status of naples bay water clarity: 2005-2014

Status of Naples Bay Water Clarity: 2005-2014 FINAL REPORT

Prepared for: The City of Naples Streets and Stormwater Department Natural Resources Division July 2016

Status of Naples Bay Water Clarity Final Report

July 2016 Cardno Document Information i

Document Information Prepared for City of Naples, Streets and Stormwater Department

Project Name Status of Naples Bay Water Clarity: 2005 - 2014

Date July 2016

Prepared for:

City of Naples 295 Riverside Circle, Naples, FL 34102

Prepared by:

Daniel G. Hammond Senior Consultant

Kristan M. N. Robbins Senior Project Scientist

Stacy M. Villanueva Project Scientist


July 2016 Cardno Table of Contents ii

Table of Contents 1 Introduction ........................................................................................................................ 1

2 Study Approach ................................................................................................................. 2 2.1 Water Clarity Parameters .................................................................................................... 2

2.1.1 Factors Affecting Water Clarity ............................................................................ 2 2.1.2 Measures of Water Clarity ................................................................................... 3

2.2 Station Descriptions............................................................................................................. 3 2.3 Approach to Analysis ........................................................................................................... 4

3 Factors Affecting Water Clarity ........................................................................................ 5 3.1 Total Suspended Solids ...................................................................................................... 5 3.2 Chlorophyll-a ....................................................................................................................... 9 3.3 Color .................................................................................................................................. 11

4 Measures of Water Clarity in Naples Bay ...................................................................... 12 4.1 Turbidity ............................................................................................................................. 12 4.2 Secchi Depth ..................................................................................................................... 14

5 Water Clarity Relationships ............................................................................................ 18 5.1 Correlation Analyses ......................................................................................................... 18 5.2 Proportional Analysis ......................................................................................................... 19 5.3 Stepwise Regression ......................................................................................................... 21

6 Implications for Naples Bay Management ..................................................................... 23

7 Literature Cited ................................................................................................................. 25

Appendices Appendix A Monitoring Location Descriptions

Appendix B Summary of Statistical Analyses

Tables Table 1. Results of AEM time series models of bimonthly TSS in Marine Segment Gordon

River and Naples Bay, 2008–2014. .................................................................................... 7

Table A-1. Monitoring Locations in Naples Bay, Marine Segment Gordon River, and Tributary Inputs, 2005–2014. ........................................................................................... A-1

Table B-1. Analysis of Variance (ANOVA) or Kruskal-Wallis results for annual geometric mean variables among Naples Bay segments, 2005–2014. ........................................... B-1


July 2016 Cardno Table of Contents iii

Table B-2. Duncan’s Post Hoc Test or Mann-Whitney Multiple Comparisons results for annual geometric mean variables by Naples Bay segment, 2005–2014. ........................ B-1

Table B-3. Wet season and dry season T-test or Mann Whitney U test results on water quality variables by Naples Bay segment, 2005–2014. ................................................... B-2

Table B-4. Kendall Tau Trend Analysis by Bay segment for annual geometric mean Secchi depth and percent of the water column penetrated by light (WC%), 2005–2014. ........... B-4

Table B-5. Spearman’s Rank Order Correlations between Secchi depth and water quality variables at current monitoring locations in Naples Bay and tributary inputs, 2005–2014. ...................................................................................................................... B-4

Table B-6. Spearman’s Rank Order Correlations between turbidity and water quality variables at current monitoring locations in Naples Bay and tributary inputs, 2005–2014. ...................................................................................................................... B-5

Table B-7. Forward, stepwise, multiple linear regression results of turbidity with chlorophyll-a, TSS, and color at current monitoring locations in Naples Bay and tributary inputs, 2005–2014............................................................................................................ B-5

Figures Figure 1. Naples Bay, Southwest Florida. .................................................................................................... 1

Figure 2. Naples Bay, Marine Segment Gordon River, and tributary input monitoring locations. ............... 3

Figure 3. Monitoring locations by Bay Segment. ......................................................................................... 4

Figure 4. Geometric mean TSS concentrations in Naples Bay. .................................................................. 5

Figure 5. Bay segment annual geometric mean TSS concentrations in Naples Bay and input tributaries, 2005–2014. ....................................................................................................... 6

Figure 6. Bay segment geometric mean TSS concentrations by season in Naples Bay and input tributaries, 2005–2014. ....................................................................................................... 7

Figure 7. Geometric mean chlorophyll-a concentrations in Naples Bay. ..................................................... 9

Figure 8. Bay segment annual geometric mean chlorophyll-a in Naples Bay and input tributaries, 2005-2014. ........................................................................................................................ 10

Figure 9. Bay segment annual geometric mean chlorophyll-a concentrations by season in Naples Bay and input tributaries, 2005–2014. .............................................................................. 10

Figure 10. Bay segment annual geometric mean color in Naples Bay and input tributaries, 2005–2014. ................................................................................................................................. 11

Figure 11. Bay segment geometric mean color by season in Naples Bay and input. tributaries, 2005–2014. ....................................................................................................................... 11

Figure 12. Geometric mean turbidity in Naples Bay. ................................................................................. 12

Figure 13. Bay segment annual geometric mean turbidity concentrations in Naples Bay and input tributaries, 2005-2014. ...................................................................................................... 13

Figure 14. Bay segment geometric mean turbidity by season in Naples Bay and input tributaries, 2005-2014. ........................................................................................................................ 13

Figure 15. Geometric mean Secchi depth (m) in Naples Bay. ................................................................... 14

Figure 16. Bay segment annual geometric mean Secchi depth in Naples Bay and input tributaries, 2005-2014. ...................................................................................................... 15

Figure 17. Bay segment geometric mean Secchi depth by season in Naples Bay and input tributaries, 2005-2014. ...................................................................................................... 15


July 2016 Cardno Table of Contents iv

Figure 18. Annual geometric mean Secchi depth at station HALDCRK, a tributary input to Naples Bay, 2005–2014. ............................................................................................................... 16

Figure 19. Geometric mean percent of water column penetrated by light (WC%) in Naples Bay. ............ 17

Figure 20. Proportion of Secchi depths greater than one meter (1.5 m for GGC and Gordon Pass segments) at stated ranges of TSS, color, chlorophyll-a, and turbidity in each bay segment, 2005–2014. ....................................................................................................... 20

Figure 21. Spatial illustration of statistically significant factors shown to affect turbidity in Naples Bay using a step-wise regression. .................................................................................... 22


July 2016 Cardno Introduction 1

1 Introduction

In 2014–2015, the Naples Bay Water Quality Analysis Project was conducted to provide a comprehensive analysis of the current status of water quality and biological community trends in Naples Bay. The final report for that project (referred to herein as “the 2015 Report” (Cardno 2015)) included a quantification of the total suspended solids (TSS) loads from the Golden Gate Canal system and identified a statistically significant increasing trend in turbidity at most of the long term monitoring locations in the Bay. The annual TSS loads to Naples Bay were calculated to be approximately 350 tons between 2009 and 2014 (Cardno 2015)1, more than six times greater than the annual TSS loading to Tampa Bay by volume, which has seen significant resource recovery in recent years. The results presented in the report were of particular concern to City of Naples resource managers because high TSS loads coupled with an increasing trend in turbidity in Naples Bay may create challenges for ongoing and future planned oyster and seagrass restoration efforts. The value of these habitats as nursery areas for commercially and recreationally important species; for substrate and shoreline stabilization and mitigation of wave action; for their contribution to water quality improvement; as well as for their inherent value to the overall health of a productive estuary, make oyster and seagrass protection and restoration an important piece of the strategy to restore Naples Bay (City of Naples 2010).

In an attempt to determine how TSS and turbidity may affect biological communities, the City requested a more in-depth investigation of the spatial and temporal patterns of TSS concentrations and turbidity in Naples Bay and the relationships between these variables and water column light penetration (as measured by Secchi depth). While concerns about large TSS loads were the impetus for this investigation, TSS is not the only factor that can affect water clarity in Naples Bay. This study details TSS trends in Naples Bay and the link between TSS and water clarity, but also includes an investigation of trends in and links between other water quality factors (chlorophyll-a and color) and water clarity measures (turbidity and Secchi depth) currently being monitored in Naples Bay.

This investigation is expected to be an important piece of the larger effort to identify how best to manage and restore the biological communities and estuarine habitats of Naples Bay. The goal is to give a more comprehensive characterization of the current status of the constituents that affect water clarity so the City can make informed management decisions and ultimately improve and protect the ecology of Naples Bay.

1 These calculations were based on Golden Gate Canal flow data from the South Florida Water Management District. Since the

2015 Report was finalized, the District revised flow estimates from the Canal, which would likely result in an increased TSS load estimate from the Canal to Naples Bay from the values reported in the 2015 Report.

Figure 1. Naples Bay, Southwest Florida.


July 2016 Cardno Study Approach 2

2 Study Approach

The main goals of this investigation are to describe (1) the current status of factors that can affect Naples Bay water clarity, (2) the current status of water clarity in Naples Bay; (3) the relationships between these variables; and finally (4) how the current status of water clarity in Naples Bay may be impacting biological communities. Each of these goals is addressed in depth in the sections that follow. Although this study recognizes other chemical, biological, and physical measures may also contribute to the observed conditions reported here, we focus on the available data and the role these measures play in the current status of Naples Bay.

2.1 Water Clarity Parameters

To describe the current status of Naples Bay water clarity and assess trends over time, three factors that can impact water clarity (TSS, chlorophyll-a, and color) and two measures of water clarity (turbidity and Secchi depth) were selected for this investigation (based on availability of data). This section provides a brief background on each water quality measurement and a framework for discussion of the results of this study.

2.1.1 Factors Affecting Water Clarity

TSS is a measure of the amount of solid particles suspended in the water column. These may be inorganic or organic and include sands, silts, phytoplankton, organic debris, and/or industrial wastes. TSS is measured in the laboratory by filtering a sample of known volume through a standard filter with specific pore size (APHA 1989). The weight of the solid particles caught on the filter divided by the volume of water filtered gives the concentration of the TSS measurement in mg/L. Most particle sizes will be caught on the filter, but it is important to note that some of the finer clays may pass through and would not be measured as TSS. However, the finer particles still impact water clarity.

Particulate matter in the water column, including particles contributing to TSS and finer particles not measured as TSS, can affect the physical and biological environment of an estuarine system like Naples Bay in many ways. It absorbs light, which makes the water warmer and restricts light passage through the water column. Warmer water has less ability to hold oxygen, which can adversely affect fish and invertebrate communities. Light restriction in the water column can adversely affect photosynthetic activity of plants including seagrass. High levels of particulate matter can also physically harm biological communities through habitat smothering when suspended particles settle out of the water column. Additionally, particulate matter in the water column can serve as attachment vehicles for other pollutants such as metals and bacteria (USGS 2015).

Like TSS, primary production is another factor that can affect water clarity: suspended algal biomass can contribute to increased turbidity and lower Secchi depths. Chlorophyll-a is typically used as a measure to represent algal biomass in the water column. At some long term stations in Naples Bay, chlorophyll-a has shown an increasing trend over time (Cardno 2015), which could be important for trends in water clarity.

Color is another parameter typically measured in Naples Bay that can be linked to water clarity. Light penetration is reduced in water with higher color which may decrease water clarity. Color can be measured in two ways: apparent and true. Apparent color is measured using a whole water sample and includes particulate and dissolved materials. True color is measured using a filtered water sample removing particulate matter and measuring just the dissolved fraction. Tannins from decaying vegetation are an example of a source of true color in a water sample. A combined field of apparent and true color is used in this investigation; data collected by the City of Naples and Collier County were recorded as apparent color, and data collected by SFWMD were recorded as true color. A sensitivity analysis of the data showed that when stations with both apparent and true color measured on the same day, using the



average of the two values (Dixon and Gordon 2016) had very little effect on the various statistical tests used in this report.

2.1.2 Measures of Water Clarity

Turbidity is a measurement of the relative clarity of a liquid and is an expression of the amount of light that is scattered by material in the water (USGS 2015). Since turbidity is a measure of water clarity, TSS is one of many measures that can affect turbidity. Turbidity is also affected by high levels of smaller particulate matter not measured by TSS, by algal biomass in the water column (typically represented by measurements of chlorophyll-a), and color. Elevated turbidity levels are an indicator of reduced light penetration and may be linked to reduced aquatic productivity (seagrass and phytoplankton) and poor aesthetic quality.

Secchi depth is a very common tool for observational measurements of water clarity. Secchi depth is measured as the depth a colored disc (usually black and white) is no longer visible or distinguishable from the surrounding water. Typically, the measurement is the average of the depth recorded when lowering the disc into the water and the depth observed when raising the disc up from the bottom. Secchi depth is a very useful tool for measuring overall water clarity, but it cannot distinguish between the sources that affect water clarity. The measurement is generally associated with the amount of light that penetrates the water column, however specific correlations between Secchi depth and light penetration are highly variable, regionally and waterbody specific, and contingent upon the sources affecting water clarity in a given waterbody.

2.2 Station Descriptions

The majority of the data for this effort were obtained from the City’s monthly Naples Bay monitoring program, including Secchi depth measurements that were not previously incorporated into the 2015 Report, and annual seagrass monitoring data. Other sources of water quality data include Collier County, the South Florida Water Management District (SFWMD), and the Florida Department of Environmental Protection (FDEP). Using multiple monitoring stations, with data collected by multiple entities, allows for a robust spatial and temporal characterization of Naples Bay and the Marine Segment of the Gordon River (Figure 2).

This study evaluates data for the 2005–2014 time period. Some stations have data outside the 2005–2014 time period, but those data were not included in this study. However, the period of record for data

Figure 2. Naples Bay, Marine Segment Gordon River, and tributary input monitoring locations.



differs among the sampling stations as a result of using data from multiple monitoring programs from different entities and relocation or discontinuation of some locations over time. This evaluation is careful

to recognize the different time periods available for each station to ensure the comparisons between and among stations are valid.

The frequency of water quality data collection by the City changed within the duration of their monitoring program: from 2006 to 2010 samples were collected every other month and samples were collected monthly from 2011 to 2014. Thus, the long-term stations include data from both monitoring frequencies while some stations with shorter periods of record only have monthly data or bimonthly data. Data from the other monitoring entities were generally collected on a monthly frequency throughout their respective periods of record. In addition to each station’s period of record, other station characteristics including depth, proximity to potential pollutant sources, proximity to potential biological community habitats, and location at tributary weirs were all considered during this study.

2.3 Approach to Analysis

For some analyses, the individual monitoring locations were grouped into bay segments based on their geographic location (Appendix A and Figure 3). Analysis at the bay segment level rather than the station level allowed for a more comprehensive characterization of the available data given the spatial and time period constraints of many monitoring locations. In general, all of the bay segments are characterized by monitoring locations that were either discontinued or initiated during the 2005–2014 time period, and also had at least one long term station. The Marine Segment Gordon River is represented by one consistent long term station (BC3) in the historic channel of the Gordon River. In addition, data from the GORDEXT and GORDPT locations can be combined to create a second long term location for this segment as was done in the 2015

Report. The only bay segment that does not include a long-term station is the Port Royal bay segment, where all available data were from the 2006–2010 time period. In most cases, the Port Royal bay segment was eliminated from the analyses because the available data do not represent current conditions and the monitoring frequency was not robust enough to draw comparisons to other bay segments with more robust datasets. However, descriptive summaries of the Port Royal data are provided.

The most appropriate spatial, temporal, and relational statistical analyses were selected based on the available datasets and the assumptions inherent in each statistical test. The type of statistical test selected for each analysis is detailed in the text with the presentation of the results, with a short description of the test if appropriate. Detailed statistical results are presented in Appendix B.

Figure 3. Monitoring locations by Bay Segment.


July 2016 Cardno Factors Affecting Water Clarity 5

3 Factors Affecting Water Clarity

3.1 Total Suspended Solids

Several sources contribute TSS loads to Naples Bay including urban stormwater runoff; the Golden Gate Canal (GGC); contributions from tributaries (Gordon River, Rock Creek, and Haldeman Creek); and wave and tidal action (resuspension). While TSS concentration data for most of these sources are available, quantitative data on the volume of water delivered to the Bay from many TSS sources are currently unavailable. As a result, TSS loads to the Bay can only be calculated for the two inputs with available flow data: the GGC and the City’s stormwater pump stations. The City’s pump stations have been estimated to contribute between 2.5 and 12 tons of TSS per year (2012–2014), while the GGC contributes an estimated 194 to 717 tons of TSS per year (2009–2014) (Cardno 2015). The lack of information about the total loadings from all sources to Naples Bay prevents a complete characterization of which sources are quantifiably most important to the observed Bay condition. Nevertheless, TSS concentration data do allow for inferences on general spatial and temporal patterns of TSS within the Bay.

The overall station geometric mean TSS concentrations in Naples Bay, the Marine Segment Gordon River, and the tributary inputs to the Bay ranged between 2.3 mg/L (Golden Gate Canal – GGCAT31) and 13.5 mg/L (Gordon Pass – GPASS6) over the 2005–2014 time period (Figure 4). Annual geometric mean TSS concentrations exhibit statistically significant differences among bay segments (ANOVA, p< 0.05; Table B-1; Figure 5). The Golden Gate Canal has significantly lower concentrations than the other bay segments, with increasing TSS moving south through the Bay; Gordon Pass had the highest TSS concentrations (Duncan’s Post Hoc Test, p< 0.05; Table B-2). The tributary inputs to the Bay (Golden Gate Canal, Marine Segment Gordon River, Rock Creek, and Haldeman Creek) all show significantly lower TSS concentrations than the Northern Bay, Southern Bay, and Gordon Pass bay segments, and higher concentrations than the Golden Gate Canal bay segment (Duncan’s Post Hoc Test, p < 0.05; Table B-2).

Figure 4. Geometric mean TSS concentrations in Naples Bay.



The increasing TSS pattern from north to south through the Bay and lower concentrations in the tributary bay inputs are likely the result of multiple hydrodynamic factors playing confounding roles. At Gordon Pass and in the Southern Bay segment, tidal and wave action are likely responsible for sediment resuspension and transport which contribute to higher TSS concentrations. The lower concentrations at the northern end of the Bay (Marine Segment Gordon River) and in the tributary inputs are in systems dominated by river inputs and stormwater runoff. Naples Bay is relatively unique in that the tributary inputs (Golden Gate Canal, Gordon River, and Haldeman Creek) all have weirs that control water input to the Bay. These water management structures likely provide some treatment for TSS by allowing suspended material to settle out of the water column prior to discharge into the Bay or Marine Segment Gordon River, lowering the TSS concentrations in the discharged water. Although the potential water treatment effect of these weirs cannot be quantified with the current dataset, the lower TSS concentrations at the tributary inputs appear to suggest some reduction is achieved.

Figure 5. Bay segment annual geometric mean TSS concentrations in Naples Bay and input tributaries, 2005–2014.

In addition to spatial differences in TSS concentrations, seasonal (wet [June–October] and dry [November–May] season) differences were also observed in the Bay and tributary inputs (Figure 6). Most bay segments, with the exception of Golden Gate Canal and Gordon Pass, have a significantly higher annual geometric mean TSS concentration in the dry season versus the wet season (T-test, p< 0.05; Table B-3). Higher volume of freshwater inputs with relatively low TSS concentrations during the wet season from the tributary sources create increased flushing through the Bay and result in lower TSS concentration measurements during wet season monitoring events. While wet season concentrations may be lower, overall loading of TSS to Naples Bay is much greater during the wet season (Cardno 2015), which is indicative of the high volume of freshwater delivery Naples Bay receives during the wet season. TSS loads delivered during the wet season may be re-suspended by boat traffic, tidal and wave action, and coupled with reduced flushing during the dry season may explain the higher TSS concentrations during this time of year.

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Figure 6. Bay segment geometric mean TSS concentrations by season in Naples Bay and input tributaries, 2005–2014.

Autoregressive Error Models (AEM) to examine trends in TSS over time were run for the four long term monitoring locations (GORDEXT/GORDPT, NBAYNL, NBAYWS, and GPASS6) in Naples Bay and the Marine Segment Gordon River. The models were run on bimonthly monitoring data to standardize the frequency throughout the dataset in the same manner as those completed during the 2015 Report (Cardno 2015). The time period for AEM model runs was limited to 2008–2014 so that flow from the GCC could be included as a covariate (flow data from GGC are not available before 2008). No statistically significant trends in TSS over time were observed at the long term stations (Table 1).

Table 1. Results of AEM time series models of bimonthly TSS in Marine Segment Gordon River and Naples Bay, 2008–2014.

Station

Total Model

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regression (Months) Est p Est p Est p Est p

GORDEXT/ GORDPT

0.16 8.07 0.05 -0.0003 0.12 -0.02 0.91 -0.05 0.13 None

NBAYNL 0.35 -0.31 0.9 0.0001 0.31 -0.14 0.15 -0.05 0.04 10

NBAYWS 0.08 6.67 0.15 -0.0002 0.38 -0.16 0.34 -0.01 0.74 None

GPASS6 0.23 4.73 0.14 -0.0001 0.56 -0.14 0.23 0.006 0.81 12

TSS is measured as a total magnitude of the suspended particles in the water column (quantified as dry weight by volume), but it cannot provide any information concerning the types of particles (sand, silt, clay, organic, inorganic, etc.) present or their source. The fact that TSS concentrations increase from north to south throughout the Bay and the tributary inputs show lower concentrations than the Bay itself is somewhat counterintuitive. Typically, river inputs serve as the source of sediment and suspended particles to estuarine environments. In the case of Naples Bay, the Bay segments furthest from the input sources to the estuary (Southern Naples Bay and Gordon Pass) consistently show the highest TSS concentrations. We hypothesize this pattern is related to different particle types that comprise the TSS measurement in different parts of the Bay.

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The weirs in the tributary inputs to the Bay (Gordon River, Golden Gate Canal, and Haldeman Creek) will provide some water treatment, reducing or preventing the heavier and larger particles (sand, larger organic debris, etc.) from discharging to the Bay, but still allowing the lighter particles (silts and clays) to discharge over the weir. Therefore, it is likely the TSS measurements in the water column from the tributaries to the Bay and the upper portions of the Bay (Marine Segment Gordon River and Northern Naples Bay) are more likely to be comprised of silts, clays, and lighter debris than would be expected if the weirs were not in place. In contrast, the TSS measurements in the southern portion of the Bay and Gordon Pass are more likely to be comprised of larger particles and sand in the water column from tide and wave action, especially in the shallower areas. Because TSS is a measurement of mass by volume, areas dominated by heavier and larger particles (e.g. sand) such as Southern Naples Bay and Gordon Pass will have higher measured TSS concentrations when compared to the silt and clay dominated areas such as in the upper portions of the Bay and the input tributaries.

Northern Naples Bay sediments are dominated by silts and clays while the Marine Segment Gordon River, Southern Naples Bay and Gordon Pass sediments are dominated by sands (Savarese et al. 2006). The sediment composition in Northern Naples Bay is the result of suspended sediments delivered through the Gordon River and boat channels along the eastern Bay (Savarese et al. 2006). Northern Naples Bay is likely the site of opposing tidal and freshwater delivery hydrodynamic forces that cause the silts and clays to settle out of the water column. Northern Naples Bay sediments being dominated by silts and clays, and Southern Naples Bay and Gordon Pass sediments being dominated by sand may help to explain why TSS concentrations increase from north to south in the Bay. Resuspension of the different types of sediments, especially in the shallow areas (where the monitoring locations tend to be), lends support to the theory that TSS concentrations differ based on the composition of the sediment types in the different portions of the Bay.



3.2 Chlorophyll-a

In the 2015 Report, an increasing trend in chlorophyll-a over time was identified at three of the four long-term monitoring stations in Naples Bay and the Marine Segment Gordon River (GORDEXT/GORDPT, NBAYNL, and NBAYWS) (Cardno 2015). The only station that did not exhibit an increasing trend was GPASS6 (Gordon Pass), but it’s possible that a higher method detection limit in the early dataset is masking the identification of any trend (Cardno 2015).

Overall geometric mean chlorophyll-a concentrations range from 2.9 µg/L to 8.8 µg/L across all monitoring stations (Figure 7). Statistically significant differences among bay segments were observed (ANOVA, p < 0.05; Table B-1), with the Golden Gate Canal, Gordon Pass, and Southern Naples Bay segments exhibiting significantly lower chlorophyll-a than the Rock Creek, Haldeman Creek, Marine Segment Gordon River, and Northern Bay segments (Duncan’s Post Hoc Test, p < 0.05; Table B-2). Chlorophyll-a concentrations decrease in the southern portion of the Bay where tidal exchange with the Gulf water is more prominent (Figure 8).

Seasonal differences were observed in chlorophyll-a concentrations in all bay segments (Figure 9). The wet season chlorophyll-a concentrations were significantly higher than dry season concentrations throughout the Bay and tributary inputs (T-test, p < 0.05; Table B-3). The largest seasonal differences and the highest wet season chlorophyll-a values were observed in Rock Creek, Haldeman Creek, and Northern Naples Bay. The higher wet season concentrations coincide with the time period when the most nutrient delivery to Naples Bay occurs, along with the warmer temperatures and increased photoperiod. The seasonal pattern in chlorophyll-a, where concentrations are higher in the wet season, is the opposite pattern that TSS exhibits.

Figure 7. Geometric mean chlorophyll-a concentrations in Naples Bay.



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Figure 8. Bay segment annual geometric mean chlorophyll-a in Naples Bay and input tributaries, 2005-2014.

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Figure 9. Bay segment annual geometric mean chlorophyll-a concentrations by season in Naples Bay and input tributaries, 2005–2014.



3.3 Color

Color measurements show a consistent decreasing pattern from north to south throughout the Bay and tributary inputs with statistically significant differences among bay segments (ANOVA, p < 0.05; Table B-1). The Golden Gate Canal, Marine Segment Gordon River, and Rock Creek segments are grouped together with the highest color measurements, and the Southern Bay and Gordon Pass are the lowest with significant differences from the other bay segments as well as from each other (Duncan’s Post Hoc Test, p < 0.05; Table B-2; Figure 10).

Color also showed statistically significant seasonal differences, with higher color observed in all bay segments during the wet season (T-test, p < 0.05; Table B-3; Figure 11). The spatial and seasonal differences in color in Naples Bay are the result of GGC flow and tributary inputs that deliver large volumes of freshwater to the Bay during the wet season. Increased tidal mixing in the Southern Bay and Gordon Pass segments explain the reduced color in these areas compared to the upper bay segments where freshwater inputs dominate.

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Figure 10. Bay segment annual geometric mean color in Naples Bay and input tributaries, 2005–2014.

Figure 11. Bay segment geometric mean color by season in Naples Bay and input.

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July 2016 Cardno Measures of Water Clarity in Naples Bay 12

4 Measures of Water Clarity in Naples Bay

4.1 Turbidity

As a measure of water clarity, tracking and understanding turbidity can be an important factor in the management of Naples Bay. This is especially true since a statistically significant increasing trend in turbidity over time was observed at three of the four long-term monitoring locations in the Marine Segment Gordon River, Northern Naples Bay, and Gordon Pass (Cardno 2015). The magnitude of the increasing trend is estimated at approximately one NTU per year. While an increasing trend is observed at most of the long-term Bay stations, turbidity measurements throughout the Bay are relatively low, with station geometric means ranging from 1.3 NTU to 4.9 NTU (Figure 12).

Overall, turbidity is relatively consistent across bay segments (Figure 13) with no statistically significant spatial differences observed (ANOVA, p > 0.05; Table B-1). Since the increasing trend over time was found at three of the four long-term stations in the Bay (Cardno 2015), it is possible the increasing trend over time is occurring with some uniformity throughout the Bay, which would explain the lack of any difference between bay segments.

In most bay segments, seasonality (wet and dry season) does not significantly affect turbidity (T-test, p > 0.05; Table B-3; Figure 14). Exceptions were the Golden Gate Canal, which showed significantly higher turbidity measurements during the wet season (T-Test, p < 0.05; Table B-3), and Southern Naples Bay, which showed significantly higher measurements in the dry season (T-test, p < 0.05; Table B-3). The difference in the patterns observed between the Golden Gate Canal and Southern Naples Bay segments is not surprising given that the GGC may not flow for long periods of time during the dry season, allowing significant residence time for settling. Localized tidal and wave action may affect turbidity during the dry season in the Southern Bay.

Figure 12. Geometric mean turbidity in Naples Bay.



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Figure 14. Bay segment geometric mean turbidity by season in Naples Bay and input tributaries, 2005-2014.

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Figure 13. Bay segment annual geometric mean turbidity concentrations in Naples Bay and input tributaries, 2005-2014.



4.2 Secchi Depth

Secchi depth is a relatively simple tool that provides a useful measurement of general water clarity. Increased Secchi depth is associated with increased water clarity, increased light penetration and improved water quality conditions that benefit ecological communities such as seagrasses. Understanding Secchi depth in Naples Bay and the factors that affect it can play an important role in the overall restoration and management of the Bay.

Statistical analysis on the Secchi depth data from most stations should be interpreted carefully because many stations had a large number of “on bottom” measurements, which are more indicative of station depth and tide stage. These particular measurements do not represent an actual Secchi depth measurement as an indication of how far light could actually penetrate at that location. In addition, Secchi depth is inherently dependent on the overall depth at each sampling location; it will therefore have a non-normal distribution at each location despite log transformation because of truncation of values. Therefore, nonparametric alternatives to the ANOVA and t-test were used in the Secchi depth analysis of differences between Bay segments and seasons. Secchi depth measurements that were recorded as being “on bottom” were estimated to be the corrected maximum sampling depth for that day (bottom vertical profile measurement depth + 0.3 m) or were excluded if no maximum sampling depth was available2. It is important to note, any perceived differences between locations could be related to large differences in total water depth at those locations, rather than differences in water clarity.

Across all Naples Bay and tributary input locations, the overall station geometric mean Secchi depth ranged from 0.8 m to 1.7 m over the 2005–2014 time period (Figure 15). A Kruskal-Wallis test (non-parametric version of ANOVA) on measured Secchi depth indicated significant differences among bay segments (Kruskal Wallis, Secchi depth, p < 0.05; Table B-1), with the Golden Gate Canal bay segment having significantly greater Secchi depth than the rest of the bay segments, except for Gordon Pass (Mann Whitney multiple comparisons, Secchi depth, p < 0.05; Table B-2). The Golden

Gate Canal bay segment showed the greatest Secchi depth, with Gordon Pass the next highest (Figure

2 Corrected maximum sampling depths were available for the City’s sampling locations; “on bottom” measurements from other

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Figure 15. Geometric mean Secchi depth (m) in Naples Bay.



16). The differences between bay segments are more indicative of the deeper station depths in the Golden Gate Canal and Gordon Pass rather than any real difference in water clarity.

The Golden Gate Canal, Rock Creek, and Southern Naples Bay segments were the only ones to show a statistically significant difference in Secchi depth between seasons (Figure 17). In the Golden Gate Canal and Rock Creek bay segments, Secchi depth was greater during the dry season, while the Southern Bay segment showed greater Secchi depth during the wet season (Mann-Whitney U test, Secchi depth, p < 0.05; Table B-3). Greater Secchi depth in the Golden Gate Canal during the dry season can be expected given the lower turbidity (see Figure 14) and the generally reduced or lack of flow during this time of year. Lower Secchi depths during the dry season in the Southern Bay segment coincide with higher TSS and turbidity (see Figures 6 and 14), which likely contribute to Secchi depths in this bay segment. Interestingly, Rock Creek, exhibited higher TSS and greater Secchi depth in the dry season. The relationships between all these variables and their potential effect on water clarity are examined in the next section.

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Figure 16. Bay segment annual geometric mean Secchi depth in Naples Bay and input tributaries, 2005-2014.

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Figure 17. Bay segment geometric mean Secchi depth by season in Naples Bay and input tributaries, 2005-2014.



Trend analyses like the AEM station-based analysis could not be conducted on the Secchi depth data with any statistical rigor because of the large number of “on bottom” measurements at many monitoring locations. Therefore, a nonparametric Kendall Tau trend analysis using annual geometric means by bay segment was performed to identify any differences or changes over time (Appendix B; Table B-4). Using this method allows for relatively accurate identification of trends while minimizing the effect of the “on bottom” measurements in the analysis. The Haldeman Creek bay segment showed a statistically significant decreasing trend in Secchi depth over the 2005–2014 time period (Tau = -0.64, p < 0.05). This trend was driven by a single station (HALDCRK) which has a long term dataset and no “on bottom” measurements (Figure 18). The Marine Segment Gordon River and Rock Creek bay segments showed increasing trends that were not significant at the p < 0.05 level, but were significant at the p < 0.1 level (Tau = 0.42, p = 0.089). No other bay segments showed any trends in either direction (p > 0.05 and 0.1).

Figure 18. Annual geometric mean Secchi depth at station HALDCRK, a tributary input to Naples Bay, 2005–2014.

As a result of the limitations on the Secchi depth data, an individual station light penetration index was created based on observed Secchi depth and the overall station depth at the time of sampling. The index values could only be calculated for stations monitored by the City because overall station depth was not recorded by any other sampling entity. Based on the City’s water quality monitoring protocols, a bottom field measurement is collected during each sampling event at 0.3 m above the bottom. Therefore, we are able to estimate total station depth for a given monitoring event by adding 0.3 m to the bottom field parameter measurement depth. The overall station depth and Secchi depth were used to estimate the Secchi depth as a percentage of total water depth using the following formula:

% of water column penetrated by light (WC%) = Secchi depth (m) / total water depth (m) * 100

Thus, Secchi measurements of “on bottom” have a WC value of 100 percent. We recognize Secchi depth does not necessarily equate to the depth of zero light penetration and several studies have estimated a range of light availability at a given Secchi depth (Buiteveld 1995; Devlin et al. 2008; Gallegos et al. 2011; Luhtala & Tolvanen 2013); however the index was used as a proxy for water column light penetration in this study in the absence of empirical light measurements (PAR). This standardization of the Secchi depth measurements allows spatial or temporal comparisons based on the relative proportion of the water column receiving light and reveals which stations regularly experience light penetration all the way to the seafloor. Based on the fact that Secchi depth was relatively consistent throughout the Bay, the differences in WC% among stations are more likely to be attributed to station depth at a given location, with a smaller percentage of the total water column being penetrated by light at the deeper stations (e.g. Port Royal, Gordon Pass). For this reason, comparing spatial differences in light penetration throughout the Bay would not be meaningful, but evaluating percent light penetration at a particular location may be useful in identifying areas of sufficient light for management activities such as seagrass restoration.

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Similar to the Secchi depth analysis, nonparametric alternatives to the ANOVA and t-test were used in the WC% analysis of differences between seasons or over time within a bay segment. Although total station depth can be biased based by tide stage at the time of sampling, we assumed over time that all tide stages would be represented and that a consistent trend in WC% would be the result of small changes in water clarity and not bias resulting from tide stage. Likewise, we assumed that differences in station depth from sample to sample due to variation in actual sampling points within a station did not bias the analysis. We also assumed overall station depth did not change over time (e.g. that a station was not dredged or filled in a way that resulted in a large change in station depth from that point on).

The overall geometric mean WC% at the City monitoring locations across all of the monitoring time frames ranged from approximately 42 percent at NBAYLLO in Port Royal to 87 percent at NBAYNL in Northern Naples Bay (Figure 19). The Golden Gate Canal segment showed a statistically significant increase in light penetration during the dry season, while the Marine Segment Gordon River, Rock Creek, and Haldeman Creek segments had increased light penetration during the wet season (Mann-Whitney U test, p < 0.05; Table B-3).

Nonparametric annual Kendall Tau trend analyses were used to identify changes in annual geometric mean WC% over time by bay segment. The Marine Segment Gordon River (Tau = 0.51, p < 0.05), Northern Naples Bay (Tau = 0.69, p < 0.05), and Haldeman Creek (Tau = 0.64, p < 0.05) all had significant increasing trends in light penetration over the 2005–2014 period (Appendix B; Table B-4). As previously stated, this analysis could only be conducted on bay segments that included the City’s monitoring locations, because light penetration index calculations were only possible for these locations. This explains the presence of a significant decreasing trend in Secchi depth for the Haldeman Creek bay segment, but a significant increasing trend in WC% for the same segment. The decreasing Secchi depth trend was driven by the HALDCRK station alone, and because this location is monitored by Collier County, not the City, it was not included in the light penetration trend analysis. However, this produces an interesting result in that the Haldeman Creek input to Naples Bay (represented by HALDCRK) is exhibiting decreasing water clarity (measured as Secchi depth) at the same time other stations in the Haldeman Creek embayment (represented by stations HALDCR and NBAYHC) are exhibiting increasing water column light penetration over time. The increasing trend in WC% at HALDCR and NBAYHC may also be attributed somewhat to the change in sampling location from NBAYHC to HALDCR over the study period (Appendix A).

Figure 19. Geometric mean percent of water column penetrated by light (WC%) in Naples Bay.


July 2016 Cardno Water Clarity Relationships 18

5 Water Clarity Relationships

Water clarity, particularly in estuarine systems, can be affected by many confounding factors. Suspended sediments (measured by TSS) can certainly affect water clarity, as can particulate organic matter in the form of algae and decaying vegetation, colored dissolved organic matter (CDOM), and even salinity. In this section, we examine the relationships between TSS, chlorophyll-a, color and two measures of water clarity currently being measured in Naples Bay: turbidity and Secchi depth.

5.1 Correlation Analyses

Correlation analyses were run on selected individual monitoring locations that represent current and/or long term conditions in the Bay and tributary inputs to the Bay including the GGC. A nonparametric correlation method (Spearman’s rank) was chosen to evaluate relationships between water quality variables (TSS) and water clarity (Secchi depth and turbidity) because Secchi depth data were truncated in many cases by “on bottom” measurements which only represent the water depth at the time of sampling for that station and not the actual Secchi depth. Therefore, the data in this analysis would not meet the assumptions of parametric correlation analysis, even with data transformations. Selected monitoring locations were used for the correlation analysis to represent the major bay segments and tributary inputs utilizing the long-term and current monitoring stations.

Although the input tributary bay segments have lower mean TSS concentrations than the major bay segments, the relationship between TSS concentrations and Secchi depth appears to be most prominent in the inputs to the Bay rather than within the Bay itself. Monitoring locations in the GGC, Marine Segment Gordon River, Haldeman Creek, and at stormwater inputs into Northern Naples Bay (CURLEW) show statistically significant negative correlations between TSS and Secchi depth (Spearman’s r, -0.22 < r < -0.52, p < 0.05; Table B-5). Conversely, none of the monitoring locations in the open portions of Northern or Southern Naples Bay, Gordon Pass, or Rock Creek exhibit a statistically significant relationship between TSS and Secchi depth (Spearman’s r, p > 0.05; Table B-5).

The relationship between TSS and turbidity in Naples Bay was also examined. Interestingly, only the Golden Gate Canal (station 3495) and Haldeman Creek (HALDCRK) exhibit a statistically significant positive relationship between TSS and turbidity (Spearman’s r, 0.28 < r < 0.38, p < 0.05; Table B-6). No other tributary input locations or Bay monitoring stations exhibit a statistically significant relationship between TSS and turbidity (Spearman’s r, p > 0.05; Table B-6). TSS and turbidity can be related in instances where the suspended solids are the main component of turbidity, but it is not surprising that they aren’t related if other components are important contributors to turbidity in certain locations. As with the relationship between TSS and Secchi depth, the relationship between TSS and turbidity appears to be stronger in tributary input locations rather than within the Bay itself.

Chlorophyll-a concentrations showed a statistically significant negative correlation with Secchi depth at monitoring locations in the Golden Gate Canal, Marine Segment Gordon River, Northern Naples Bay, Rock Creek, and Haldeman Creek bay segments (Spearman’s r, -0.31 < r < -0.59, p < 0.05; Table B-5). Similar to TSS, chlorophyll-a was more related to Secchi depth in monitoring locations representing inputs to the Bay rather than within the Bay itself. The same pattern was observed in the relationship between chlorophyll-a and turbidity, with a statistically significant positive relationship in many locations representing inputs to Naples Bay (Spearmen’s r, 0.26 < r < 0.65, p < 0.05; Table B-6). In this instance, one station within the Bay itself (NBAYNL in Northern Naples Bay) also showed a significant positive relationship between chlorophyll-a and turbidity.

Relationships between color and Secchi depth measurements were observed in almost all bay segments, again mostly representing inputs to the Bay. A statistically significant negative correlation was observed from at least one monitoring location in the Golden Gate Canal, Marine Segment Gordon River, Rock



Creek, and Gordon Pass bay segments (Spearman’s r, -0.30 < r < -0.58, p < 0.05; Table B-5). Color was positively correlated with Secchi depth in Haldeman Creek (HALDCRK) (Spearman’s r, 0.41; p < 0.05; Table B-5). Color showed also showed mixed relationships with turbidity. Color was positively correlated with turbidity in the Golden Gate Canal and Haldeman Creek (station HALDCRK) bay segments (Spearman’s r, 0.34 < r< 0.41, p < 0.05; Table B-6), but was negatively correlated with turbidity at locations in Rock Creek (BC2), Northern Naples Bay (CURLEW), and Southern Naples Bay (NBAYWS) (Spearman’s r, -0.24 and -0.41, p < 0.05; Table B-6).

Given that turbidity and Secchi depth are both measures of water clarity, it is not surprising that turbidity exhibited a consistent relationship with Secchi depth throughout the Bay and input tributaries with a statistically significant negative correlation at almost all monitoring locations (Spearman’s r, -0.32 < r < -0.65, p < 0.05; Table B-5). The only exceptions were stations BC-3 and GORDPT in the Marine Segment Gordon River and HALDCRK located at the weir in Haldeman Creek. As turbidity increases, the amount of light scatter in the water column also increases and the Secchi depths decrease.

5.2 Proportional Analysis

While correlation analyses help to identify if the data indicate certain relationships are present, they alone may not tell a comprehensive story about what affects water clarity in Naples Bay. Based on the great variation in station depths and the large number of “on bottom” Secchi measurements at many locations throughout the Bay, in addition to the natural variation in the datasets, it’s possible the correlation analyses with Secchi depth may be biased. Also, the mere identification of a relationship falls short of the goal of informing management decisions. To further explore the observed relationships and provide more pertinent information for resource managers, a proportional analysis was conducted (at the bay segment level) to determine the likelihood of achieving a certain Secchi depth given ranges of the variables affecting water clarity. In addition to identifying a relationship between these factors, this analysis is useful to identify the magnitude at which the effect is observed. As a management tool, the proportional analysis can help to identify thresholds of TSS, chlorophyll-a, color, or turbidity that coincide with a desirable Secchi depth.

The proportional analysis calculated the proportion of Secchi depths greater than a named threshold (>1 m or > 1.5 m) for observations where TSS, chlorophyll-a, color, or turbidity were within predefined ranges (or bins). Several alternate Secchi depth thresholds were examined for use in the analysis, and > 1 m was chosen for most stations (> 1.5 was used for Gordon Pass and the GGC locations because of the deeper station depths). In general, Secchi depth at most stations was almost always greater than 0.5 and less than 1.5 or 2. For this analysis, monitoring events with “on bottom” recorded for the Secchi depth were removed. Also, in order to provide a condition more representative of the bay segment as a whole, if only a single measurement was available for a given parameter range, it was eliminated from the proportional representation. This analysis was limited to the same monitoring stations as the correlation analyses.

In general, for most bay segments, at greater magnitudes of TSS, color, chlorophyll-a, and turbidity, the proportion of Secchi depth measurements greater than one meter (1.5 m for Gordon Pass and GGC) are lower (Figure 20). Exceptions to this were typically the result of a limited sample size for a given range or parameter. The strongest pattern was observed between turbidity and proportion of Secchi depths greater than 1 or 1.5 meters. Secchi depth measurements greater than 1 or 1.5 meters were greatly reduced when turbidity increased into the six to eight NTU and higher ranges.



Figure 20. Proportion of Secchi depths greater than one meter (1.5 m for GGC and Gordon Pass segments) at stated ranges of TSS, color, chlorophyll-a, and turbidity in each bay segment, 2005–2014.

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5.3 Stepwise Regression

Given that turbidity reflects the sum of all factors that affect water clarity (including TSS, chlorophyll-a, and color) attempting to identify which factors are most influencing turbidity is an important management goal. A forward, stepwise regression analysis was conducted for each current and long term monitoring location used in the correlation analysis to determine which measured constituents may play a larger role in predicting the observed turbidity in Naples Bay and the input tributaries. For each location, the forward stepwise regression attempted to determine what relative effect chlorophyll-a, TSS, and color had on predicted turbidity (all variables log10-transformed; Appendix B and Table B-7). The standardized coefficients (b*, scaled to range of values) for each statistically significant regression model (p < 0.05) were used to illustrate the relative importance of each explanatory variable in predicting turbidity at each station (Figure 21). For some stations, the resulting model had relatively good fit to observed turbidity (r2 >0.5, 3495 and HALDCRK), but at other stations, the models were only moderately well-fit (0.25 > r2 0.5, GORDEXT, CURLEW) or poorly fit (r2 < 0.25, GGCAT31, BC3, OYSBAY, NBAYNL, NBAYWS, HALDCR). This means that there are other missing factors not included in these models that would help predict turbidity.

At most of the current monitoring locations in Naples Bay and the tributary inputs, chlorophyll-a plays the largest role in predicting observed turbidity (Figure 21). This was observed in the Golden Gate Canal, Marine Segment Gordon River, Northern Naples Bay, and Haldeman Creek segments. TSS was most likely to play a role in predicting turbidity at stations representing inputs to the Bay (Haldeman Creek, Golden Gate Canal, and Marine Segment Gordon River) as well as station NBAYNL in Northern Naples Bay near a pump station input to the Bay. In all cases where chlorophyll-a and TSS were included as predictors of turbidity, the relationship was positive meaning that as chlorophyll-a and/or TSS goes up, the turbidity also goes up. The observed increasing trend in chlorophyll-a concentrations (Cardno 2015) and the regression model result that indicates chlorophyll-a plays a large role in turbidity and therefore Secchi depth, may have important implications for Naples Bay management.

Color was also a significant predictor of turbidity at several of the monitoring locations, but with the opposite effect from chlorophyll-a and TSS. In most cases where color was identified in the models as a predictor of turbidity, the relationship was negative, meaning that as color increases, the turbidity decreases. This pattern may be the result of higher color freshwater inflow that may receive some treatment from the weirs (settling) at the tributary inputs prior to entering Naples Bay.

None of the factors used in the regression model (chlorophyll-a, TSS, and color) were significant in predicting turbidity in Gordon Pass or Rock Creek. Thus, factors other than TSS, chlorophyll-a, and color are driving turbidity in these areas. Interestingly, even though TSS concentrations are highest in Southern Naples Bay and Gordon Pass (see Section 3.1), TSS was not a significant variable in explaining turbidity in this area. Since turbidity appears to play an important role in Secchi depth (and therefore light penetration), identifying, measuring, and understanding the factors that impact water clarity in the Southern Bay are important management steps that could have important biological implications.



Figure 21. Spatial illustration of statistically significant factors shown to affect turbidity in Naples Bay using a step-wise regression.

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July 2016 Cardno Implications for Naples Bay Management 23

6 Implications for Naples Bay Management

Water clarity is an important component of an overall Naples Bay management plan to protect and restore the estuarine ecosystem. The City of Naples recognizes the ecological value and importance of healthy seagrass and oyster communities in Naples Bay. Since the 1950’s, Naples Bay has lost approximately 90 percent of its seagrass beds and 80 percent of its oyster reefs (Schmid et al. 2006) which have been attributed to hydrologic alterations and urbanization (Baum 1973, Simpson et al. 1979, and SFWMD 2007). The City has an aggressive and ongoing management plan that includes water quality and water clarity improvements; shoreline protection; and seagrass and oyster restoration projects (City of Naples 2010). The results of this study are expected to be useful for informing the overall management plan for Naples Bay and provide insight for ongoing seagrass and oyster restoration efforts. Seagrass communities can be affected by depth, water clarity, sediment characteristics, tidal and wave action, and boat traffic. Only the first two factors are considered in this study, but our results can be combined with analyses of the other factors to generate a robust understanding of effects on seagrass in Naples Bay.

Naples Bay is a shallow, narrow estuary with an average depth of approximately 1.7 m at the monitoring locations in the Marine Segment Gordon River, Northern Naples Bay, and Southern Naples Bay segments. The Port Royal segment has somewhat deeper depths, and Gordon Pass is approximately 3.2 m deep at the GPASS6 monitoring location. The distribution of known seagrass is limited to the shallow areas of the Southern Naples Bay segment with typically less than five percent cover, using the Braun-Blanquet scale (Cardno 2015). Within the existing seagrass beds in Naples Bay, the deep edge of bed is more likely limited by the presence of the boating channel than it is by water clarity (Cardno 2015). However, in the shallow water outside of the channel, water clarity likely plays a major role in whether or not enough light penetrates to the seafloor to support seagrass growth. Water quality and clarity in Southern Naples Bay is represented by a single long-term monitoring location (NBAYWS) with an average water depth of 1.6 m and an average Secchi depth of 1.1 m. With Secchi depths reaching approximately 70 percent of the water column, in an area less than two meters deep, it is possible reduced light availability could be contributing to the low seagrass density in this area.

Secchi depths throughout the Bay are related to turbidity, which is the sum of all factors affecting water clarity, including color, chlorophyll-a, and TSS. Chlorophyll-a is a large contributor to turbidity at most monitoring locations, although color and TSS were significant at some locations. TSS appeared to be a significant factor in turbidity in and around the tributary inputs. This result is not unexpected given that the tributary inputs (including the GGC) act as sources of suspended sediments, color, and nutrients to the Bay. During the wet season, when the tributary inputs deliver a high volume of freshwater, TSS is delivered to the Bay in very low concentrations but high loads during a relatively short period of time each year. Because the weirs in the tributaries and GGC likely provide some water treatment for sediments, the low concentration and high loads delivered to Naples Bay are likely to consist of smaller silts and clays that take longer settle out of the water column which may contribute to turbidity, but may not be measured in a laboratory TSS measurement. The dominance of silts in the sediments of the Northern Naples Bay and Haldeman Creek areas (Savarese et al. 2006), suggests that these are areas where smaller sediment particles settle out of the water column, which could smother potential seagrass habitat while also creating pockets of loose, fine material that is easily re-suspended with tidal and wave action as well as boat wakes. Chlorophyll-a concentrations are also significantly elevated during the wet season (indicating more abundant algal populations) which also contribute to turbidity.

The increasing trends in turbidity and chlorophyll-a over time (Cardno 2015) are potentially problematic for seagrass and oysters given the significant role chlorophyll-a plays in turbidity and the statistically significant relationship between turbidity and Secchi depth throughout the Bay. As a preliminary planning tool, the proportional analysis can be used to predict changes in Secchi depths if turbidity continues to increase according to the current trend. At the current rate of increase (approximately one NTU per year),


July 2016 Cardno Implications for Naples Bay Management 24

the average turbidity in Naples Bay can conservatively be expected to reach six to eight NTU in approximately five to ten years, which according this analysis, is associated with a dramatic decrease in the proportion of Secchi depths greater than one meter. As water clarity is diminished, light penetration is decreased in the shallow areas of the Bay that could potentially support seagrass, which creates management issues for current seagrass beds as well as planned restoration activities. We recognize this scenario is preliminary based on the current information available, and that an optical model considering all of the factors that affect water clarity and seagrass growth in Naples Bay would be necessary. Specifically, data establishing the relationship between actual light penetration in the water column (e.g. PAR) and other measures affecting water clarity (e.g. TSS, turbidity, and chlorophyll-a) would be necessary to identify management targets based on the physiological light requirements of seagrass in Naples Bay.

Although TSS was only shown to play a significant role in turbidity in some of the tributary input locations, the increasing concentrations from north to south within the Bay and the overall loading of TSS to the Bay may still be a factor for seagrass and oyster restoration activities. Loading calculations for TSS are currently only possible for the GGC, and overall loading from all sources including all tributaries and stormwater inputs would be a helpful tool in understanding the overall role TSS plays in Naples Bay. TSS was significant in explaining turbidity at the tributary inputs, which suggests that TSS may be a localized factor and may affect biological communities near the sources of TSS to the Bay. Loading calculations from these localized sources (e.g. Haldeman Creek) would be necessary for understanding how they may be affecting seagrass where it is currently being monitored in Southern Naples Bay.

In addition to more detailed TSS loading data, more information about sediment resuspension in the southern portion of the Bay may also explain some of the TSS spatial patterns noted in this report. The southern portion of Naples Bay is the most affected by tidal action and most likely experiences the greatest amount of boat traffic of all the bay segments as vessels travel to and from Gordon Pass. Both factors occur frequently and could be significant contributors to high TSS concentrations due to sediment resuspension. However, the spatial and temporal extent of sediment resuspension and its impact on TSS concentrations cannot be captured in monthly grab samples. A directed sampling program with more frequent (or continuous) monitoring of TSS and/or hydrology would be necessary to determine how sediment resuspension (from tidal action, boat wakes, or other physical drivers) affects conditions in Southern Naples Bay.

This study provides information for resource managers on the factors affecting water clarity in Naples Bay. This effort was limited to the factors currently being measured. In order to provide a more robust characterization of water clarity and the potential effects on biological communities, further studies relating these factors to light availability for seagrass growth are recommended. However, this effort was successful in identifying the role of TSS, chlorophyll-a, and color in water clarity and in identifying relationships among variables that can have an effect on seagrass. Although no direct cause and effect relationship with the observed seagrass distribution or density in Naples Bay could be established at this time, this study lays the groundwork for additional ongoing efforts to create water quality and water clarity thresholds that will ultimately allow for seagrass community restoration in Naples Bay.


July 2016 Cardno Literature Cited 25

7 Literature Cited

American Public Health Association (APHA). 1989. Standard Methods for the Examination of Water and Wastewater. 17th ed. American Public Health Association, American Water Works Association, Water Pollution Control Federation publication. APHA, Washington D.C.

Baum, E.L. 1973. Early Naples and Collier County. Collier County Historical Society. Naples, Florida.

Buiteveld, H. 1995. A Model for Calculation of Diffuse Light Attenuation (PAR) and Secchi Depth. Netherlands Journal of Aquatic Ecology. 29:55-65.

Cardno. 2015. Naples Bay Water Quality and Biological Analysis Project. Prepared for the City of Naples Streets and Stormwater Department, Natural Resources Division. August 2015. 151 pp.

City of Naples. 2010. A Twenty Year Plan (and Visionary Guide) for the Restoration of Naples Bay. Naples, Florida. 28 pp.

Devlin, M.J., J. Barry, D.K. Mills, R.J. Gowen, J. Foden, D. Sivyer, and P. Tett. 2008. Relationships Between Suspended Particulate Material, Light Attenuation, and Secchi Depth in UK Marine Waters. Estuarine Coastal and Shelf Science. 79:429-439.

Dixon, L.K. and D.J. Gordon. 2016. Water Quality and Clarity of Naples Bay, FL: Evaluation with Respect to Existing Seagrass. Technical Report prepared for City of Naples, Natural Resources Division. Mote Marine Laboratory Technical Report No. 1945.

Gallegos, C.L, P.J. Werdell, and C.R. McClain. 2011. Long-Term Changes in Light Scattering in Chesapeake Bay Inferred from Secchi Depth, Light Attenuation, and Remote Sensing Measurements. Journal of Geophysical Research. 116:C00H08.

Luhtala, H. and H. Tolvanen. 2013. Optimizing the Use of Secchi Depth as a Proxy for Euphotic Depth in Coastal Waters: An Empirical Study form the Baltic Sea. ISPRS International Journal of Geo-Information. 2:1153-1168.

Schmid, J.R., K. Worley, D.S. Addison, A.R. Zimmerman, and A.V. Eaton. 2006. Naples Bay past and present: a chronology of disturbance to an estuary. Technical Report to the City of Naples, funded by the South Florida Water Management District. p. 58.

Savarese, M., B. Fielder, and T. Dellapenna. 2006. Substrate and Subsurface Mapping of Naples Bay Using Geophysical Techniques: Implications for Oyster Reef Restoration. Submitted to the South Florida Water Management District, July 14, 2006.

Simpson, B.L., R. Aaron, J. Beltz, D. Hicks, J. van de Kreeke, and B. Yokel. 1979. The Naples Bay Study. The Collier County Conservancy.

South Florida Water Management District. 2007. Naples Bay: Surface Water Improvement and Management Plan. South Florida Water Management District, 10–29p.

United States Geological Survey Water Science School. 2015. http://water.usgs.gov/edu/turbidity.html.

Status of Naples Bay Water Clarity

APPENDIX

A MONITORING LOCATION DESCRIPTIONS


July 2016 Cardno A-1

Appendix A Monitoring Location Descriptions

Table A-1. Monitoring Locations in Naples Bay, Marine Segment Gordon River, and Tributary Inputs, 2005–2014.

Station Name Date Range Station Descriptor

Golden Gate Canal 3495 2005–2014 upstream of GGC1 weir

GGCAT31 2005–2014 upstream of GGC1 weir BC4 2005–2009 downstream of GGC1 weir

Marine Segment Gordon River

BC3 2005–2014 downstream of Golden Gate Pkwy weir

GORDEXT 2011–2014 GORDPT 2006–2010 GORDPK 2006–2010

NB4 2009–2004 GORDJOE 2006–2010

Rock Creek ROCKCR 2011–2014 upstream of confluence with Bay

BC2 2005–2014 at confluence with Bay Northern Naples Bay

CURLEW 2011–2014 dead end canal at stormwater input OYSBAY 2011–2014 dead end canal at stormwater input NBAYCC 2006–2010 NBAYNL 2006–2014

BC1 2005–2009 NBAY33 2006–2014 NBAY29 2006–2010 NBAYKF 2006–2010

Haldeman Creek HALDCRK 2005–2014 upstream of weir at SR 41

BC5 2005–2013 downstream of weir HALDCR 2011–2014 just upstream of confluence with Bay

NB2 2009–2014 just upstream of confluence with Bay NBAYHC 2006–2010 at confluence with Bay

Southern Naples Bay NBAYWS 2006–2014 NBAY21 2006–2010 NBAYBV 2006–2010

Port Royal NBAYLLO 2006–2010 NBAYTC 2006–2010 NBAY13 2006–2010

Gordon Pass GPASS6 2006–2014

Status of Naples Bay Water Clarity

APPENDIX

B SUMMARY OF STATISTICAL ANALYSES


July 2016 Cardno B-1

Appendix B Summary of Statistical Analyses

Table B-1. Analysis of Variance (ANOVA) or Kruskal-Wallis results for annual geometric mean variables among Naples Bay segments, 2005–2014.

ANOVA

Parameter Sum of

Squares Degrees of Freedom

Mean of Squares F p-value

TSS (mg/L) 829 6 138 20.0 <0.001

Turbidity (NTU) 6 6 1 1.6 0.17

Chlorophyll-a (µg/L) 92 6 15.4 6.6 <0.001

Color (PCU) 9590 6 1598 17.5 <0.001

Kruskal-Wallis

Parameter Degrees of Freedom H p-value

Secchi Depth (m) 6 31.0 <0.001

Red indicates statistical significance at p < 0.05

Table B-2. Duncan’s Post Hoc Test or Mann-Whitney Multiple Comparisons results for annual geometric mean variables by Naples Bay segment, 2005–2014.

Bay Segment Mean Value Groupings

1 2 3 4 Duncan’s Post Hoc Test

TSS

Golden Gate Canal 3.2 ****

Marine Segment Gordon River 4.6 ****

Haldeman Creek 4.8 ****

Rock Creek 5.7 ****

Northern Naples Bay 8.4 ****

Southern Naples Bay 10.9 ****

Gordon Pass 13.7 ****

Turbidity - No Significant Differences (ANOVA, p > 0.05)

Chlorophyll-a






Rock Creek 6.0 ****


Color




Appendix B Status of Naples Bay Water Clarity Summary of Statistical Analysis Final Report


Bay Segment Mean Value Groupings

1 2 3 4 Northern Naples Bay 32.0 ****

Rock Creek 35.8 **** ****



Mann Whitney Multiple Comparisons

Secchi Depth




Rock Creek 1.11 ****


Gordon Pass 1.29 **** ****


Table B-3. Wet season and dry season T-test or Mann Whitney U test results on water quality variables by Naples Bay segment, 2005–2014.

Bay Segment Mean Dry

Mean Wet

Test value

Degrees of

Freedom p-value Valid N Dry

Valid N Wet

Std. Dev. Dry

Std. Dev. Wet

T-test

Log TSS

Golden Gate Canal 0.52 0.50 0.97 284 0.335 167 119 0.26 0.22

Gordon Pass 1.18 1.08 1.19 73 0.236 40 35 0.34 0.35

Haldeman Creek 0.74 0.62 3.34 361 0.001 211 152 0.36 0.30 Marine Segment

Gordon River 0.72 0.58 3.74 300 0.000 170 132 0.32 0.31

Northern Naples Bay 1.02 0.78 5.71 326 0.000 186 142 0.37 0.37

Port Royal 1.06 0.87 2.88 82 0.005 49 35 0.28 0.30

Rock Creek 0.86 0.64 4.61 159 0.000 92 69 0.33 0.28

Southern Naples Bay 1.11 0.88 3.65 128 0.000 71 59 0.34 0.35

Log Turbidity

Golden Gate Canal 0.12 0.32 -5.51 175 0.000 104 73 0.23 0.25

Gordon Pass 0.34 0.30 0.38 74 0.702 41 35 0.47 0.39

Haldeman Creek 0.33 0.30 1.12 208 0.266 124 86 0.25 0.18 Marine Segment

Gordon River 0.32 0.32 -0.10 223 0.924 126 99 0.27 0.26

Northern Naples Bay 0.39 0.35 1.61 287 0.108 164 125 0.20 0.22

Port Royal 0.25 0.19 0.80 90 0.426 54 38 0.37 0.21

Rock Creek 0.35 0.30 0.89 104 0.376 61 45 0.27 0.26

Southern Naples Bay 0.42 0.31 2.64 142 0.009 78 66 0.29 0.19 Log Chlorophyll-a


Gordon Pass 0.48 0.64 -3.08 73 0.003 40 35 0.21 0.24

Haldeman Creek 0.69 0.99 -9.71 315 0.000 191 126 0.26 0.29 Marine Segment

Gordon River 0.66 0.79 -3.27 276 0.001 159 119 0.33 0.36

Northern Naples Bay 0.62 0.88 -8.04 336 0.000 193 145 0.25 0.33

Port Royal 0.55 0.80 -4.31 89 0.000 53 38 0.23 0.34



Bay Segment Mean Dry

Mean Wet

Test value

Degrees of

Freedom p-value Valid N Dry

Valid N Wet

Std. Dev. Dry

Std. Dev. Wet

Rock Creek 0.70 0.92 -4.69 144 0.000 86 60 0.25 0.32

Southern Naples Bay 0.50 0.72 -5.43 139 0.000 75 66 0.19 0.29

Log Color


Gordon Pass 0.89 1.25 -4.96 74 0.000 41 35 0.20 0.41

Haldeman Creek 1.34 1.63 -7.33 310 0.000 184 128 0.42 0.20 Marine Segment

Gordon River 1.51 1.82 -9.52 319 0.000 182 139 0.32 0.21

Northern Naples Bay 1.33 1.68 -13.49 338 0.000 194 146 0.21 0.27

Port Royal 1.06 1.43 -6.16 90 0.000 54 38 0.22 0.36

Rock Creek 1.32 1.78 -8.78 156 0.000 91 67 0.39 0.19

Southern Naples Bay 1.06 1.52 -9.06 141 0.000 78 65 0.23 0.37

Mann-Whitney U test

Secchi

Golden Gate Canal 1.76 1.51 5191 413 0.000 268 147 0.53 0.46

Gordon Pass 1.39 1.64 427 62 0.328 37 27 0.66 0.85

Haldeman Creek 1.10 1.09 11201 412 0.394 164 250 0.28 0.25 Marine Segment

Gordon River 1.10 1.16 6834 296 0.175 126 172 0.27 0.24

Northern Naples Bay 1.12 1.14 11270 353 0.760 152 203 0.24 0.27

Port Royal 1.26 1.37 707 84 0.091 50 36 0.44 0.34

Rock Creek 1.05 1.11 2078 193 0.036 79 116 0.25 0.22

Southern Naples Bay 1.10 1.24 1210 112 0.019 59 55 0.40 0.25

Water Column %

Golden Gate Canal 0.82 0.73 4464 371 0.000 241 132 0.20 0.21

Gordon Pass 0.51 0.57 437 61 0.496 36 27 0.30 0.31

Haldeman Creek 0.74 0.79 2964 216 0.023 98 120 0.17 0.18 Marine Segment

Gordon River 0.75 0.82 1603 145 0.218 66 81 0.20 0.17

Northern Naples Bay 0.57 0.62 8535 321 0.242 135 188 0.22 0.23

Port Royal 0.49 0.53 673 77 0.395 46 33 0.17 0.19

Rock Creek 0.75 0.89 316 71 0.022 37 36 0.19 0.14

Southern Naples Bay 0.72 0.72 1289 100 0.984 55 47 0.24 0.20 Red indicates statistical significance at p < 0.05



Table B-4. Kendall Tau Trend Analysis by Bay segment for annual geometric mean Secchi depth and percent of the water column penetrated by light (WC%), 2005–2014.

Bay Segment

Secchi Depth Light Penetration Percent

N Kendall

Tau p-value N Kendall

Tau p-value Golden Gate Canal 10 0.38 0.13 9 0.00 1.00

Gordon Pass 9 0.21 0.46 9 0.11 0.68

Haldeman Creek 10 -0.51 0.04 10 0.64 0.01

Marine Segment Gordon River 10 0.24 0.33 10 0.47 0.05

Northern Naples Bay 10 -0.11 0.65 10 0.69 0.01

Port Royal 6 0.33 0.35 5 -0.40 0.33

Rock Creek 10 0.42 0.09 9 0.33 0.21

Southern Naples Bay 10 -0.33 0.18 9 -0.17 0.54 Red indicates statistical significance at p < 0.05

Table B-5. Spearman’s Rank Order Correlations between Secchi depth and water quality variables at current monitoring locations in Naples Bay and tributary inputs, 2005–2014.

Station ID Bay Segment Turbidity TSS Chlorophyll-a Color

3495 Golden Gate Canal

-0.62 -0.44 -0.32 -0.56

GGCAT31 -0.38 -0.03 -0.31 -0.58

BC3


-0.25 -0.02 -0.13 -0.33

GORDEXT -0.41 -0.50 -0.59 0.11

GORDPT -0.22 -0.45 -0.49 -0.02

NBAYNL

Northern Naples Bay

-0.32 -0.20 0.03 0.18

CURLEW -0.65 -0.52 -0.12 0.21

OYSBAY -0.36 0.03 -0.40 -0.30

ROCKCR Rock Creek

-0.62 0.00 -0.46 -0.29

BC2 -0.36 0.07 -0.11 -0.30

HALDCR Haldeman Creek

-0.54 -0.04 -0.05 -0.01

HALDCRK -0.02 -0.22 -0.37 0.41

NBAYWS Southern Naples Bay -0.42 -0.08 0.06 0.23

GPASS6 Gordon Pass -0.55 -0.16 -0.25 -0.34

Red Indicates significance at p < 0.05



Table B-6. Spearman’s Rank Order Correlations between turbidity and water quality variables at current monitoring locations in Naples Bay and tributary inputs, 2005–2014.

Station ID Bay Segment Secchi TSS Chlorophyll-a Color

3495 Golden Gate Canal

-0.62 0.38 0.51 0.36

GGCAT31 -0.38 -0.08 0.32 0.34

BC3


-0.25 0.02 0.27 0.09

GORDEXT -0.41 0.20 0.49 -0.10

GORDPT -0.22 -0.04 -0.10 0.12

NBAYNL

Northern Naples Bay

-0.32 0.20 0.26 -0.07

CURLEW -0.65 0.28 0.08 -0.41

OYSBAY -0.36 0.17 0.10 -0.21

ROCKCR Rock Creek

-0.62 0.08 0.27 0.06

BC2 -0.38 0.16 0.44 -0.29

HALDCR Haldeman Creek

-0.54 0.21 0.16 -0.22

HALDCRK -0.02 0.28 0.65 0.41

NBAYWS Southern Naples Bay -0.42 0.03 -0.02 -0.24

GPASS6 Gordon Pass -0.55 0.18 0.22 0.16

Red Indicates significance at p < 0.05

Table B-7. Forward, stepwise, multiple linear regression results of turbidity with chlorophyll-a, TSS, and color at current monitoring locations in Naples Bay and tributary inputs, 2005–2014.

b* Std. Err. b Std. Err. t p-value

Station ID: 3495 R²= 0.519; F(3,41)=14.750 p<0.00000

Intercept -0.513 0.180 -2.846 0.007

logChla 0.563 0.110 0.401 0.078 5.113 0.000

logColor 0.247 0.116 0.250 0.117 2.140 0.038

logTSS 0.209 0.117 0.293 0.164 1.784 0.082

Station ID:GGCAT31 R²= 0.233; F(2,56)=8.5035 p<0.00060

Intercept -0.541 0.186 -2.897 0.005

logColor 0.328 0.118 0.320 0.115 2.787 0.007

logChla 0.320 0.118 0.302 0.111 2.726 0.008

Station ID: BC2 R²= 0.06; F(1,44)=2.9165 p<0.09473

Intercept 0.074 0.111 0.668 0.507

logChla 0.25 0.146 0.219 0.128 1.707 0.094

Station ID: BC3 R²= 0.155; F(2,53)=4.8698 p<0.01144

Intercept -0.651 0.426 -1.524 0.133

logChla 0.331 0.126 0.287 0.110 2.619 0.011

logColor 0.196 0.126 0.380 0.245 1.552 0.127

Station ID: CURLEW R²=0.256; F(2,39)=6.7209 p<0.00310

Intercept 1.082 0.203 5.321 0.000

logColor -0.540 0.148 -0.494 0.136 -3.637 0.001

logChla 0.261 0.148 0.165 0.093 1.762 0.086

Station ID: OYSBAY R²=0.175; F(2,43)=4.5665 p<0.01591

Intercept 0.698 0.142 4.929 0.000

logColor -0.525 0.186 -0.350 0.124 -2.816 0.007

logChla 0.503 0.186 0.287 0.106 2.699 0.009



b* Std. Err. b Std. Err. t p-value

Station ID: ROCKCR R²= 0.110; F(2,43)=2.6522 p<0.08200

Intercept 0.415 0.165 2.519 0.016

logChla 0.395 0.171 0.213 0.083 2.303 0.026

logColor -0.220 0.171 -0.015 0.117 -1.284 0.205

Station ID: GORDEXT R²= 0.318; F(2,42)=9.7800 p<0.00033

Intercept -0.022 0.083 -0.264 0.793

logChla 0.406 0.139 0.305 0.105 2.906 0.005

logTSS 0.257 0.139 0.135 0.073 1.844 0.071

Station ID: NBAYNL R²= 0.138; F(3,70)=3.7446 p<0.01482

Intercept 0.375 0.158 2.378 0.020

logChla 0.368 0.125 0.257 0.087 2.953 0.004

logColor -0.212 0.129 -0.156 0.095 -1.642 0.105

logTSS 0.144 0.116 0.077 0.062 1.242 0.218

Station ID: NBAYWS R²= 0.085; F(1,71)=6.6221 p<0.01216

Intercept 0.663 0.106 6.291 0.000

logColor -0.292 0.114 -0.200 0.078 -2.573 0.012

Station ID: HALDCR R²= 0.243; F(3,43)=4.6091 p<0.00697

Intercept 0.631 0.216 2.916 0.005

logColor -0.491 0.168 -0.401 0.137 -2.927 0.005

logChla 0.498 0.164 0.405 0.132 3.050 0.003

logTSS 0.155 0.139 0.097 0.087 1.118 0.269

Station ID: HALDCRK R²= 0.530; F(3,54)=20.367 p<0.00000

Intercept -1.428 0.663 -2.153 0.035

logChla 0.551 0.110 0.322 0.064 5.016 0.000

logTSS 0.209 0.107 0.221 0.113 1.951 0.056

logColor 0.170 0.096 0.757 0.427 1.771 0.082

Station ID:GPASS6 R²=0.057; F(2,72)=2.1810 p<0.12033

Intercept -0.087 0.201 -0.433 0.666

logTSS 0.191 0.115 0.240 0.144 1.667 0.100

logChla 0.133 0.115 0.245 0.211 1.159 0.250

status of naples bay water clarity: 2005-2014

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