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Draft Technical Report on the Scientific Basis for Alternative San Joaquin River Flow and Southern Delta Salinity Objectives

Public Board WorkshopJanuary 6-7, 2011

January 6 and 7, 2011 Workshop

Focus of Workshop

Focus: Discuss technical basis for developing alternative San Joaquin River flow and southern Delta salinity objectivesOther Issues: including non-technical, environmental review, economics, policy and procedural issues focus of subsequent steps in processAdditional comments: Due by noon, Feb. 8


CommentsCA Farm Bureau Fed.CA Sportfishing Protection Al./CA Water Impact Net.Central Delta Wtr. Ag.Central Valley Clean Water Assoc.City of StocktonCity of TracySF Pub. Util. Com.South Delta Water Ag.State Wtr. Contractors/San Luis Delta Mendota Wtr. Nat. Marine Fish. Serv.

Coalition for a Sustainable DeltaContra Costa Wtr. Dist.Dept. Fish and GameDept. Water ResourcesJohn LettyStockton East Wtr. Dist.North. CA Water Assoc.San Joaquin R. Grp. Auth.Glenn-Colusa Ir. Dist.Bay Institute/Natural Res. Def. CouncilDept. of Interior


Panel Participation RequestsNational Marine Fisheries ServiceDepartment of Fish and GameBay Institute/Natural Resources Defense CouncilDepartment of Water ResourcesDepartment of InteriorState & Federal Water Contractors

California Sportfishing Protection Alliance/ California Water Impact NetworkSouth Delta Water AgencyU.S. Environmental Protection AgencyAmerican RiversSan Joaquin River Group Authority


Proposed Questions National Marine Fisheries ServiceDepartment of Fish and GameBay Institute/Natural Resources Defense CouncilDepartment of InteriorSF Public Utilities Commission

California Sportfishing Protection Alliance/ California Water Impact NetworkSouth Delta Water AgencyU.S. Environmental Protection AgencySJR Group AuthoritySJR Exchange Contractors


Next Steps

Following workshop submit revised Technical Report for independent peer reviewDraft Substitute Environmental Document expected by end of 2011Consideration of approval of final Substitute Environmental Document and any changes to San Joaquin River flow and southern Delta salinity objectives by spring of 2012

Chapter 2: Hydrologic Analysis of San Joaquin River Basin


Outline

1. Project area and unimpaired flow2. Typical hydrograph3. Annual, monthly, and daily flows4. Major tributary contributions to Vernalis5. Flow downstream of Vernalis6. Summary


Project Area

Vernalis

Stanisl

aus

Tuolum

ne

Merced

Upper

San Jo

aquin

Fresno

Chowchilla


Unimpaired Flow

“The flow that would occur absent the affects of dams and diversions”Not adjusted for changes in channel geometry, levees, valley floodingData Source

DWR. 2007. “Central Valley Unimpaired Flow”DWR, CDEC website “Full Natural Flow”


Unimpaired Flow

Tributaries calculated using gage data downstream of the major dams

Adjusted for evaporation, storage, and diversions“Valley Floor” based on factors for west side streams and Fresno Slough, however does not incorporate groundwater interactionVernalis = Sum of tributaries, valley floor, minor streams, and Tulare Basin outflow


Outline



0

2

4

6

8

10

12

O-04 N-04 D-04 J-05 F-05 M-05 A-05 M-05 J-05 J-05 A-05 S-05

Water Year 2005 (Wet)

Flow

(100

0 cf

s)

Unimpaired Flow

Observed Flow @ Ripon Peak 19,300 cfs

Winter Storm

Fall Storm Flow s

Rain on Snow

Spring Snow melt

Summer Baseflow

Typical Hydrograph – Stanislaus


Outline



Annual Flows at Vernalis Changes in Storage within SJR Basin

0

2

4

6

8

10

1930 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005Water Year

Tota

l Ava

ilabl

e St

orag

e C

apac

ity (m

af)

Cummulat ive Reservoir Storage

New

Mel

ones

New

Don

Ped

r o

New

Exc

hequ

er

Fria

nt D

am

Tri-D

ams,

and

Che

rry

Valle

y

Mad

era

Can

a

Kern

Can

al


0

2

4

6

8

10

1930 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005Water Year

Annu

al d

iffer

ence

from

uni

mpa

ired

flow

/ st

orag

e ca

paci

ty (m

af)

Dif ference from Unimpaired Flow

Cummulat ive Reservoir Storage

New

Mel

ones

New

Don

Ped

r o

New

Exc

hequ

er

Fria

nt D

am

Tri-D

ams,

Che

rry

Valle

y

Mad

era

Can

a

Kern

Can

al

Annual Flows at Vernalis Changes in Storage within SJR Basin

1987 = 84%

1993 = 20%

Vol

ume

stor

ed, d

iver

ted,

co

nsum

ed (

maf

/ yr)

Volume stored, diverted, consumed

~3.3 maf~2.4 maf


0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

Mon

thy

Flow

(maf

/mo)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

Monthly Flows at VernalisUnimpaired FlowActual Observed Flow

Median

75th %tile

25th %tile

50% of years


Monthly Flows at Vernalis

During 75% of years (~19 of past 25 yrs)April : < 40% of Unimpaired Flow May : < 25% of Unimpaired Flow June : < 30% of Unimpaired Flow

May was never more than 60%June was never more than 55%


Daily Flows – Tuolumne Wet Year (2005)

0

5

10

15

20

25

30

O-04 N-04 D-04 J-05 F-05 M-05 A-05 M-05 J-05 J-05 A-05 S-05

October 1 thruogh September 30

Flow

(100

0 cf

s)

Unimpaired Flow

Observed Flow @ Modesto

Page 20


0

5

10

15

20

25

30

O-07 N-07 D-07 J-08 F-08 M-08 A-08 M-08 J-08 J-08 A-08 S-08

October 1 thruogh September 30

Flow

(100

0 cf

s)

Unimpaired Flow

Observed Flow @ Modesto

Page 21

Daily Flows -Tuolumne Critically Dry Year (2008)


Annual Peak Daily Flows at Vernalis

Return Period

% Reduction from Unimpaired Flow (Annual 1-day Peak Flow)

1.5yr 70%

2yr 76%

5yr 53%10yr 65%

Unimpaired peak flows from USACE, 2002. “Sacramento San Joaquin Comprehensive Study” compared to 1984-2008 gage data.


Outline



Upper SJR at Friant Monthly Average Percent Contibution to UF and Observed Flow at Vernalis (1984-2008)

0%

10%

20%

30%

40%

50%

Perc

ent C

ontri

butio

n (%

)

UF 39% 31% 27% 24% 23% 23% 27% 31% 37% 45% 45% 45%

OBS 9% 7% 7% 6% 7% 8% 11% 13% 20% 22% 17% 14%


Merced Monthly Average Percent Contibution to UF and Observed Flow at Vernalis (1984-2008)

0%

10%

20%

30%

40%

50%

Perc

ent C

ontri

butio

n (%

)

UF 14% 14% 12% 15% 15% 15% 16% 16% 15% 14% 14% 12%

OBS 17% 16% 16% 16% 13% 13% 15% 17% 13% 11% 10% 11%


Tuolumne Monthly Average Percent Contibution to UF and Observed Flow at Vernalis (1984-2008)

0%

10%

20%

30%

40%

50%

Perc

ent C

ontri

butio

n (%

)

UF 33% 33% 26% 31% 31% 32% 31% 32% 32% 27% 27% 27%

OBS 25% 21% 22% 26% 29% 26% 29% 26% 19% 20% 21% 22%


Stanislaus Monthly Average Percent Contibution to UF and Observed Flow at Vernalis (1984-2008)

0%

10%

20%

30%

40%

50%

Perc

ent C

ontri

butio

n (%

)

UF 20% 19% 20% 21% 20% 21% 21% 18% 14% 11% 11% 14%

OBS 22% 22% 25% 20% 19% 24% 27% 31% 36% 36% 33% 27%


STANISLAUS RIVER MERCED RIVER

UPPER SJR TUOLUMNE RIVER

Observed Flow

Unimpaired Flow

Tributary Contribution to Vernalis Flow


Outline



HOR

USGS Gage @ Vernalis

Barriers


Summary

Natural variability and magnitude reduced

Seasonal peak flows shifted in time

Tributary contributions altered

Flows downstream of Vernalis altered

Chapter 3: Scientific Basis for Developing Alternate San Joaquin River Delta Inflow Objectives


OutlineFocus, Problem and Approach for Chap. 3Salmon and Steelhead Life History Salmon and Steelhead Population TrendsSan Joaquin River Basin Inflow NeedsImportance of the Natural Hydrograph


Focus, Problem and Approach Focus: San Joaquin River flows at Vernalis for fall-run Chinook salmon & steelhead

Problem: Reduced flows & changes in natural flow regime impairing fish and wildlife

Approach: Evaluated existing scientific literature on inflows and protection of fish & wildlife and used to develop range of potential flow alternatives


OutlineFocus, Problem and Approach for Chap. 3Salmon and Steelhead Life History Salmon and Steelhead Population TrendsSan Joaquin River Basin Inflow NeedsNatural Hydrograph Importance


Generalized Life History SJR basin Fall-Run Chinook Salmon and Central Valley Winter-Run Steelhead


Population Trends SJR basin Fall-Run Chinook Salmon


Population Trends SJR basin Central Valley Winter-Run Steelhead


Fall-Run Chinook Inflow Needs

Primary limiting factor for San Joaquin River fall-run Chinook salmon survival and abundance is reduced flows during spring

State Water Board review focused on inflows to Delta from February through June


Functions Supported by Spring FlowsSalmon have adapted to natural flows These flows provide several functions

Cues for outmigrationImproved transport downstreamImproved edge habitat and food productionMaintenance of channel habitat and transport of sediments, biota and nutrientsIncreased turbidity and reduced predationImproved water quality


Salmon Abundance

Additional flow is neededThe primary influence on adult escapement is flow two and a half years earlier

NMFS 2009

Fall-Run Chinook Salmon Escapement shifted 2 yearsin relation to water year

NMFS 2009


Salmon Survival

Hankin et al. 2010

SJRGA 2007

Combined Differential Recovery Rate (CDRR) are point estimates of survival


Supporting StudiesStudy ConclusionKjelson et al. 1981 Additional flow increased use of

estuary and survival of juvenilesKjelson and Brandes 1989

Salmon escapement and Vernalis flow correlated

Anadromous Fish Restoration Program 1995

Salmon declines attributed to inadequate streamflow – more flow needed

Brandes and McLain 2001

Relationship between survival and river flow statistically significant


Supporting StudiesStudy Conclusion

Mesick 2001 Recruitment correlated with springtime flows

Mesick et al. 2008; Mesick 2009

Winter and spring flows highly correlated with smolt production

Newman 2008 Positive association between flow and survival


Supporting Studies

VAMP Peer ReviewIncreased flows have a positive effect on salmon survivalHigher flows through the Stockton Deep Water Ship Channel could benefit salmon

VAMP Acoustic EvaluationsSurvival of tagged fish has remained lowDry conditions can lead to increased predation


Previous Flow Recommendations

Increase flows at Vernalis to achieve salmon doubling goal

DFG: 7,000 to 15,000 cfs AFRP: 1,744 to 17,369 cfs TBI/NRDC: 5,000 cfs to an average of 10,000 cfs

Increase flows at Vernalis to protect fish and wildlife beneficial uses

60 percent of unimpaired


Importance of the Natural Flow Regime

A more natural flow regime would improve ecosystem functions

Fish communitiesFood webHabitat connectivityFluvial hydrogeomorphological processesTemperature


Importance of the Natural Flow RegimeFish Communities

Native communities have adapted to flow variabilityA natural flow regime protects genetic variability

Food WebHigh pulse flows benefit the lower trophic levelsFloodplain inundation provides organic matter



Habitat connectivity (lateral and longitudinal)Riparian and floodplain activation allows for energy flowImproved juvenile fish survivalBeneficial migration transportLess hostile rearing conditionsGreater net downstream flow



Fluvial hydrogeomorphological processesIncreased complexityMobilization of the streambedLess homogenous channel

TemperatureDecreased temperatures provide cold water refugia


Conclusions

A higher and more naturally variable inflow regime from the SJR is neededAny flow objectives will incorporate adaptive managementA range of alternative SJR flow objectives expressed as percentages of Unimpaired Flow will be analyzed

Chapter 4: Southern Delta Salinity


Existing Salinity Objectives

0 1 2 3 4 5 Miles³

#

Tracy

#

Stockton

!O

SJR @ Airport Way Bridge, Vernalis

!O

Old River near Middle River

!O

Old River @ Tracy Road Bridge

#

Manteca

!O

SJR @ Brandt BridgeLegal Delta

Boundary

South Delta Water Agency Boundary

San Joaquin County BoundarySan Joaquin County Boundary


Southern Delta (SD) Salinity

Outline:Characterizing SD salinity degradationSalt Loading from NPDES dischargesEffects of salinity on agricultural usesEffects of salinity on municipal uses


Factors Affecting SD Salinity

Salinity of SJR at VernalisEvapo-concentration from agricultural useNet flows in SD channels

Barrier operationsProject pumping

NPDES point sources


Salinity Regression AnalysisMonthly Average Data - April through August

y = 1.16x + 79.76R2 = 0.82

y = 1.17x + 183.89

0

200

400

600

800

1000

1200

1400

0 200 400 600 800 1000 1200 1400Observed EC (µS/cm) at Vernalis

Obs

erve

d EC

(µS/

cm) a

t OLD

85% prediction line:

best fit regression line:


Salinity Regression AnalysisMonthly Average Data - September through March

y = 0.92x + 164.28R2 = 0.71

y = 0.92x + 291.67

0

200

400

600

800

1000

1200

1400

0 200 400 600 800 1000 1200 1400Observed EC (µS/cm) at Vernalis

Obs

erve

d EC

(µS/

cm) a

t OLD

85% prediction line:

best fit regression line:



Outline: Estimating SD salinity degradationSalt Loading from NPDES dischargesEffects of salinity on agricultural usesEffects of salinity on municipal uses


Loading from NPDES Discharges

2007 Regional Board led DWR study:City of Tracy WWTP estimated to increase salinity 3 to 11 µS/cm at full capacity

Mass balance analysisAssumed permitted maximum salinity loads from Tracy, Deuel, and Mountain HouseCompared to estimated of salt load entering SD at the head of Old River


Mass Balance Analysis Results

0

500

1,000

1,500

2,000

2,500

3,000

O N D J F M A M J J A S

Month

Sal

t Loa

d (to

ns/m

onth

)

0%

5%

10%

15%

20%

25%

30%

Per

cent

of H

OR

Sal

t Loa

d (%

)

Point Source Salt Load (tons/mo) Percent of HOR Salt Load (%)


Salt Sensitivity of Crops in SD

1976 2007

Most salt sensitive crops grown in SD: - dry bean - almond, - walnut, - apricot

From Figure 3.4, Hoffman (2010)


Findings from Hoffman, 2010No adverse effects from following factors:

Saline/sodic soilsShrink/swell soils (bypass flows)Chloride/sodium toxicityShallow groundwater

Current salinity levels suitable for all cropsPotential for boron toxicity


Findings from Hoffman, 2010 con’t

Drains in western part of SD averaged LF = 0.21 to 0.27; minimum = 0.11Relatively high leaching fractions (LF) associated with SD irrigation practicesStudies of dry bean salt tolerance outdatedNo studies on early growth stagesStudies recommended on bean tolerance, leaching fraction, and boron toxicity


Soil Water Salinity ModelingRecommends steady-state approach:

using “exponential” water uptake equationincluding rainfall

For dry bean, alfalfa, and almond in SD:no loss yields at EC=1.0 dS/m and LF > 0.205% yield loss with low rainfall at LF = 0.15

Salt dissolution could increase soil water salinity by 5% over steady-state estimate


Impacts on Municipal Uses

Municipal and domestic supply beneficial use identified by Basin Plan for SDNo municipal intakes in immediate area, but SWP and CCWD intakes are in vicinityUSEPA maximum contaminant level (MCL):

Recommended MCL = 0.9 dS/mUpper MCL = 1.6 dS/m

Chapter 5: Water Supply Impact Analysis


Water Supply Impact Analysis

Outline:Overview of ApproachEstimating Additional Flows RequiredEstimating Reduction in Return FlowTotal Water Supply Impact Analysis



Conservative estimate of combined impact of flow and salinity objective alternatives.Additional flow above current conditions compared against diversions.Does not identify where or how additional flow will be obtained.Post-processing of CALSIM II model run representative of current conditions.


CALSIM II Operations Model

SJR module of CALSIM II was developed by USBR as operations planning modelImposes current infrastructure, regulations, delivery constraints and estimates demandAssumes historical conditions from 1922 to 2003 representative of futureUses CALSIM II output from 2009 SWP Delivery Reliability Report


CALSIM vs. Observed - Vernalis Flow

0

200

400

600

800

1000

1200

1400

1600

1800

2000

Oct

-83

Oct

-84

Oct

-85

Oct

-86

Oct

-87

Oct

-88

Oct

-89

Oct

-90

Oct

-91

Oct

-92

Oct

-93

Oct

-94

Oct

-95

Oct

-96

Oct

-97

Oct

-98

Oct

-99

Oct

-00

Oct

-01

Oct

-02

Date

Mon

thly

Flo

w (t

hous

and

acre

-feet

Observed

CalSIM II

Peak: 3,700 taf


CALSIM vs. Observed - Vernalis Salinity

0.00

0.20

0.40

0.60

0.80

1.00

1.20

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03Date

Mon

thly

Ave

rage

EC

(dS

/m)

Observed

CalSIM II



Outline: Overview of ApproachEstimating Additional Flows RequiredEstimating Reduction in Return FlowTotal Water Supply Impact Analysis


Additional Flow for Meeting Flow Objective Alternatives

-1,000

-500

0

500

1,000

1,500

2,000

2,500

3,000

Oct-77 Oct-78 Oct-79 Oct-80 Oct-81 Oct-82 Oct-83 Oct-84

Flow

(TA

F/m

o)

CALSIM Output @ Vernalis 40% Vernalis Unimpaired Flow Shortage (Feb. thru June)


Additional Flow for Meeting Salinity Objective Alternatives

Three-step calculation on monthly time-step:1. Use regression equations to determine

required EC at Vernalis2. Calculate low-salinity flows needed to

achieve required EC at Vernalis3. Subtract flows already being provided to

meet flow objective alternative


Return Flow ReductionsAssumes required additional flows to come from reduced diversionsProportional reduction in return flows (requiring additional diversion reduction)Also assumes increase in irrigation efficiency in response to reductionsAdds approximately 11% to the total water supply impact estimate


Total Water Supply Impact

Sum of the following:Additional flow to meet flow objectivesAdditional flow to meet salinity objectives(not already being provided for flow objectives)Estimated reductions in return flows


Total Water Supply Impact% Unimpaired Total Annual Volume by Water Year Type

Flow (average in thousand acre-feet)Alternative W AN BN D C

for flow objectives only60% 1,531 1,723 1,496 981 79350% 944 1,226 1,088 683 58440% 462 766 709 409 38930% 162 373 363 194 21420% 23 83 101 49 69

additional required for salinity objectives in combination60% 80 155 173 189 20850% 80 155 181 203 22340% 80 158 197 235 23730% 81 158 221 271 26520% 88 172 249 306 329


Total Water Supply Impact% Unimpaired Percent of Diversions by Water Year Type

Flow (average in percent)Alternative W AN BN D C

for flow objectives only60% 76 83 71 45 4950% 47 59 51 32 3640% 23 37 33 19 2430% 8 18 17 9 1320% 1 4 5 2 4

additional required for salinity objectives in combination60% 4 7 8 9 1350% 4 7 8 9 1440% 4 8 9 11 1530% 4 8 10 12 1620% 4 8 12 14 21


Questions?

draft technical report on the scientific basis for ... · other issues: including non-technical,...

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