrology relationships studied, and added studies of interactions between biotic groups and of biological responses to waterbody geomorphology. Overall, four principal environmental drivers of LEB aquatic ecosystems were consistently identified through statistical modelling: hydrology, season, geomorphology and salinity. These four drivers were common to all biotic groups even given their very different life-histories (trophic level, mobility, age at first reproduction, growth rate, longevity, etc) and sensitivities to local versus regional effects and seasonal versus inter-annual events. Discussion of the roles of these four environmental drivers form the backbone to ARIDFLO – the general model of biotic response to natural flow variability. Hydrology Hydrology is a key driver of aquatic ecosystems in the LEB given that the provision of water is both limited and highly variable in this arid environment. The extreme variation in annual flood size in the LEB is reflected in the adaptations shown by many of the biota and in the nature of the ecological processes in these rivers. Traits such as tolerance of extremes of water quality and food availability, generalism, mobility, reproductive flexibility, opportunism, rapid response and adaptive life-stages are examples of organism-level responses to this stochastic environment, while boom-bust dynamics exemplify ecosystem processes. There were several main patterns of biotic response to a variable hydrology detected in the statistical analyses. Biotic communities are principally structured both by the connecting and homogenising effects of large flows (which drive dispersal and successful reproduction) and the disconnecting and diverging effects of droughts (which increase the regulatory influence of biotic interactions such as predation and competition).

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Large floods result in a boom in richness and abundance of the five taxonomic groups systematically studied, although dispersal of mobile individuals can reduce abundance estimates for some taxa (e.g. fish and waterbirds) due to dilution effects. Movement of aquatic organisms and/or their propagules (e.g. some fish migrations and downstream transport of algae) occurs with every flow and this process has an important role in maintaining (or increasing) diversity along the river system. Flows also connect and homogenise communities over large distances, resetting successional sequences and facilitating the long term persistence of taxa by counteracting the impact of localised population depletions or extinctions. Also, flow events of any size and spatial extent (whether catchment wide or localized inflow due to thunderstorms), play a vital role in topping up waterbodies thereby ensuring their persistence for a longer period. After the cessation of flow, waterbodies and populations of aquatic organisms therein (with the exception of waterbirds and some highly mobile insects) become increasingly disconnected from the rest of the river system until flow resumes. A mosaic of wetlands with a diverse range of habitats is produced, each with different successional stages depending on the time since loss of connection. Disconnected conditions of reduced habitat area and resources result in the decrease in richness and abundance of most taxa, although the concentration of mobile organisms within refuges can result in localized increases in abundance estimates for some taxa (e.g. fish). In general, during disconnection, local habitat conditions and biotic interactions are considered to become more influential and assemblage structure diverges along different successional trajectories in isolated waterholes according to the compositions of assemblages and populations at the time of disconnection, species life-history traits and the ecological processes that control species abundance and distribution. This dynamic mosaic of waterbodies and flow paths of varying connectivity is critical for the maintenance of biological diversity in the LEB. One the one hand there are the refuges critical to the continued local persistence of water-dependent species, while on the other hand the continually shifting mosaic provides a dynamic variety and continua of habitats in which the capabilities of organisms are continually tested. This variability abates deterministic processes that would otherwise lead to the dominance by a few species and exclusion of all others – a pattern typically observed in stable environments. Persistence of biota under such variable conditions is dependent on whether organisms are able to tolerate the local environmental conditions (biotic and/or abiotic) and/or whether some of the population can successfully disperse to track the shifting mosaic of suitable conditions. LEB rivers typically receive flows every year, but it is the irregular extreme flood and drought events which have the most widespread and long-lasting effects on the biota. This does not mean that years of average flows and floods are not important, but rather that larger changes in the biota occur with more extreme hydrological events. Extreme events are able to trigger successional pathways and biotic responses that smaller in-channel flows do not. For instance, when the Georgina and Diamantina catchments were connected during the floods of 2001, the Diamantina fish community was invaded by thousands of individuals of two Georgina fish species, which previously had only been infrequently recorded in the lower Diamantina. Such invasions are rare and potentially ephemeral, but they could (even) include the connection of catchments and biota through Lake Eyre itself, on the rare occasions when the lake is flooded but only moderately saline. Such connections would have long-term implications for regional biodiversity.

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The counterpoint to large floods is extended droughts. Although these are much rarer in the recent record than large floods, the occurrence of such droughts means that the survival of the LEB biota is critically reliant on the persistence of drought refuges. The interannual hydrological variability of the LEB rivers is highest in their lower reaches, and so the distribution patterns and local persistence of many species and entire assemblages may be in a continuous state of flux or disequilibrium. Over the short to medium term (i.e. 1-5 years), the maintenance of water levels and salinity concentrations in shallower (non-refuge) waterholes can also be significantly related to the occurrence of runoff from local rainfall events. Such events increase the probability of waterbody persistence until the next flow event and can thus prevent the local extirpation of some aquatic biota. Given the rarity of truly permanent refuges (which are fixed in their location), these spatially unpredictable event-specific refuges may prove to be equally important in the maintenance of biodiversity in the LEB as the permanent refuges. Over successive drought events, the shifting spatial distribution of these event-specific refuges will promote greater biodiversity by setting in train different successional and dispersal processes when the next flood event occurs. Hydrological persistence The influence of large floods persists well into the next flood season and year. A range of complex mechanisms and relationships are likely at work, but the persistence of large areas of aquatic habitat, along with lags in biological responses, ecological succession and extended recruitment and growth schedules for long-lived organisms, all combine to foster and maintain high levels of abundance and richness across most taxa. Large floods also activate, mobilise and transport large amounts of nutrients which can become bio-available in the early summer of the following flood season. Additionally, hydrological persistence identifies a “ramping” response, whereby large population sizes attained on (for example) the 2000 flood are able to produce equally big or even bigger responses on the smaller 2001 floods. Ramping up of fish numbers was observed during flood clusters in both the Dry/Wet and ARIDFLO survey periods. For instance the Dry/Wet study in the lower Cooper observed ramped increases in the abundance of four native fish species during a cluster of large floods through 1989-1991, and a parallel decrease in the abundance of the exotic fish species, plague minnow (Gambusia holbrooki). A hypothesis was advanced that hydrological persistence (in terms of successive large floods) provides a recruitment advantage for native species over the exotic species, plague minnow (Puckridge et al. 2000). The data collected during the ARIDFLO project tested and supported this hypothesis over a different time period for the same river reach, as well as for different river reaches within the LEB. The time frame over which extreme hydrological events can continue to influence biotic groups exceeds the temporal scope of ARIDFLO sampling. For instance, large floods can replenish significant algal seedbanks and zooplankton eggbanks that can remain viable for decades. Similarly, some fish species (such as LEB golden perch) and waterbirds with high longevities can have particularly successful years of recruitment on large regional floods, and this produces strong year-classes that can persist and influence population dynamics for decades. The contraction of populations under drought is just as significant, and may result in localised extinctions of certain species that may or may not be replaced by dispersers (potential new colonisers) on the next big flood.

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An improved understanding of the influence of such long-term outcomes of extreme hydrological events requires a commitment to long term ecological monitoring. Season The rivers of the LEB show strongly seasonal fluctuations in temperature and rainfall/streamflow. The variations in air and water temperature between winter and summer periods are pronounced and the winter minima are correlated with lower fish activity and less algal growth. These changes have profound effects on the rest of the food chain. As water temperature rises in spring and summer, fish activity increases, seasonal breeding take place, and algal growth rates and abundance increase. Again these seasonal changes have cascading effects. The increase in fish numbers increases predation pressure on macroinvertebrates and zooplankton while the increase in algal abundance increases primary production. Although the general pattern of seasons can be considered predictable, there is considerable interannual variability in the intensity and onset timing of the seasons and summer flows, and this has significant effects on the biota. Such inter-annual seasonal variation affects timing of breeding, extent of breeding, success of breeding, availability of food resources, etc, and is capable of precipitating very different community dynamics and biotic responses between years even with a roughly similar sequence of seasons and flows. Furthermore, different biotic responses may eventuate depending upon prevailing conditions in preceding years, and so interpretation of biotic data collected from single sampling events can be hazardous if considered in isolation. For example, the high winter macroinvertebrate and waterbird abundance estimates in August 2000 are likely reflecting the recession of the large 2000 flood event rather than being typical of winter conditions in years of average flow. However, as only one winter sampling trip was completed during ARIDFLO sampling, further data are needed to test this postulate. Geomorphology There are two major water-transport systems in the large rivers of the LEB: deep, narrow integrated primary channels and broad, shallow floodways on the floodplain. The primary channel system carries flows during all events and the floodplain system only during the larger events. Bankfull depth, bankfull width and the cease-to-flow depth separate five waterbody types (macrohabitats): refuge waterholes, main channel waterholes, off-channel waterholes, floodplain and lakes. The rivers of the LEB have headwaters in areas of relatively low elevation and over the majority of their courses they lie in a flat landscape with very low gradients. One geomorphological consequence of these conditions is the distinctive anastomosing channel form which dominates the wide floodplains of the Channel country and which is well represented in the lower Diamantina reach. Where the Cooper enters the Strzelecki dunefields as seen in the Coongie Lakes region, another equally distinctive river-floodplain morphology has developed.

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There, major disjunctions between alternate flow paths have developed, and while these may reconnect downstream, they do so over much greater distances then in the classic anastomosing forms of the Channel Country. Blocs of sand dunes serve to isolate the various flood paths within this section of the lower Cooper, and so while the combined area of the floodplain is still considerable, the floodplain is highly dissected These distinctive morphologies have major influences on many biotic processes. For instance:

• Large floods result in massive increases of aquatic habitat available to juvenile fish, and support distinctive floodplain algal and zooplankton assemblages. The large transmission losses characteristic of LEB rivers are mainly due to storage (ponding) in waterbodies in channels and on the floodplain. Only subtle topographic variations in such flat landscapes – in the form of bars, sills, levees, gilgais, sand deposits and deflation hollows – are required at first to enable wetland filling and then to promote subsequent disconnection on a receding event.

• Low gradients and complex flow paths result in a mosaic of waterbodies with differing frequencies of inundation and drying, and which are replenished by floods of differing sizes.

• Low gradients also result in slow travel times and, in combination with ponding, this increases the persistence of water on the floodplain to time-scales that allow utilisation of these waterbodies by a wide range of biota (e.g. breeding waterbirds). Not only is there a mosaic of waterbodies with different frequencies of inundation and drying, but also the complexity of and lags in the alternate flow paths combine with the slow passage of a flood to present a series of waterbodies, within close physical proximity, at different stages of filling and recession, providing a wide range of staggered habitats and food resources (a ‘shifting mosaic’).

• Hydrological persistence interacts with the flood path complexity of the multiple lake and channel systems in the Coongie Lakes to present an even greater range of habitats in the one or two flood years following a major flood (such as occurred in 2000). While even quite small regional flow events will normally push new floodwaters into the main lakes in the Coongie system, there will be other, peripheral lakes and floodpaths going through a drying phase, such that a great variety of wetland habitats and resources are simultaneously available to highly mobile organisms such as birds.

Although the relative importance of macrohabitat and microhabitat varies across biotic groups, a spatial mosaic of habitat patches at different successional stages is critical to the maintenance of regional diversity in all biota. Available micro- and macrohabitats should not be considered static entities but as dynamic features of the riverscape that change under varying flow conditions. For instance, microhabitat diversity changes with water level (higher water levels inundate the riparian vegetation whereas lower water levels often result in reduced microhabitat complexity and a dominance of bare banks). Similarly, although the macrohabitat-defined waterbodies are fixed in space (unlike some of the microhabitat categories), their availability as wetland habitat varies dramatically according to the size of flood and extent of floodplain inundation or time since last flow. Changing flow patterns alters the relative roles that local habitat conditions (macrohabitat and microhabitat) play in determining biological responses.

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As mentioned previously, under disconnected conditions local habitat becomes more important in structuring communities, but during large flood events where there is widespread longitudinal (upstream-downstream) and lateral connection (main channel-outer channel/floodplain) so organisms are capable of dispersing over large distances and the role of local habitat is greatly diminished. Salinity The majority of the waterbodies sampled by ARIDFLO were fresh, with salinities generally <500mg/L, and none of the upper reach Cooper or upper reach Diamantina waterbodies sampled had elevated salinities (>1000mg/L), even when sampled at low water levels. However the three South Australian reaches all contained some waterbodies that showed large and fluctuating salinities, up to hypersaline (>70,000 mg/L). There are differences in the mechanisms introducing salt to the waterbodies of the three affected South Australian reaches. The salt in the Neales-Peake appears to be introduced into the catchment by diffuse leakage from the Great Artesian Basin, and it is then stored in the channel and bank sediments. This salt is mobilised during flow events and moves longitudinally into the waterholes during the low flow of the recession. The salt in the Warburton is probably stored in the floodplain sediments and is introduced laterally into the waterholes following large flood events. The salt in the lakes of the Coongie Lakes wetlands accumulates over longer periods by evapo-concentration. However, despite these different mechanisms, salinity fluctuations in the channelised waterholes of the Neales and lower Diamantina reaches share certain similarities, which substantially affect the aquatic biota:

• Affected waterholes are saline and only become fresh when flushed by flows. In contrast, the downstream lakes of the Coongie Lakes wetlands (e.g. Apanburra and Goolangirie) can be considered fresh and only increase significantly in salinity at very low water levels.

• Salinity of the waterholes does not rise significantly until inflow rates are quite low, the flow velocity within the waterhole is effectively zero and there is rapidly declining connection between waterholes. Possibly connection is closed to larger fish due to the low inflow rates when salinity rises to levels >1500-2500mg/L.

• In the Neales, the larger the flood event, the more rapid is the post-flow rate of rise in salinity as well as the magnitude of the salinity rise. It is uncertain to what extent salinity increases in the waterholes of the Warburton River are related to the size of the previous flood.

Thus while salinity had a large impact on the assemblage composition of many of the biotic groups, it was an influence restricted to the lower sections of the South Australian reaches. To survive saline conditions, aquatic organisms must possess physiological mechanisms capable of tolerating the high salinities, or have the ability to disperse to fresher habitats, or be able to deposit seeds or eggs capable of germinating or hatching upon the return of fresher conditions. High salinities generally result in a switch to alternative community states composed of salt-tolerant taxa and which are sometimes less diverse than the freshwater communities (e.g. lower taxa richness for fish and zooplankton).

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However, this is not always so, e.g. there is no significant change in taxa richness for algae until very high levels of salinity, although the assemblage composition is different at moderate salinities. All biotic groups have salt tolerant taxa (to at least hypersaline levels of around 70,000 mg/L, 100,000µS/cm) and thus there is generally only a weak correlation between the abundance of a group and the salinity of sites. This demonstrates the ability of salt-tolerant taxa to take advantage of the shifting patterns of saline conditions in the LEB surface waters and to increase their abundance at the expense of less salt-tolerant taxa.

Major findings by biotic group Rapid response algal assemblages The ARIDFLO project provides the first comprehensive survey of planktonic and benthic algae in the three South Australian reaches of the LEB. Algae have specific ecological tolerances to such variables as salinity, flow, light and temperature, turbidity and nutrient status and, if identified correctly, can indicate the status of a particular water body in the absence of physico-chemical measurements. The algae of the LEB were no exception. Algae are, for the most part, cosmopolitan and occupy the same niches in Australia as in lakes and wetlands in other parts of the world. An example of this is the Rift Valley Lakes region in Ethiopia (Kebede, 1996), where not only was the overall diversity of algae almost identical to that in the LEB but many of the same taxa were found in sites of similar water quality. The algal community of all three LEB reaches was moderately diverse with upwards of 240 taxa from 123 genera in seven phyla (divisions) identified in the study area This compares to approximately 400 genera recorded from Australia as a whole (Entwisle et al. 1997). 50% of the genera were common to all three reaches and only 14% were collected in one reach only. (Algae were identified for the two Queensland reaches but not on all sampling occasions and so the Queensland results were not included in the statistical analyses). At the reach scale the lower Cooper (Coongie Lakes) reach had the highest mean generic richness and the highest mean relative abundance, and the Neales the lowest. The higher richness and production of the Coongie Lakes wetlands results from a combination of the lacustrine nature of the environment and the large floods which probably allow the release of a greater store of nutrients and spores from lakebed sediments than from other habitats. The lakes will also receive nutrients through a full flooding-drying cycle, due both to their depositional nature and the focussed activities of consumers higher in the food chain. It was concluded that the rich and distinctive algal assemblage in the lakes in the two summers following the large 2000 flood had resulted from a combination of higher temperatures and available light, nutrient inputs, sedimentation processes and lake stratification. A high proportion of the algae collected were of benthic origin as samples were collected close to shore. In April 2002 comparisons were made in all three of the Coongie Lakes between the samples collected at the usual depth near shore and those from mid-lake. The littoral/benthic samples had approximately twice the number of genera as the mid-water/planktonic samples and were dominated by euglenids (species of Euglena, Phacus, Lepocinclis and Trachelomonas), benthic diatoms (Nitzschia and Navicula) various green algae (Pediastrum) and cyanobacterial of benthic origin (Oscillatoria, Cylindrospermum, Anabaena).

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Genera of the euglenid group are indicative of waters rich in organic nutrients, suggesting that the nutrient load from the avian and bovine faecal material observed around the shoreline of Coongie Lakes is impacting upon the composition and relative abundance of the littoral algal assemblage. In addition to the regular plankton trawls, opportunistic samples of visible accumulations of filamentous cyanobacteria, green algae and diatoms were collected from the margins of waterholes and lakes (the "bathtub ring"), submerged stones and vegetation and the shells of a freshwater turtle (Emydura macquarii emmottii). Cluster analyses identified four major algal assemblage groups in the South Australian samples:

1. A moderately diverse assemblage of saline tolerant taxa (principally from the Neales and lower Diamantina), collected from sites with salinities >2,000μS/cm. These were the cyanobacterial filaments Anabaenopsis, Nodularia, Spirulina and certain species of Anabaena, the diatoms Nitzschia Entomoneis and Gyrosigma, and the dinoflagellate Gymnodinium. Due to the presence of salt-tolerant taxa, in general increasing salinity results in major changes in assemblage composition but not in overall taxon richness. However, at high salinities, (>50,000µScm-1 or approximately seawater), taxa richness declines sharply.

2. Moderately diverse assemblages at sites with low salinities. These sites were principally from the lower Diamantina and Neales and were characterised by one of three criteria: (1) collected during the winter trip (August 2000), (2) collected from isolated sites without flow for some months, (3) collected from sites that received recent inflow from local rainfall. The linking factor between all three criteria was low fish numbers and abundant microfauna which suggests that increased grazing by microfauna and invertebrates was responsible for the lower algal diversity.

3. Highly diverse assemblages at low to moderately saline sites that were flowing or had received some flow in the previous few weeks. The diversity of euglenids again suggests high organic nutrient levels for sites in this group. Other genera significantly correlated with this group were Anabaena (cyanobacteria), Pediastrum and Eudorina (green algae) and Aulacoseira and Synedra (diatoms). Sites from the lower Cooper also formed a distinctive cluster within this group.

4. A low diversity group consisting of only four sites.

Drought significantly influences the LEB algal assemblage. Major changes in algal composition were recorded as reaches progressively dried out during the later sampling trips, particularly in the lower Diamantina where richness substantially decreased. In contrast, current and recent flow has a major influence on increasing the richness of the LEB algal assemblage probably through two mechanisms; (1) stimulation of algal germination from resting spores in waterbodies and floodplain/channel sediments, and (2) transport of algae from aquatic refuges into downstream positions. In relation to the first mechanism, a variable flow regime (i.e. sequences of wetting and drying) and an undisturbed channel/floodplain system may be important features in maintaining algal diversity.

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In relation to the second, maintaining both river connectivity and aquatic refuges is critical in maintaining algal diversity. The rapid response of the algal community to changing hydrological conditions is best demonstrated by the samples collected from drought-affected waterbodies with low water levels on the Neales in February 2003. The drought samples contained only a few saline tolerant taxa yet, within a few days of the arrival of a regional flood, taxon diversity markedly increased with the emergence of many algae typically found at lower salinity levels. The saline tolerant taxa had disappeared. The cyanobacteria (blue-green algae) were of particular interest in the study because of the potential of some species to form dense surface scums (blooms) that are toxic to stock, waterbirds and any small animals drinking the water. Allergic reactions are known in humans. Decomposition of these blooms can cause severe oxygen depletion with subsequent stress on fish populations. The eventual progression to anaerobic conditions in the sediments may result in conditions conducive to the proliferation of the causative organism of botulism which is lethal to waterbirds. Toxic cyanobacterial blooms reported in other parts of Australia have occurred predominantly in regulated systems such as the Murray-Darling or in estuaries, lakes and farm dams which receive high loads of phosphorus and nitrogen either directly from effluents or indirectly as a result of land use practices (e.g. Young 20001a). In contrast the natural regime of LEB rivers, so far as can be deduced from the results of this study, has not resulted in the development of toxic blooms, despite the large load of nutrients recycled from the activities of waterbirds (Reid & Gillen 1988). The cyanobacteria in the LEB occurred over a wide salinity range but were not found in abundance until the drought conditions of April 2002 and February 2003. Nodularia spumigena and Anabaena circinalis, both of which are potentially toxic to stock, were of common occurrence on two occasions, the former at two higher salinity sites (>10,000μ EC) and the latter in two lower salinity sites (<1000μ EC). Most of the time however, the potentially toxic species were recorded as rare and did not dominate the plankton assemblage at any stage during the study period. A bloom of Planktothrix cf. perornata, of unknown toxicity, was observed in the North West branch of Cooper Creek in February 2003. Blooms of non-toxic species were observed in April 2002 in Lake Goolangirie (Anabaena aphanizomenoides) and in February 2003 in Yelpawaralinna Waterhole (Microcystis cf. panniformis). Riparian vegetation characteristics The rivers of the LEB are generally characterised by low abundance and diversity of macrophytes because of the high turbidity of the surface waters (Bunn et al. 2003). In the absence of macrophytes, the riparian vegetation types provide important aquatic microhabitats for several biotic groups, depending on the current water level. Therefore, understanding the relationship between waterbody morphology, flow regime and riparian vegetation patterns can improve our understanding of assemblage dynamics for several biotic groups as well as for the riparian vegetation itself. The major structural elements of the riparian zone showed distinctive vertical zonation relative to geomorphological levels. Generally, the coolibah zone occurred around the bankfull depth and the base of the lignum zone occurred around the cease-to-flow level of the waterbodies. Red gums also occurred just above the cease-to-flow level and nearly always below bankfull depth.

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More ephemeral vegetation, such as cyperus (Cyperus gymnocaulos), polygonum, grasses and herbs occurred between the lignum level and current water level. Observations suggest that to some extent, cyperus and polygonum are both able to retreat or advance along the bank profile as the water level varies and so maintain a position close to the current water level over a range of conditions. Rank abundance measures of 20 woody plant species (plus nardoo and sedges) were taken in 73 quadrats at 54 waterbodies. Three species - coolibah, lignum and river coobah - were present in over half of all quadrats. Ordination analyses of the long-lived woody plant species were carried out to produce sites scores for analyses. These scores can be considered ‘regime’ environmental variables as, being derived from long-lived woody vegetation data, they are invariant within the time scale of the ARIDFLO project. Queensland waterbodies were found to be associated with nardoo and Queensland blue-bush. The Neales waterbodies were often correlated with the halophytic samphire, reflecting the saline nature of several sites. Finally, refuge waterholes on all river systems tend to be associated with river red gum, coolibah, Queensland beantree, Broughton Willow and lignum. First study to identify LEB zooplankton Zooplankton were only identified for the three South Australian reaches. Overall 423 taxa were recognised from samples collected during the first six field trips. At least 21 new species were recorded - 20 rotifers and one microcrustacean. A further 10 species of microcrustaceans had unusual features and are potential new species. Range extensions included new records for eight rotifer taxa in Australia and one for a microcrustacean taxon. Virtually all the microfauna identified are first records for the LEB. The total number of microfaunal species identified in the ARIDFLO sampling is similar to multi-site, species-resolution studies of other arid and semi-arid basins. Comparable Australian surveys were of ephemeral floodplain waterbodies of the Murray-Darling Basin (Shiel et al. 1998) and of a range of wetland types (river-fed, lakes, claypans) in the Carnarvon Basin, WA (Halse et al. 2000). Notably however, the mean taxon richness per sample site in the ARIDFLO survey was higher than for the MDB and Carnarvon Basin surveys. Of the three SA reaches, the lower Diamantina had the highest total taxon richness, and the Neales the lowest. The lower diversity in the Neales may be a function of both the smaller catchment size of the Neales and its higher proportion of saline waterbodies which reduce zooplankton richness. The percentage composition of the major zooplankton groups – Protista, Rotifera, Crustacea and Other (typically juveniles of aquatic insects or predatory water mites) – also varied between trips. During the April trips (during or soon after floods) the relative proportion of rotifers was high compared to microcrustaceans. However during the winter (August 2000) and early summer trips (November 2000, 2001), this relative proportion was reversed and the overall taxa richness was lower. This may reflect responses to season such as changes in predation pressure (by either macroinvertebrates or larval fish), and/or could represent responses to hydrology.

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For instance, rotifers predominate in flowing waters (April trips), whereas microcrustaceans do better in low or no flow (August and November trips). However, predatory corixid macroinvertebrates were also very abundant in August 2000 and may well have imposed significant top-down predation pressure on zooplankton. In a related pattern, overall zooplankton diversity was highest during the large flood events of April 2000 and through the following summer floods, then both flood sizes and overall diversity decreased through 2001-2002 as drought conditions developed. The floodplain macrohabitat had the highest number of significantly associated taxa (i.e. indicator species: 12), off-channel waterbodies were next (5), then lakes (1), and main channel waterbodies had none. This implies that floodplain habitats have a distinctive zooplankton assemblage. It is not known to what degree this diverse assemblage is the result of the large flood event of 2000 transporting a diverse microfauna downstream, and/or to what degree it results from floodwaters stimulating the hatching of zooplankton from desiccation-resistant eggs in the floodplain sediments. There is no reliable estimate of the viability or longevity of the various components of the egg bank in LEB (or other Australian) conditions, but it is likely that the LEB microfauna is capable of surviving extended dry periods in sediments. Cluster analyses identified four major assemblage groups in the South Australian samples:

1. High diversity samples which belong to the flood-related April trips on all reaches, although this group was associated most strongly with the small flood of 2001 rather than with the big flood of 2000. The predominance of April samples could be ascribed to either a seasonal factor and/or an effect of the late phase of annual flooding.

2. High diversity samples from lower Cooper sites, and mainly from Trip 3 (December 2000). Trip 3 conditions were characterised by receding water levels (after the large floods of 2000) and a diverse algal assemblage.

3. Low diversity assemblages from sites with elevated salinity.

4. Low diversity assemblages from a variety of trips, but predominantly from sites characterised by extended periods of disconnection and falling water levels. Compositional changes due to competitive interactions and predation are likely on the receding limb of floods, particularly after waterbodies become disconnected. With declining water levels habitat diminishes, population densities increase and resource partitioning becomes more critical.

Macroinvertebrate diversity driven by microhabitat complexity Some 136 taxa were recognised and, basin-wide, the cumulative taxon richness was asymptotic from Trip 4 onwards, i.e. very few new macroinvertebrate taxa were detected. This suggests that the sampling program captured most of the macroinvertebrate taxa (at the level of taxonomic resolution adopted) in the sampled areas by this trip. Of the five ARIDFLO study reaches, the lower Diamantina had the highest cumulative taxon richness (100 taxa), followed by the Thomson (91), Neales (85), Coongie Lakes (83) and upper Diamantina (55). The mean taxon richness per waterbody for each of the ARIDFLO reaches is generally equal to or greater than that determined for the Murray, Darling, Diamantina and Cooper catchments in previous surveys (Sheldon, unpublished).

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The mean sample taxon richness at the reach scale showed significant variation between trips and reaches, but mean taxon richness per reach generally declined over the sampling period. This decline reflects the decrease in flow volumes and onset of drought conditions. High macroinvertebrate richness is associated with large floods whereas low richness is associated with drought. The highest mean sample taxon richness per reach (the lower Diamantina excepted) was recorded on Trip 2 (August 2000). This was a winter trip in the lower Cooper and lower Diamantina and sampled the still-flowing recession tail of the large 2000 flood. The waterbodies sampled in the other reaches were all relatively recently disconnected and still at moderately high water levels. Flooding can cause large and rapid swings in the composition of the macroinvertebrate fauna. Samples from the Neales on Trip 7 (at the end of the 2002-2003 drought) are a good example of this. Sites that were extremely saline and had no macroinvertebrate fauna when initially sampled were, a few days later, teeming with Branchinella, conchostracans, Triops and beetle larvae. These macroinvertebrates had obviously been washed into the river from the floodplain. The trip with lowest mean sample taxon richness was Trip 7 (February 2003), which in the SA reaches corresponded with a major drought. Queensland samples were collected just after flooding and in those samples there was no obvious effect of the 2002/2003 drought on taxon richness. Given the exceptional hydrological variability of the LEB, its macroinvertebrates have to deal with dramatic and rapid changes in microhabitat over time. The types and extent of riparian microhabitats available for littoral macroinvertebrates depends greatly on flow conditions and water levels. Typically during sub-bankfull flow, the water level is amongst the lignum, red gums and ephemeral/herbaceous vegetation. However after the cessation of flow and falling water levels, few microhabitats are available apart from bare banks. The upper Diamantina had a significantly lower mean sample taxon richness than other reaches, which is likely attributable to the lower diversity of microhabitats on this reach. Upper Diamantina waterholes sampled were typically deep, steep-sided main channel waterbodies with high discharges during floods and bare banks offering little microhabitat complexity. Over all ARIDFLO reaches, samples collected from bare microhabitats accounted for about 40% of all samples. The remainder in decreasing order were; coolibah (20%), lignum (14%), Cyperus (9%), snags (6%), herbs (4%), tea-tree - Melaleuca trichostachya (4%) and Polygonum (3%). Bare microhabitat samples tended to have the lowest mean sample taxon richness (varying between 5-15) whereas the highest (33) was recorded from the Thomson on Trip 2 from Cyperus. Three other high values for richness are Polygonum (29, Coongie Lakes, Trip 6), lignum (27, Coongie lakes, Trip 6) and herbs (27, Neales, Trip 5). On Coongie Lakes, the upper Diamantina, and the lower Diamantina in August 2000, the corixids had very high relative abundances - 45%, 72% and 43% respectively, of all fauna collected. The high abundances of these predators probably have some influence on the low taxon richness of zooplankton collected during this trip.

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Salinity is an important driver of the Neales macroinvertebrate assemblages. The saline waterbodies (>10 000µScm-1) generally had a mean sample taxon richness of 0-11, the less saline waterbodies 5-20. There were fewer saline waterbodies on the lower Diamantina and they had mean sample taxon richnesses of 3-8. The four taxa that are indicator species for saline waterbodies, Necterosoma, Berosus, Culicoides and Tanytarsus were all found on the Neales reach. Cluster analyses identified five major macroinvertebrate assemblage groups:

1. Samples particularly from the Neales with high salinity, bare microhabitats, low taxa richness, but not necessarily low abundances. Indicator species include the beetle Necterosoma, chironomid Tanytarsus and Culicoides which are correlated with water conductivities >10,000µScm-1.

2. Samples tending to have low to medium taxon richness and abundance and being principally from the later trips to waterbodies with low water levels and long periods of disconnection. Indicator species include the chironomid Harnischia and the small bivalve Corbiculina.

3. Samples with variable richness and abundance but associated with recent flood events. A characteristic of many of these flow events is that they were sourced from relatively localised rainfall events from a limited catchment area. Most such sites were from Queensland reaches and the Neales where relatively fast discharge rates and velocities may be important. The indicator species, Aedes (mosquito) and the three crustacean taxa; Branchinella, Triops, and conchostrachans are more commonly creatures of the floodplains. They are highly susceptible to fish predation when they are washed into waterholes and rivers. On Trip 5, two of the waterholes on the Neales (COOT and BIRR) had an abundance of Branchinella in them and the few fish that were present were very fat. The gastropod Notopala and chironomid Parakiefferiella are also indicator species for this group.

4. Samples tending to be of medium to high taxon richness and abundance. There are 23 indicator taxa, three of which are also indicator species for water conductivity. The chironomid Nanocladius and the caddisfly Triplectides are correlated with water conductivities of <500 µScm-1 and the chironomid Coelopynia pruinosa is correlated with water conductivities of 500-2,000µScm-1. The correlation with low water conductivity suggests this group is possibly structured by flood dispersal or invertebrate booms due to big floods, as low water levels are often associated with rising salinities, particularly in the shallower water bodies.

5. Samples with low taxon richness and abundance and from the later drier trips (3-7) and bare microhabitats. There was only one indicator species, the shrimp Macrobrachium australiense.

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Abundant native fish Native fish in LEB Rivers are abundant and indicative of good ecological health. Of the fifteen native species known to occur in the Cooper, Diamantina and Neales Rivers, all were detected during ARIDFLO. Further, discovery of a potential new grunter species or hybrid (Scortum sp.) may increase the species list to sixteen. Range extensions and confirmation of isolated distribution records were also made for seven native species, helping extend our knowledge base for LEB fishes. The abundance of native fish in the LEB is demonstrated by the total size of the ARIDFLO catch: 103,869 native fish over seven surveys and five river reaches. A similarly broad-scale project, the NSW Rivers Survey (Harris and Gehrke 1997), collected only 29,788 fish (including exotics), yet used more efficient techniques (electrofishing) with greater sampling effort. However, ARIDFLO fish abundance estimates varied widely across waterbodies and surveys. Although standard sampling typically captured between 150 and 300 native fish per waterbody, the range spanned from zero to over two thousand, reflecting variability in the environmental conditions encountered at different waterholes. Although LEB Rivers possess a rather limited total number of fish species, waterholes along these rivers have a relatively high species count at local scales. That is, most fish species are captured across a range of macrohabitat types and their distributions appear less restricted than fish of the Murray-Darling Basin (with the notable exception of the LEB Cooper Catfish, which is associated only with deeper refuge waterholes). The total number of fish species in the LEB is only half that of the Murray-Darling Basin, yet when ARIDFLO catch results were compared to the NSW Rivers Survey (Harris and Gerhke, 1997), sites on the Cooper and Diamantina yielded more species per sampling effort (average 5.3 and 4.5 respectively) than the Murray (3.1) and only slightly fewer than the Darling (6.3). This locally high species richness is partly due to the mobility of most LEB fishes, but is also considered characteristic of a relatively pristine ecology, where species still maintain viable populations. Upstream LEB reaches were also found to have higher average species richness than downstream reaches (Cooper 6 versus 5, Diamantina 4.9 versus 4.3), as conditions become more extreme and deep-water refuges less common downstream. This is principally a function of these rivers being endorheic (internally draining), flowing into increasingly arid areas and having diminishing flow volumes, smaller, less defined channels and less diverse habitats downstream. Remote waterholes a long distance from refuge waterholes were also found to be relatively species poor, for although most native fishes are exceedingly mobile, their dispersal capabilities and behavioural preferences vary considerably over distances of hundreds of kilometres. There have been recent concerns about a lack of quantitative evidence for the use of floodplains by native fish in the Murray-Darling Basin (e.g. Humphries et al. 1999). However, ARIDFLO clearly demonstrated that in an environment where natural connectivity between the river and its floodplains has not been disrupted, native fishes, particularly juveniles, actively disperse into floodplain habitats. Floodplains in the LEB were found to harbour almost as many species (4.50±0.57SE) as were found on average in deep refuge waterholes (4.99±0.22SE). Whilst generally variable in character, floodplains in the lower reaches are typically vast low-lying areas of terrestrial and semi-terrestrial vegetation (e.g. lignum) subject to shallow inundation during floods.

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This vegetation may dry within weeks or days following flooding, environmental conditions can be harsh, and any fishes using such ephemeral habitats run the risk of being stranded. However, such habitats provide a bounty of plankton, micro- and macroinvertebrate food resources for larval and juvenile fish and shelter from larger predatory fishes. Across all five reaches, fish assemblages were generally found to be highly variable in their species composition and abundances, shaped by prior hydrological history at each site. Localised invasions and extinctions are expected and do occur. For example, the first few individuals of native glassfish (Ambassis spp.) appeared in the lower Cooper during the large floods of 1990-91 (Puckridge et al. 1999), and by the time of ARIDFLO sampling (2000-2003) had become ubiquitous in the Coongie Lakes fish community. Localised species losses were also recorded as waterbodies dried and lost their fish fauna (e.g. Bobbiemoonga on the lower Diamantina in 2001). These sites are dependent upon receiving new fish colonisers on the next flow or flood event. In general, both species abundance and richness estimates were higher when a flow pulse was occurring or had recently occurred, most likely due to flood-induced movements and breeding. Such increases are attributable to ecological ‘mass effects’, caused by the capture not only of resident fish, but also of other fish passing through the sampling site, particularly juveniles. For example, in April 2001 flood-waters from the Georgina River entered Goyders Lagoon via Eyre Creek and travelled towards Lake Eyre along the Warburton River. Although the flood was relatively small by the time it reached Goyders Lagoon, it carried many thousands of Georgina River rainbowfish, glassfish and banded grunters. This demonstrates how the typically fragmented fish assemblages of the LEB can be rapidly reconnected on large flow events. Lurking exotic fish Exotic fish species constitute only a minute fraction of the fish community in the hydrologically undisturbed LEB Rivers. Over the seven ARIDFLO surveys, only 2 goldfish and 751 plague minnow were collected, 0.7% of the total catch. In comparison, the Murray River fish assemblage is dominated by exotics in many areas (97% of the catch, McKinnon, 1993; 57.5% of the catch, Harris and Gehrke 1997). In terms of regional distribution patterns, the only species expected to occur in particular reaches but not collected during ARIDFLO surveys turned out to be exotics. The notoriously invasive plague minnow formed only sporadic and usually small populations in the Cooper and the Neales Rivers and was not recorded at all on the Diamantina River, even though it has previously been recorded in several bore drain habitats in the upper Diamantina. Goldfish have previously been recorded from the upper Cooper, typically in modified habitats such as the Lloyd Jones Weir on the Alice River, but during ARIDFLO only 2 individuals were collected from Coongie Lakes. In disturbed catchments in Australia and overseas, exotic species are increasing at the expense of natives. But is the increase in exotic species a symptom of poor river health or a cause of decline in native species? The large spatial scale of ARIDFLO and relatively long temporal scale of study of the Coongie Lakes reach (17years) provided a unique opportunity to study the controls on abundance and distribution of exotic fish in virtually natural rivers, free from significant hydrological alteration.

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The presence of exotic species per se has not led to a decline in native fish diversity or abundance in the Coongie Lakes over the last seventeen years. In fact, the frequency of detection of goldfish in the lower Cooper has actually declined from one-in-nine samples to one-in-ninety-six between the Dry/Wet survey of 1986-1992 and the ARIDFLO survey of the same sites in 2000-2003. Further, although plague minnows have not shown any significant decline between the 1987-1992 and 2000-2003 time-periods, their populations have remained at low abundances. This provides some evidence that poor river health (disrupted ecological function), rather than the presence of exotic species, is a driver of increased exotic fish abundances and reduced native populations in regulated rivers. In contrast to native species in the LEB, it also appears that exotic fish such as plague minnow and goldfish are unable to capitalise as effectively on flood clusters. On the Thomson, Coongie Lakes and Neales reaches, exotic species showed no response to the large floods of early 2000 and follow-up floods of 2001. The ‘catchability’ or abundance estimates did not increase following these events as it did for native species. Indeed, plague minnow abundances in the lower Cooper showed significant relative declines following clusters of large floods in both the Dry/Wet and ARIDFLO surveys. We hypothesise that plague minnow are disadvantaged by floods because high water levels reconnect their disconnected and shallow refuges, leaving them vulnerable to native predators. Furthermore, their reproductive strategy of live-bearing a limited number of young with a gestation period of 28 days may delay their response to the bounty of zooplankton and other larval-fish food produced by flood events. As plague minnow and goldfish occur at low but variable abundances in the LEB, they can be viewed as ‘sleeper’ exotic species. i.e. they are established components of the fish assemblage but are not as yet having a significant impact on ecosystem processes. Perhaps this is because the extreme hydrological variability and/or the strong populations of native predators suppress exotics. More generally, the unregulated hydrology of the LEB Rivers is likely to contribute strongly to sustaining the integrity of their indigenous fish faunas. However, the ‘sleeper’ status of the two exotics implies that human intervention could tip the balance in favour of these pests and their distribution and abundance in the LEB Rivers should be closely monitored. In particular, the artificial persistence and stability of weir pool environments may well be supporting the maintenance of pest fish species in the LEB. Natural outbreaks of fish disease Large-scale disease outbreaks are natural occurrences in LEB Rivers, particularly following the disconnection phase after large floods. Disease is not necessarily an indicator of a ‘health problem’ in the ecosystem, rather diseases and parasites of fish are indigenous components of healthy ecosystems. However disease outbreaks remain a symptom of stressful environmental conditions, and the challenge for managing LEB River systems is to discriminate anthropogenic from natural causes of such stress and to decide if, when and how to intervene. For example, although widespread flooding can open up new habitats and food resources for fish, the falling flood may bring such stressors as overcrowding, low dissolved oxygen levels, high temperatures and poor water quality. Extended exposure to such stressors may leave individuals susceptible to disease and death. This may be a natural process, but may also be exacerbated by human-changes such as increased nutrient levels, enhanced algal blooms and reduced water quality. During ARIDFLO surveys in August 2000 and April 2001, large numbers of fish were affected by necrotic bacterial and fungal lesions in recently flooded waterbodies on the Diamantina and the Coongie Lakes reach. Sick individuals were from a range of species, although golden perch and grunters appeared to be particularly sensitive. Disease outbreaks reached a peak several months after the beginning of a flood pulse and then decreased as

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environmental conditions stabilised during disconnection. Flooding appears to result in the development of sub-lethal but stressful environmental conditions, and over several months these protracted conditions lead to disease outbreaks and occasionally fish-kills. This lagged development of disease followed by fish-kills contrasts with the pattern in tropical northern Australia (e.g. in Magela Creek) where kills typically occur with the first flushing flows, which have lethally low dissolved oxygen levels. However, this is not to say that rapid fish-kill events do not occur in LEB Rivers, as evidenced by the fishkill of hundreds of Golden perch at Longreach in November 2002. These locally catastrophic events are more typically associated with drying waterholes, low water levels and lack of flow, where anoxic conditions develop, often from the high nocturnal oxygen demands of algal blooms. Thus, environmental conditions stressful to native fish can develop at many points through the hydrological cycle, including flows and floods as well as drought. In contrast to the Diamantina and lower Cooper, very little disease was recorded on the Neales over the 2000-2003 period. The moderately high salinities on this reach may reduce osmotic stress for freshwater fish and directly suppress some of the common pathogens such as Saprolegnia. The few cases of disease recorded in February 2003 were from fish in small, rapidly drying pools, where temperatures were high, oxygen levels low and fish were over-crowded. Spectacular booms of waterbirds in Coongie lakes Seventy one waterbird species were recorded during systematic ground surveys on selected ARIDFLO waterbodies in the LEB. A further six species were recorded incidentally on other waterbodies, and several other wetland-dependent landbirds were also recorded. These 77 waterbird species comprise the majority of the non-vagrant, inland Australian waterbird fauna. The large floods initiated in the LEB in the summer of 1999/2000 in the Cooper and Diamantina and in 2000/01 in the Georgina River-Eyre Creek provided an enormous amount of wetland habitat. Forty-five of these 77 species were recorded breeding in this habitat, and over 40 sites of colonially nesting waterbirds were documented. These breeding sites included many previously unknown to science but well known to the LEB resident community. The LEB wetlands are now known to support hundreds of thousands to several million waterbirds from a wide range of species, and to support breeding of most of them. In Lake Eyre itself, breeding of 18,000 pairs Banded Stilts and the fledging of 50,000 of their progeny took place in 2000 after a partial filling of the lake. Many colonies of Australian Pelican were also recorded in the ARIDFLO Channel Country study region, with as many as 100,000 pairs breeding over 2000 and 2001. Three very large (>10,000 pairs) mixed-species nesting colonies – with up to 13 species breeding together, the largest comprising at least 50,000 pairs – were established in 2000 and 2001 in the Queensland Channel Country, while many smaller colonies were recorded in both States.

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The extensive floodplains of the Channel Country are now known to be a major powerhouse for waterbird breeding in the national context, and the more extensive and more regularly inundated components in Queensland are more important, in this respect (reproduction), than the heralded Coongie Lakes system in South Australia. Fourteen species detected over the study have special conservation significance, either nationally or within State jurisdictions, and migratory shorebirds have conservation significance under international agreements. Many of these sightings were on the lower Cooper (Coongie Lakes) reach. Eight of these species were noted breeding in the study period. The lower Cooper reach (Coongie Lakes) dominated the waterbird results in species richness and total waterbird abundance. Only one of the 71 species (Pectoral Sandpiper) was not recorded there – 83% of all waterbirds counted during systematic site visits were on the Coongie Lakes waterbodies. These waterbodies dominate ARIDFLO’s waterbird results because of the rich shallow wetland habitats provided by the lakes; no other reaches have comparable habitats. Of the three South Australian reaches the lower Diamantina was intermediate after Coongie Lakes in cumulative species richness and abundance, the Neales last in cumulative species richness and markedly so in total abundance. The catchment area, flow volumes, waterbodies and floodplain of the Neales are all much smaller than those on the Diamantina-Warburton. Also the western drainages of the LEB are more isolated from the continental network of major Australian wetlands than are the eastern rivers. These factors probably explain the Neales’ lower cumulative species richness and abundance. The Queensland reaches have steeper topographic gradients, higher flow rates and shorter water-residence times than further downstream, so wetlands capable of supporting large numbers of waterbirds are rarer (it should be noted that these study sites lie upstream of the Channel Country). Cumulative species richness was similar for both reaches but total waterbird abundance was several times as great on the upper Diamantina as on the Thomson. When abundance is corrected for survey effort, both Queensland reaches support a more abundant fauna than the Neales. Five major groupings (containing 14 sub-groups) could be recognised from the analysis of waterbird assemblage composition. Species richness was a structuring influence, and three of the major groups (II-IV) consisted of a small number of depauperate counts from the Neales catchment, and are probably due to chance co-occurrences of a few species drawn from a larger species pool. Most other observations were allocated to the four sub-groups in Major Group V, which comprises observations with moderate to high species richness and high abundance. Waterbird diversity and abundance increased markedly in response to the one in ten year floods at the start of the ARIDFLO study period, with increases in both these measures at waterbodies in the four reaches on the Cooper and Diamantina between Trips 1 & 2. These trends were probably driven by the draining of floodwaters off the floodplains of all five reaches by August 2000, with birds converging on the more reliable waterbodies. Also, the LEB wetlands were probably being actively colonized from outside the region throughout this first half of 2000, initiated by the large flooding events late in 1999 and early in 2000. Therefore, more species in greater abundances could be detected in August 2000. While species richness also increased at Neales River sites, mean abundance declined slightly over the same period, and this may have represented an emigration of waterbirds from the western Lake Eyre drainages east to the Diamantina and Cooper systems. Breeding by many species was recorded in this period.

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Following large flood events, spectacular recruitment of waterbirds occurs in the LEB wetlands. Since most of the species involved are highly mobile, virtually the whole population of a given species has the capability of flying into the region from elsewhere at these times and of emigrating once breeding has been completed and wetlands dry out. Hence the dynamics of the LEB waterbird fauna are classically ‘boom and bust’ and, significantly, have the capacity to play a major role in waterbird production and changes in population size throughout the continent. Mean abundance per waterbody and species richness were both lowest during the first survey, when the area of inundated floodplain was at its maximum. This result was probably due to (1) a lag in the colonisation of the newly flooded LEB wetlands, (2) waterbird populations being dispersed over a vast area of newly inundated floodplain, and (3) the fact that extreme rainfall and flooding truncated waterbird survey effort in the Coongie Lakes reach. In fact flooding allowed access to only four of the eight regularly surveyed Coongie Lakes sites on this April 2000 trip. Two other trips had low abundances, namely Trips 4 (March-April 2001) and 7 (January-April 2003). In 2001 at the time of ground surveys, there was a major flood in the Georgina River-Eyre Creek system and moderate sized floods along the Cooper and Diamantina were also in progress, and so many birds had probably dispersed onto recently filled wetlands. Certainly many waterbirds appeared to shift to the Eyre Creek wetlands, judging by the results of the aerial surveys. By the final trip in early 2003, the LEB was in drought – the ‘boom’ period of 2000-01 was over and the ‘bust’ was firmly entrained. Therefore, while the mean abundance per waterbody on the final trip was over twice that on the first trip, basin-wide total population was (on aerial survey) an order of magnitude or two lower than on the first trip. The highest abundance was recorded on the sixth ground survey (April 2002) when 90,932 individuals were counted, and 96% of these were in the Coongie Lakes system. Another 11,000 birds were counted during incidental surveys of four other lakes to the east of Lake Goolangirie in this reach. The greatest count from a single waterbody was obtained on this occasion, with ca 53,000 individuals counted on Lake Goolangirie. The general result of recorded low densities at flood maxima and high densities in draw-down and bust periods seems at first counter-intuitive, but in reality is testimony to the pitfalls of not considering all and relevant spatial scales, and ARIDFLO deliberately undertook aerial surveys of the wider Channel Country and Lakes region (‘Channel Country’) of the mid-lower LEB to obtain this broader perspective on waterbird spatial dynamics. Aerial survey results indicated that in excess of 4 million waterbirds were present in the Channel Country at the height of flooding in early 2000, and the true figure is believed to be closer to 8 million waterbirds (of all species) –more waterbirds than have been estimated in any region of Australia before. The 2000/01 Georgina River-Eyre Creek floods resulted in at least 1.5 million waterbirds, probably closer to 3 million, flocking to these wetlands (on this river system alone), and several new breeding colonies were discovered on the Eyre Creek floodplain in autumn 2001. A major finding of significance is that the Channel Country wetlands, particularly in Queensland, are of primary importance to waterbird breeding effort in Australia. It is likely that further research will reveal that these Channel Country wetlands are more productive for waterbird recruitment than most other parts of Australia and, as such, the future prospects of many inland Australian waterbird species will be shown to depend greatly on the continued health and vigour of these wetlands at times of extensive flooding.

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By contrast, lakes support a great abundance of waterbirds in drying phases (2002-03) when little or no floodplain habitat is available to waterbirds. Under drought conditions, all lakes may eventually dry – and Coongie Lake itself went dry early in 2003 – and so most waterbirds have to depart the LEB if they are to survive. On the last trip the remaining waterbirds in the LEB had retreated to the deeper waterbodies, demonstrating the drought-refuge value of these sites. For example, 88% of all waterbirds counted on the last trip were on the shallow rapidly drying waters of Coongie Lake. At this time only one other large, still inundated wetland remained in the ARIDFLO study region - Lake Hope, and the densities of waterbirds recorded on this lake in January 2003 were exceptional. Most surviving waterbirds had vacated the LEB, and the conservation significance of drought-refuge wetlands around the periphery of the continent is brought into sharper focus as a consequence of this observation.

New turtle record for the Diamantina During Trip 7 (February 2003), Mel White, a turtle researcher from the Applied Ecology Research Group, University of Canberra, accompanied the ARIDFLO research team to examine turtle populations in the lower Cooper and lower Diamantina reaches. Based on information provided to ARIDFLO scientists by the local land manager, an intensive survey at Yammakira (Clifton Hills Outstation) on the lower Diamantina yielded the capture of two turtles (Emydura sp.) in baited traps. Apart from a few anecdotal reports, turtles had not previously been recorded in the Diamantina, and so these catches officially established their presence. The specimens are the same species of Emydura as in Cooper Creek, E. emmotti. Only two were caught, one a juvenile and the other a mature male, but capture of a juvenile at least 5 years old suggests that turtles are breeding in this river. To persist in dryland rivers, turtles must have evolved special traits which allow them to survive unpredictable and extreme fluctuations in flow. Emydura persists in the Cooper’s boom-bust environment by congregating in permanent waterholes and only migrating between ephemeral and semi-permanent waterholes during floods. Because of the isolation of the permanent waterholes, any turtles that remain in ephemeral waterholes after a flood are unlikely to survive the intervening drought, so there is strong selection for a propensity to stay close to permanent water. The University of Canberra’s research on Cooper Creek has demonstrated that permanent waterholes are consistently dominated by adult turtles in high densities, semi-permanent waterholes are dominated by juveniles at low densities, and ephemeral waterholes contain no turtle populations. The turtle data gathered on the ARIDFLO field trip accords with the above findings. In the Coongie Lakes system, large adult turtles were caught in the deeper waterholes of the North West Branch of Cooper Creek and around Innamincka. Cullymurra Waterhole, the deepest in Cooper Creek, supports a dense turtle population in which the majority are large adults. Without these important refuge waterbodies, turtles would not exist in the LEB rivers. Although the native water rat Hydromys chrysogaster has not been intensively studied, it is likely that it has a similar distribution pattern and adopts a similar strategy to the Cooper turtle. Both turtles and water rats were observed commonly in Lake Goolangirie during the early parts of the study, yet there were no sightings of either species during Trip 6, and it is concluded that both species had retreated further upstream in response to falling water levels and increasing conductivity.

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Important considerations for monitoring LEB river health Monitoring programs need to be specifically developed or modified for use in arid zone rivers with naturally high levels of hydrological variability. Any monitoring program is dependent on the researcher having first articulated the desired state to which the system should conform. "State" in this respect should not be construed necessarily as steady state - a dynamic range of responses is desirable. This approach requires having sufficient knowledge of the system’s attributes and behaviour (structure, composition, function and dynamics), either gained through intensive prior study (baseline surveys) or through modelling (which itself must be based on a combination of sound theory and intensive study of comparable systems elsewhere). Important components of a sound adaptive management cycle include theory-driven hypothesis articulation (conceptual models of river function, health and predicted responses); focussed study (gap identification, data acquisition, information gain); indicator selection; target setting (incorporating ecosystem modelling) and monitoring of selective indicators. In this way the twin objectives of (i) increasing understanding of how and why ecosystems function, and (ii) refinement of indicators and their expected response to drivers of change, can be met through time with each repetition of the management cycle. Particular issues pertinent to monitoring ecological health in LEB rivers include:

scale• : i.e. appropriate spatial and temporal resolutions. Riverscapes must be viewed from an organism rather than an exclusively anthropocentric perspective (ideally not based on political jurisdictions or boundaries) (Wiens 2002). The range of scales over which indicator organisms are likely to be reliable needs to be explicitly considered. Which are useful in the short-term (e.g. algae, zooplankton, macroinvertebrates), which in the long-term (e.g. trees, birds, fish), and which respond to local hydrology, say in a particular wetland (e.g. trees), and which to hydrology on a much larger scale (e.g. waterbirds)?

context• : What stage(s) of the flood cycle is the system in, and what season should be monitored? This determines the magnitude or direction of expected response of those indicators sensitive to hydrological and seasonal variation, eg fish breeding response. “When to monitor” may be driven by events, e.g. floods or periods of no flow, rather than according to a fixed calendar schedule.

reference state• : How can this be defined? Recognition and description of an undegraded condition is particularly difficult in highly variable semiarid ecosystems (Rogers & Biggs 1999).

indicator choice• : What assemblages should be chosen and how can they be calibrated and validated? How quickly will these assemblages respond and will the same assemblages be able to provide early warning, assess compliance, and diagnose causes (Boulton 1999)? Do biotic components need to be monitored or are there more efficient surrogates? Some indicators should be chosen for which a change in variance, rather than in mean or median, may be important.

sensitivity:• The power of any test of an environmental impact is constrained by data variability, the magnitude of the putative effect and the number of independent sampling events (Osenberg et al. 1994)

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cost effectiveness• : There are numerous budgetary trade-offs to be considered when deciding upon the scale and limitations of potential monitoring programs. Cost-benefit analyses should be included in any monitoring program.

values• : Scientific and community values are both important, but are not necessarily the same.

Key sites within any monitoring program for LEB rivers should include:

• Refuges, deep waterholes or spring-fed waterbodies connected to the river.

• Modified waterholes, such as those with weirs and large waterholes are located near towns. These are likely to show the first signs of human pressure and thereby provide some ‘early warning’.

• Waterbird colonies. These lend themselves to monitoring of breeding activity (size and number of species) and success.

• Habitat for endangered or otherwise significant species, assemblages and ecosystems (e.g. Cooper catfish).

• Parts of the catchment subject to high stressor activities (e.g. land clearance, farm dam developments).

Hydrological monitoring The types of threats to the hydrological health of the LEB can be classified into two types operating at different spatial and temporal scales: o Broad scale or diffuse changes in the flow regime and sediment transport of a

catchment or reach. This could result from changes in land use in the catchment, farm dams and storages that capture rainfall runoff, or large-volume extraction from stream flow.

o Spatially explicit or specific threats to key wetlands and waterbodies from local changes in flow patterns (e.g. from building levees, changing flow sills) or by over-extraction of water from a waterbody (e.g. pumping water from refuges during drought).

Given the sparsity of gauging stations in the catchments of the LEB, identification of changes in the flow regime of reaches may not be possible using historical and current gauged data. The Cooper Creek catchment has the most gauging stations and also the highest degree of land clearing and so should be investigated to see if sufficient data are available to investigate the effects of land clearing on the flow regime. Current hydrological models of the LEB catchment (e.g. ARIDFLO hydrological models, QNRM model of Cooper Creek catchment) do not have the capacity to determine how land use changes may impact upon the flow regime. This is because of the lack of data on the spatial distribution of catchment characteristics affecting runoff and streamflow, and the lack of gauging station data available for model calibration.

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Healthy native fish identified by an Index of Biotic Integrity The Index of Biotic Integrity (IBI) developed during the NSW Rivers Survey (Harris and Gehrke 1997; Harris and Silveira 1999) was used in ARIDFLO as a template for the preliminary assessment of health of the LEB fish communities. The IBI is most commonly used to assess biotic integrity response across a gradient of anthropogenic disturbance. However, ARIDFLO used the IBI to assess biotic integrity response across a gradient of natural disturbance. From this initial mapping of environmental conditions across the LEB, a more sensitive and powerful monitoring protocol can be developed. Such a protocol may then be able to detect the range of impacts of human disturbance over and above the naturally noisy signal of biotic variation. Calculation of IBI scores for the waterbodies sampled by ARIDFLO yielded an initial quantitative assessment river health. The approach identified sites of excellent environmental conditions and good biotic integrity. These were typically large, deep refuge waterholes. This approach also provided insight into which component measures of the IBI perform well in an undegraded river system and which require further modification or exclusion to make the IBI a more powerful monitoring tool. Graphical analysis of IBI score response to selected environmental factors demonstrated a strong deterministic component to fish community assemblage organisation in addition to the expected stochastic variation. The main conclusions reached from applying an IBI to the ARIDFLO fish data were:

• LEB fish communities are healthy, and environmental variability is the key to their good health.

• LEB fish communities are resistant and resilient to natural environmental disturbances. Resistance is demonstrated by maintenance of that diverse and abundant fish communities in refuge waterholes, even during severe droughts. Resilience is demonstrated by recolonisation of sites by several species, only a few months after complete drying and extirpation of the previous fish fauna.

• LEB fish communities are nevertheless vulnerable. During drought, persistence of the entire LEB fish fauna is reliant upon a relatively small number of refuges with a drastically reduced area of available habitat. It is critically important to ensure that the biotic integrity of refuge waterholes is maintained, especially in the upper reaches of the Cooper and Diamantina where increasing demands are being made on their resources. Furthermore, the reliance of the fish communities of downstream reaches upon the quality and integrity of upstream refuges, means that any future water extraction plans will impact the fish fauna of the whole river, not just the local site where the water extraction is planned. Therefore effective management of LEB rivers requires recognition that local-scale decisions will potentially impact at much larger spatial scales

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Major Recommendations arising from the ARIDFLO project 1. Compile and maintain an inventory of refuge waterholes A comprehensive inventory should be conducted of the positions of all refuge waterholes (e.g. defined by cease-to-flow depths of >3m or >4m). Data to identify such sites could be drawn from ARIDFLO, the CRC for Freshwater Ecology’s Dryland River Refugia Project (Upper Cooper, Warrego and Border rivers) and community knowledge. This would enable a ranking to be made on the relative importance of waterbodies based on their abundance in a reach or a catchment, or on some other criteria of interest. For instance, the mid-upper Diamantina and the mid Cooper reaches have relatively higher numbers of deep refugia whereas the lower reaches have far fewer deep waterholes. Isolated or single refugia are very vulnerable to catastrophic events (e.g. illegal fishing, pollution, over-extraction of water). Some catchments are particularly vulnerable (e.g. Neales with only Algebuckina waterhole as a deep water refuge) and some, such as the Macumba, anecdotally do not contain any deep refugia and are therefore dependent on coincident reflooding with the Neales or Warburton for recolonisation after extended droughts. 2. Commitment to, and the expansion of, the acquisition of hydrological data Given the sparsity of gauging stations in the catchments of the LEB, identification of changes in the flow regime of reaches may not be possible using historical and current gauged data. Current hydrological models of the LEB catchment (e.g. ARIDFLO hydrological models, QNRM model of Cooper Creek catchment) do not have the capacity to determine how land use changes may impact upon the flow regime because of the lack of data on the spatial distribution of catchment characteristics affecting runoff and streamflow, and the lack of gauging station data available for model calibration. Recommissioning of some gauging stations is recommended with appropriate improvements in the ratings of these stations. As a bare minimum, Glengyle on the Georgina River in Queensland, should be recommissioned to monitor effects on any upstream hydrological changes on flows into South Australia and on the ecologically important wetlands downstream of Glengyle (Lakes Mipia, Koolivoo, Muncoonie Lakes). However, recommissioning of gauging stations at Diamantina Lakes (upper Diamantina River) and Roxborough Downs (Georgina River) would also provide invaluable data for improving hydrological modelling. We do not have information on the costing of recommissioning gauging stations but it is likely to be in the range of tens of thousands of dollars. Additional low-cost depth loggers could be installed at a number of other sites to augment the gauging station network at a cost of $1000 - $5000 per site depending on the type of water level logger used. Visiting the gauging station sites for maintenance and data downloading is required at least on a six monthly basis and is a significant expense in these remote locations. However, increasing the number of water level logger sites in a catchment means that more data can be collected for incremental increases in field time for those visiting these sites.

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3. Commitment to long-term ecological monitoring To understand or predict long-term changes in the dynamics of biological communities with land-use, water extraction and water diversion changes, repeated observations are required on a medium- to long-term scale (Fruget et al. 2001). This is particularly true given that the most useful biotic indicators for monitoring LEB ecological condition will incorporate a wide range of groups, time scales and spatial areas (e.g. from relatively short-term algal and cyanobacterial indicators, through mid-term macroinvertebrate indicator response to flow, to longer-term following of fish growth and recruitment and colonial waterbird breeding success). The enormous spatial and temporal variability of flows in LEB rivers and the importance of preceding conditions at time of sampling (historical legacy and hydrological persistence) requires commitment to a multi-annual, if not decadal, monitoring program. Further to this, a much more explicit connection needs to be developed between terrestrial and aquatic ecology with the recognition that aquatic systems are intrinsically linked with their terrestrial catchments (Boulton et al. 1999, Belliard et al. 1999): 4. Pastoralist-insight reporting network The rivers of the LEB are remote, relatively inaccessible and costly to regularly sample by non-resident scientific teams. Anecdotal help from pastoralists would be valuable in documenting the shifting extent of available aquatic habitat. Pastoralists through their daily activities and concern for the land have knowledge that to date has not been adequately represented and incorporated into scientific forums. For example, occasional reports could contain observations of when waterholes dry, which waterholes have been topped up with local thunderstorm activity, relative flood heights or areas of flood-extent, etc. all of which are currently under-reported in this sparsely gauged region. Establishment of fixed photo points would be another effective and inexpensive means of addressing data knowledge gaps, fragmented temporal records and high data gathering costs. Further, a well managed community reporting network could also be tied in with simple water quality sampling or installation of automatic water level loggers to provide additional quantitative data capability. 5. Assessment of sustainability of current and future water extraction levels The storage and extraction of water is under the control of state legislation and monitored by state government authorities and so will not be directly addressed in this report. However, ARIDFLO recommends that the sustainability of current water extraction levels be carefully monitored, especially during times of extended drought as was experienced in 2002/2003. Remnant aquatic habitats and deep water refugia are particularly vulnerable to over-extraction during disconnected conditions and need to be afforded greater protection. Over-extraction can result in fish-kills, algal blooms and water quality problems, and at such times, the loss of fauna from only a small number of waterholes may be enough to significantly impact regional biodiversity. Suitable protection might include legislating a water allowance for the environment, setting minimum-depth extraction limits on waterholes, encouragement of water-economic practices and penalising water-wasteful practices.

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Appropriate participatory and inclusive procedures (communications, meetings) will be a vital aspect in the successful community-wide adoption of wiser water-use practices. Within an inclusive protective framework for environmental values, there is also much scope for continued and improved education (for scientists and community alike). For instance, the Lake Eyre Basin Ministerial Forum in Birdsville 2002, successfully fostered free discussion and exchange not only of specific knowledge but also an improved understanding of differing values and shared concerns. If the outcomes of such forums can be integrated successfully into the knowledge base of the wider community, then the environmental health of LEB rivers will become more secure. 6. Further analyses of ARIDFLO data set and publication of results Despite the large volume of data, analyses and results presented herein, further laboratory processing, analyses and integration across biotic groups are required to obtain full value from the ARIDFLO investment. In particular, replicate macroinvertebrate samples from Trips 2-7 remain unsorted and await enumeration, while quantitative processing of zooplankton samples has been deferred (quantitative algal samples were not collected). Given the quantitative approach taken to macroinvertebrates, fish and birds, estimates of abundance of plankton would add greatly to the value of the ARIDFLO study, and allow more authoritative description of biotic response to flow variability in LEB rivers. Report outline Chapter 1 gives a general overview and introduction to the LEB, its rivers and the ARIDFLO project’s aims. The hydrological and biological methodologies of the project are detailed in Chapter 2. Hydrological modelling results (IMAGHYD) are presented in Chapter 3, biotic results and observations for each taxonomic group in Chapter 4. Chapter 5 presents the results of REML statistical modelling, that describes the strength, direction and magnitude of the effect of hydrological and other environmental variables on selected biotic responses. These models help to identify the main environmental drivers of biology–hydrology relationships. These key drivers are emphasised in a conceptual model of LEB ecosystem structure and functioning as discussed in Chapter 6. Graphical conceptualisations of these major findings and putative relationships are also presented in Chapter 6. Finally, Chapter 7 sets out the basis for environmental monitoring of the health of LEB rivers, and includes an account of the preliminary trial of one river health assessment tool, the index of biotic integrity for fish.

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