S T A T

E O F C A L I F O

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N I A

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R Q U A L I T Y C O

N T R O L B O A R D ★ ★

CENTRAL

V ALLEY REGION



### Staff Report of the



### C ALIFORNIA 

### E NVIRONMENTAL 

### P ROTECTION 

### A GENCY



## R EGIONAL 

## W ATER 

## Q UALITY 

## C ONTROL 

## B OARD


## C ENTRAL 

## V ALLEY 

## R EGION



# T OTAL 

# M AXIMUM 

# D AILY 

# L OAD

FOR 

# S ELENIUM IN THE



# L OWER 

# S AN 

# J OAQUIN 

# R IVER

August 2001State of California

California Environmental Protection Agency

REGIONAL WATER QUALITY CONTROL BOARD

CENTRAL VALLEY REGION

Robert Schneider, Chair Karl E. Longley, Vice Chair Beverly Alves, Member
Susan Azevedo, Member
Alson Brizard, Member Christopher Cabaldon, Member Mark Salvaggio, Member

Gary M. Carlton, Executive Officer

3443 Routier Road, Suite A

Sacram ento, California 95827-3003

Phone: (916) 255-3000

CalNet: 8-494-3000

DISCLAIMER

This publication is a technical report by staff of the California Regional Water Quality Control Board, Central Valley Region. No policy or regulation is either expressed or intended.

### Staff Report of the



### C ALIFORNIA 

### E NVIRONMENTAL 

### P ROTECTION 

### A GENCY



## R EGIONAL 

## W ATER 

## Q UALITY 

## C ONTROL 

## B OARD


## C ENTRAL 

## V ALLEY 

## R EGION



# T OTAL 

# M AXIMUM 

# D AILY 

# L OAD

FOR 

# S ELENIUM IN THE



# L OWER 

# S AN 

# J OAQUIN 

# R IVER

August 2001

REPORT PREPARED BY:
Matthew J. McCarthy, Land and W a ter Use Analyst Leslie F. Grober, Senior Land and W a ter Use Analyst San Joaquin River TMDL Unit

## Table of Contents

Executive S u mmary

.............................................................................................................. ... iv TMDL Summary

................................................................................................................... .... v
P r o b l e m S t a t e m e n t

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...... 1

Environm ental Setting and TMDL Scope............................................................................... 1 Regulatory History

............................................................................................................. ..... 2

T a r g e t A n a l y s i s

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .......... 3 Source Analysis

................................................................................................................ ......... 6

Sources of Selenium

............................................................................................................ ... 6 Subsurface Agricultural Return Flows

............................................................................... 6 Surface Agricultural Return Flows and Wetland Discharges

............................................ 7

Groundwater Accretions

..................................................................................................... 7 Tributary Inflows

.............................................................................................................. .. 7 San Joaquin River Selenium Loads

........................................................................................ 8 Discharge

...................................................................................................................... ...... 8

S

e l e n i u m L o a d i n g

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Selenium Concentration

.................................................................................................... 12

L o a d A l l o c a t i o n s

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ....... 14

Data Sources

................................................................................................................... ...... 15 Seasonal Variations and Flow Regimes

................................................................................ 16 Violation Rate and Design Flow

........................................................................................... 17 Calculating the TMML

......................................................................................................... 18 Background Load

.............................................................................................................. 19 Margin of Safety

............................................................................................................... . 2 1

Load Allocation

................................................................................................................ . 2 1 Linkage Analysis

............................................................................................................... ...... 21 Implementation Plan

............................................................................................................ .. 25 Regional Components

....................................................................................................... 28 District Level Components

................................................................................................ 28 Farm Level Components

................................................................................................... 28

Performance Measures and Feedback

.................................................................................. 28 Public Participation

........................................................................................................... ..... 28

References

..................................................................................................................... ........... 30

i

## List of Tables

Table 1. Selenium W a te r Quality Objectives 1 (in bold) and Perform a nce Goals (in italics)

........ 6 Table 2. Annual discharge 1 (thousand acre-ft) of three locations in the lower San Joaquin River

Basin

.......................................................................................................................... ............. 9

Table 3. Annual selenium loading 1 (pounds) at three locations in the lower San Joaquin River

Basin

.......................................................................................................................... ............. 9

Table 4. Differences in selenium loading 1 (pounds) between three locations in the lower San Joaquin River Basin

............................................................................................................ .. 10

Table 5. Percent difference in selenium loading 1 between three locations in the lower San Joaquin River Basin

............................................................................................................ .. 10

Table 6. Annual selenium concentrations (μg/L) from three locations in the lower San Joaquin

R i v e r B a s i n

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ........ 12

Table 7. Unm easured selenium concentrations 1 (μg/L) from three locations in the lower San Joaquin River Basin

............................................................................................................ .. 14 Table 8. Year type, seasonal grouping, percentile rank, design flow and the num ber of violations over a 30 year period for the San Joaquin River at Crows Landing

..................................... 19

Table 9. Flow from various sources used to calculate background loads of selenium in the lower San Joaquin River Basin

....................................................................................................... 2 0

Table 10. Annual values for the calculation of lo ad allocations for four water year types

......... 21

Table 11. Calculation of load allocation for each month and year typ e

...................................... 22 Table 12. Stepwise calculation of load a llocation, including design flow, TMML, background

load and m a rgin of safety

...................................................................................................... 23

Table 13. Annual load allocations from this TMDL and 2001 Tentative W a ste Discharge Requirem e nts (W DR) (CRWQCB-CVR, 2001)

................................................................... 26

ii

## List of Figures

Figure 1. Location m a p of the lowe r San Joaquin River Basin

...................................................... 2 Figure 2. Wetland water supply schem a tic before Grassland Bypass Project

................................ 4 Figure 3. Wetland water supply schem a tic after Grassland B ypass Project

................................... 5 Figure 4. Annual selenium loading from four lo cations in the lower San Joaquin River Basin

. 11 Figure 5. Monthly selenium concentrations for the Drainage Project Area and the San Joaquin

River near Vernalis

............................................................................................................ ... 13 Figure 6. Com p arison of m onthly historical con centration, linkage analysis concentration and the water quality objective from water year 1986 through water year 1999 for the SJR at Crows Landing

.................................................................................................................. .... 24 Figure 7. Load allocations and com p liance dates for the Grassland Bypass Project (GBP) as outlined in the 2001 Draft Use Agreem ent for the San Luis Drain (USBR-SLDMW A , 2001)

and 2001 Tentative W a ste Discharge Re quirem e nts (CRW QCB-CVR, 2001)

.................... 27



## List of Appendices

Appendix A. Monthly Flow Data for Load Allocation calculations Appendix B. Monthly Flow Data for Background Load calculations Appendix C. Linkage Analysis calculation of Background Selenium Load Appendix D. Linkage Analysis calculation of Crows Landing Selenium Load and Concentration Appendix E. Linkage Analysis calculations for se lected daily periods, Calculation of Daily Load Appendix F. Linkage Analysis calculations for selected daily periods, Calculation of Crows Landing Concentration
(Appendices G through R available separately upon request)
Appendix G. 1995 Agreem ent for Use of the San Luis Drain Appendix H. 2001 Draft Agreem ent for Use of the San Luis Drain Appendix I. 1998 W a ste Discharge Require m e nts for the Grassland Bypass Project Appendix J. 2001 Tentative W a ste Discharge Re quirem e nts for the Grassland Bypass Project and 15 August 2001 Revisions Appendix K. Regional Board 1996 Basin Plan Am endm ent for the Control of Agricultural Subsurface Drainage Discharges, Com m e nt Letters Received Appendix L. Regional Board 1996 Basin Plan Am endm ent for the Control of Agricultural Subsurface Drainage Discharges, Response to Com m e nts Appendix M. Regional Board 1996 Basin Plan Am endm ent for the Control of Agricultural Subsurface Drainage Discharges, Adm i nistrative Record Appendix N. 2001 EIS/EIR for the Grassland Bypa ss Project, Public Hearing Dates and List of

C o mme n t e r s Appendix O. 2001 EIS/EIR for the Grassl and Bypass Project, Response to Com m e nts Appendix P. Selenium Total Maxim u m Daily Load W o rkshop held on 16 May 2001 Appendix Q. 2001 W a ste Discharge Requirem e nt s for the Grassland Bypass Project, Regional Board Meeting Agenda Item , 6-7 Septem ber 2001 Appendix R. 2001 W a ste Discharge Requirem e nts for the Grassland Bypass Project, Letter to Regional Board

iii

## Executive Summary

The lower San Joaquin River (SJR) is listed on the Federal Clean W a ter Act’s 303(d) list as

im paired for selenium , which is toxic to waterfowl at high levels. The im pairm e nt extends from the Salt Slough confluence to the Airport W a y Bridge near Vernalis. The 303(d) listing requires developm ent of a Total Maxim u m Daily Load (TMDL) for selenium in the lower SJR. The

m a jor source of selenium is from an area called the Drainage Project Area (DPA) that is currently under regulations to reduce selenium loading. Load allocations have been developed to specif y how m u ch selenium can be discharged while still m a intaining a healthy ecosystem

. Based on these load allocations, waste discharge requirem e nts are assigned to the DPA’s drainage system , the Grassland Bypass Project (GBP). This report outlines the developm ent of a TMDL f o r the lower SJR to reduce the selenium im pairm e nt in the river and outlines load

allocations that will be im plem ented f o r the GBP.

Selenium is a naturally occurring trace elem ent known to be hazardous to waterfowl at elevated

levels. Death and deform ities of waterfowl at Kesterson W ildlife Refuge in 1983 first focused attention on agricultural drainage and selenium . The Central Valley Regional W a ter Quality Control Board (Regional Board) has adopted the U.S. Environm ental Protection Agency aquatic

lif e criterion f o r total selenium of 5 μ g/L f our-day average as the selenium water quality objective for the lower SJR. W h ile selenium occurs naturally throughout the lower SJR Basin,

elevated concentrations of selenium occur in the shallow groundwater in the 97,000 acre DPA

contained within the Grassland W a tershed. Subsurface agricultural drainage discharges from

this area are the m a jor source of selenium

.

Load allocations for agricultural subsurface drainage discharges from the DPA were first developed in a 1994 Regional Board report. The load allocations in this TMDL are based on the

m e thods used in the 1994 report; they are designed to m eet selenium water quality objectives

downstream of the Merced River confluence. Th e m e thods group a thirty year historical flow record by water year type and season, resulting in m onthly load allocations for the DPA as displayed in the TMDL Summary section. A linkage analysis was developed as a check of the

load allocation m e thods. This linkage analysis considers historical discharges, background

selenium loads, and estim ated load allocations. The analysis conf irm e d the ability of the load

allocations f o r m eeting m onthly selenium water quality objectives.

The program to im plem ent this TMDL was adopted by the Regional Board in a 1996 Basin Plan

Am endm ent for the Control of Agricultural Subsurface Drainage Discharges. Included in this

program is a com p liance tim e schedule for m eeting the four-day average and m onthly m ean water quality objectives for selenium . Landowners within the DPA form ed a group called the

Grassland Area Farm ers and developed a plan to divert drainage from wetland supply channels and direct all of the drainage through the GBP into Mud Slough, a tributary of the lower SJR. The Regional Board assigned waste discharge requirem e nts to the GBP in 1998 that require the

Grassland Area Farm ers to reduce the discharge of selenium from pre-GBP load levels. The waste discharge requirem e nts are currently being revised using the load allocations included in

this TMDL. Reductions in selenium loading will be achieved through use of blending, drainage recycling, and selenium extraction technologies.

iv

## TMDL Summary

W a ter body: San Joaquin River

Total Size: 330 m iles

Im paired: 50 m iles from the Salt Slough confluence to the Airport W a y Bridge near

Vernalis

Pollutant: Selenium

Source: Major: Subsurface agricultural return flows (tile drainage) from the 97,000-acre Drainage Project Area of th e Grassland W a tershed (88% of total load)

Minor: Distributed inputs throughout the San Joaquin River Basin

Schedule: Level 1 (three year tim efram e )

Priority: High

Report Date: August 2001

The following load allocations for the Drainage Project Area are based upon m eeting a 5 μg/L

f our-day average water quality objective f o r the lowe r San Joaquin River. There is no waste load

allocation f o r this Total Maxim u m Daily Load.

Drainage Project Area Monthly Load Limits (pounds) Water Year Type Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

C r i t i c a l 151 9 3 9 2 1 0 1 1 0 5 6 9 7 0 7 5 5 7 5 5 5 5 1 5 2 Dry/Below N o r m a l 319 1 8 5 1 8 4 1 9 3 1 9 7 1 3 0 1 3 1 1 3 7 2 3 5 2 3 3 2 3 3 3 1 9

Above N o r m a l 398 4 7 2 4 7 2 4 9 0 4 9 7 2 1 2 2 1 4 2 2 5 2 6 4 2 6 0 2 6 0 3 9 8

W e t 211 4 8 8 4 8 8 5 0 6 5 1 2 3 5 4 3 5 6 3 6 6 3 3 2 3 2 8 3 2 8 2 1 1

v

## Problem Statement

The lower San Joaquin River (SJR) is listed in accordance with Section 303(d) of the Clean

W a ter Act for exceeding selenium water quality objectives. Areal extent of the im pairm e nt was
listed as 50 river m iles from the Salt Slough confluence to the Airport W a y Bridge near Vernalis. This water quality lim ited segm ent was listed in 1988 as part of the water quality assessm ent and 303(d) listing process.



### Environm ental Setting and TMDL Scope
The southern part of the Central Valley of Calif ornia is com p rised of two hydrologic basins: the

SJR and the Tulare Lake Basins. The SJR Ba sin (Figure 1) is drained by the SJR, which discharges to the Sacram ento-San Joaquin Delta. The Tulare Lake Basin is for the m o st part an internal drainage basin that occasionally overf lows into the SJR Basin during extrem ely high flood flow periods.

The SJR Basin is bounded by the Sierra Nevada Mountains on the east, the Coast Ranges on the west, the Delta to the north, and the Tulare Lake Basin to the south. From its source in the Sierra Nevada Mountains, the SJR flows southwesterly until it reaches Friant Dam

. Most of the water

is diverted at Friant Dam into the Friant-Kern Canal and out of the SJR Basin. Only flood flows during wet years continue to flow into the SJR Basin. Below Friant Dam

, the SJR flows westerly to the center of the SJR Basin near Mendota, where it turns northwesterly to eventually join the Sacram ento River in the Sacram ento-San Joaquin Delta. The m a in stem of the SJR is

about 300 m iles long and drains approxim a tely 13,500 square m iles. The geographic scope of

this TMDL is 50 m iles of the lower SJR from the Salt Slough confluence to the Airport W a y Bridge near Vernalis. This reach of the SJR drains an area of approxim a tely 2.9 m illion acres. Mud Slough and Salt Slough are tributaries to the SJR that drain the 370,000-acre Grassland

W a tershed. These sloughs contain a m i x of agricultural return flows, runoff from m a naged wetlands, rainfall runoff, and flood flows. Mud Slough discharges to the SJR approxim a tely two

m iles upstream of the confluence between the SJR and the Merced River. Salt Slough flows into the SJR approxim a tely 6 m iles upstream of the Mud Slough confluence. Flow in the lower SJR

is lim ited by the presence of Mendota Dam and Sack Dam

, both of which are located upstream of the Salt Slough confluence.

Soils on the west side of the SJR Basin are derived from rocks of m a rine origin in the Coast Range that are high in selenium and salts. Major land uses in the watershed include agriculture

and m a naged wetlands. Dry conditions m a ke irrigation necessary for nearly all crops grown

com m e rcially in the watershed. Irrigation of the soils derived from these m a rine sedim e nts
leaches selenium and salt into the shallow groundwater. Subsurface drainage is produced when

farm ers drain the shallow groundwater from the root zone to protect their crops. This subsurface agricultural drainage water is high in naturally occurring salts and selenium . Soils and shallow groundwater with the highest concentrations of selenium in the SJR Basin are located in a 97,000-acre area that has alternately been called the Drainage Study Area, Drainage Problem Area, and m o st recently, the Drainage Project Area (DPA).

Selenium is a highly bioaccum u lative trace elem ent, which, under certain conditions, can be

m obilized through the food chain, and cause both acute and chronic toxicity to waterfowl.

1Def o rm ities and deaths of waterf owl have been linked to toxic concentrations of selenium . The lower SJR was placed on the Section 303(d) list in 1988 because water routinely exceeded the

U.S. Environm ental Protection Agency’s (U.S. EPA) criteria for total selenium of 5 μg/L. The

effects of selenium on waterfowl are the driv ing force behind current criteria. Subsurface agricultural drainage is the prim ary source of selenium in the lower SJR Basin although selenium sources at low concentrations (less than 2 μg/L) are widespread.

Sta n i s

l a u s

R

i v

e

r

Tu o l u m n e R i v e r

Me r c

e

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R

i v

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Ve r n a l i s

S J R at L and er SJ R n e a r Pa t t e r s o n

Ores t i m

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a C r eek

S an Joaq u

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e

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r a m C r e

e

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Mu d

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Sa l t

S l oug h

M e nd o t a D a m Sa c k D a m

D r a i na ge P r o j e c t A r e a ( 3 70, 000 ac r e s )

( 9 7, 0 00 a c r e s) S J R at Cr o w s L and i n g Si e

r r a

N

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v

a

d

a

C

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s

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a nge 

## N

Figure 1. Location map of the low e r San Joaquin Riv e r Basin



### Regulatory History

Selenium in subsurface agricultural drainage wa s found to be the cause of waterfowl death and

deform ity at Kesterson Reservoir in 1985. Subsurface agricultural drainage was conveyed from

W e stlands W a ter District in the Tulare Lake Basin to Kesterson Reservoir via the partially

com p leted San Luis Drain. Discovery of the adverse im pacts of selenium in agricultural drainage water resulted in the closure of the Kesterson Reservoir and cessation of the use of the San Luis Drain to convey water from W e stlands W a ter District. W e stlands W a ter District is just

south of the DPA and the two areas share sim ilar characteristics in agricultural drainage water

2quality. Subsurface agricultural drainage water in the Grassland W a tershed has historically

drained to the SJR via a network of constructed and natural channels. These sam e channels are also used to convey fresh water supplies for m a naged wetlands.

Regional Board staff com m e nced a program of m onitoring and assessm ent of waterbodies in the

Grassland W a tershed in 1985. A 1988 Regional Board Basin Plan Am endm ent for the Control of Agricultural Subsurface Drainage Discharges identified water conservation m e asures as a

m eans of reducing selenium concentrations and loads in the SJR and wetland supply channels.

From 1985 to 1996, channels in the Grassland W a ter District were used to alternately convey agricultural drainage water and freshwater (Figure 2). An agreem ent between Grassland W a ter District and agricultural districts in the DPA a llowed use of a series of wetland supply channels to convey drainage through the north and south portions of the Grassland W a ter District. Drainage water was alternately conveyed to Mud Slough via the San Luis and Santa Fe Canals or to Salt Slough via the Blake-Porter Bypass. This flip-flop system was used to try to keep freshwater supplies separated from subsurface agricultural drainage water. The increased

dem a nd for freshwater supplies, and continued environm ental concern with this arrangem e nt, led to developm ent of the Grassland Bypass Proj ect (GBP) and the Regional Board’s 1996 Basin

Plan Am endm ent for the Control of Subsurface Agricultural Drainage (1996 Basin Plan

Am endm ent).

The GBP was im plem ented in Septem ber 1996 to divert agricultural drainage water from the

DPA out of the Grassland W a ter District water supply channels (Figure 3). This diversion allows refuge m a nagers greater control over their supply and release operations, so they can receive and apply all of their fresh water allocations according to optim um habitat m a nagem e nt schedules. Diversion of agricultural drainage water away from the Grassland W a ter District

channels reduces the selenium exposure to fish, wildlife, and hum ans in the wetland channels and Salt Slough. Other pollutants of concern in the drainage water, such as salt and boron, m a y also be reduced. Com b ining agricultural drainage flows into a single concrete-lined structure, the San Luis Drain, allows for better m onitoring, potentially leading to a m o re detailed

evaluation as well as effective control of selenium and agricultural drainage. The establishm ent of an accountable drainage entity has provided the fram ework necessary for responsible

watershed m a nagem e nt in the Grassland W a tershed.

Total Maxim u m Daily Load (TMDL) reports have been com p leted for selenium in Salt Slough and the Grassland Marshes (CRW QCB-CVR, 1999 and 2000). These TMDLs have been

im plem ented through the Regional Board’s 1996 Basin Plan Am endm ent. In accordance with

the 1996 Basin Plan Am endm ent, W a ste Discharge Requirem e nts for discharges from the GBP were issued in July 1998.



## Target Analysis

W a ter quality objectives were adopted in the Regional Board’s 1996 Basin Plan Am endm ent.
The am endm ent contained selenium water quality objectives for Mud Slough (north), Salt Slough and wetland supply channels in the Grassland W a tershed and for the m a in stem of the

SJR from Sack Dam to Vernalis. The U.S. EPA aquatic life criterion of 5 μg/L was adopted as the SJR objective. This objective, which was approved by the State W a ter Resources Control

Board and the Office

3S a nt a F e Ca n a l



### Dra i na ge P r oj e c t A r e a Ag a t h a C a n a l Ca m p 13

Ca n a l 

### • Nor t h

G r ass la n d

Wa te r D i st ri ct

Sout h

G r ass la n d

Wa te r D i st ri ct • Sa n L u i s C a n a l Sal t S l o ugh 

### Sa n J oaqu i n R i v e r

M u d Sl oug h (n o r t h )

S a n L u i s Dr ai n



### • •

CCI D M a i n C a n a l 

### • B l a k e- P o r t er By p a s s S a n L u i s Ca na l

Fr e m o n t C a n a l

Sa n t a

Fe

Ca n a l

Figure 2. Wetland w a ter supply schematic before Grassland By pass Project

4S ant a F e Ca nal



### D r ain a g e Pr o j ect A r ea A gat ha C a n a l Ca m p 1 3

Ca nal 

### • Nor t h

Gr assl an d

Wat e r
D i st r i ct

South

Gr assl an d

Wat e r
D i st r i ct • S an Lui s Ca n a l Sa l t S l ough 

### San J o a qui n R i v e r

M ud Sl ough ( nor t h )



### • •

CC I D M a i n C a n a l 

### • S an Lui s Dr ai n

B l a k e- P o r t er By pa s s Sa

n

L u i s C a n a l

Fr e m o n t C a n a l

Sa

n t a Fe

Ca n a l

G r as s l and B y pa s s

Figure 3. Wetland w a ter supply schematic after Grassland By pass Project

of Adm i nistrative Law, is a four-day average concentration of 5 μg/L (CRW QCB-CVR, 1998a). This TMDL uses the four-day average 5 μg/L objective as the num eric target. Targets adopted

5for other im paired waterbodies in the SJR Basin include 2 μg/L m onthly m ean for the Grassland wetland supply channels, 2 μg/L m onthly m ean for Salt Slough, and 5 μg/L four-day average for Mud Slough. Selenium water quality objectives and perform a nce goals are shown in Table 1.

Table 1. Selenium Water Quality Objectiv es 1 (in bold) and Performance Goals (in italics)

Water Body/Water Year Type 10 January

1997 01 October

2002 01 October

2005 01 October

2010 Salt Slough and Wetland Water Supply Channels listed in Appendix 40 of the Basin Plan 2 μg/L monthly mean

San Joaquin River below the Merced River; Above Normal and Wet Water Year types 5 μg/L

m onthly m ean 5 μg/L four-day

av erage

San Joaquin River below the Merced River; Critical, Dry and

Below Normal Water Year types 8 μg/L

m onthly m ean 5 μg/L

m onthly m ean 5 μg/L four-day

av erage

Mud Slough (north) and the San Joaquin River from Sack

Dam to the Merced River 5 μg/L four-day

av erage

1 Copy of table found in the W a ter Quality Control Plan for the Sacram ento and San Joaquin Rivers (CRW QCB-CVR, 1998a)



## Source Analysis

Subsurface agricultural return flows from the DPA in the Grassland W a tershed are the prim ary source of selenium in the lower SJR Basin. There are no m unicipal or industrial sources.

Selenium is a naturally occurring elem ent found in sedim e nts of the Coast Ranges on the west

side of the lower SJR Basin. Selenium can th erefore be found in surface runoff and groundwater throughout the west side of the lower SJR Basin. Although selenium exists naturally in the soils of this watershed, som e land use practices m a y accelerate its m ovem e nt to ground water and

surface water.



### Sources of Selenium

Selenium is added to the lower SJR from a wide range of sources including subsurface agricultural return flows, surface agricultural return flows, wetland discharges, groundwater accretions, and tributary inflows.

Subsurface Agricultural Return Flows Subsurface agricultural return flows, also known as tile drainage, occur as the result of efforts to control groundwater levels to m a intain agricultural productivity. Tile drains are installed in areas of high groundwater to lower the water table be low the root zone. The lower SJR Basin has

m a ny areas with high groundwater levels due to poor ly drained soils and application of irrigation water. Tile drainage m a y have high selenium concentrations, especially in the Grassland

W a tershed. Drainage f r om tile drains in the DPA is the prim ary source of selenium in the

Grassland W a tershed and the SJR. A survey of tile drainage in the lower SJR Basin (Chilcott et al., 1988) found the highest concentrations of sele nium in the Grassland W a tershed. Eighty-two

6percent of the sam p les collected at 173 tile drainage sites in the Grassland W a tershed had

selenium concentrations ranging from 11 to 500 μg/L. Six percent of the sam p les had selenium concentrations above 500 μg/L and twelve percent had selenium concentrations below 11 μg/L. Tile drainage from areas outside of the Grassland W a tershed has selenium concentrations significantly lower than the Grassland W a tershed and the DPA. A survey of agricultural drainage found that the range of selenium concentra tions in tile drainage that discharges directly

to the SJR from areas north of the DPA was 0.2 to 9.3 μg/L, with a m e dian of 2.2 μg/L (W estcot et al., 1989).

Surface Agricultural Return Flows and Wetland Discharges Surface agricultural return flows and wetland discharges from the west side of the SJR have the

sam e selenium concentration as the source water. The selenium concentration depends on whether the source is groundwater, SJR diversions, or the Delta-Mendota Canal. A survey of agricultural discharges to the SJR (W estcot et al., 1989) found the m ean selenium concentration of surface return flows, with source water from a m i x of SJR and Delta-Mendota Canal water, to be 2.2 μg/L, with a range from 1.8 to 2.7 μg/L.

Subsurface agricultural return flows were alternately discharged to Mud Slough and Salt Slough before use of the GBP. Monthly selenium concentrations averaged 14 μg/L for Salt Slough and 7 μg/L for Mud Slough (Grober et al., 1998) from 1986 to 1995. W ith use of the GBP, Salt Slough no longer received subsurface agricultural re turn flows, only surface agricultural return flows and wetland discharges. Mud Slough received no surface agricultural return flows

upstream of the San Luis Drain confluence; flows are now com p rised m o stly of wetland discharges. Annual selenium concentration was 1 μg/L for Salt Slough during water year 1997 (Chilcott et al., 1998). Annual selenium concentration was 1 μg/L for Salt Slough and 1 μg/L for Mud Slough upstream of the San Luis Drain during water year 1998 (Chilcott et al., 2000).

Groundwater Accretions The lower SJR, downstream of the Grassland W a ters hed, is generally a gaining stream . The U.S. Geological Survey (USGS) investigated the qua lity and quantity of groundwater inflow to the

SJR from Newm an to Patterson (Phillips et al., 1991). Average groundwater inflow was 2.0

cfs/m ile, with a range of 1.1 to 3.2 cfs/m ile. This flow translates to about 1,500 acre-ft/m ile annually and 75,000 acre-ft for the im paired 50 m ile stretch of the SJR. The concentration of

selenium in the groundwater was estim ated to be 0.9 μg/L. Assum i ng a m ean groundwater

inflow of 2.0 cfs/m ile at a selenium con centration of 0.9 μg/L, groundwater contributes approxim a tely 200 pounds of selenium per year along the im paired 50-m ile stretch of the SJR.

Tributary Inflows A survey of the water quality of ephem e ral west side SJR tributaries between 1984 and 1988 (W estcot et al., 1991) found m e dian selenium concentrations generally less than or equal to 1.0 μg/L for Del Puerto, Orestim ba and Hospital Creeks. Ingram Creek had a m e dian selenium concentration of 4.3 μg/L. The m a xim u m annual load contributed to the SJR by these and 36 other ephem e ral stream s was estim ated to be approxim a tely 600 pounds per year. Little data is

available on selenium concentrations for the Merced, Tuolum ne and Stanislaus Rivers. Most of

the sam p les collected from these rivers between 1985 and 1988 (USGS, 1988 and USGS, 1991)

had selenium concentrations below the detection lim it of 1.0 μg/L but som e sam p les from each

7tributary had concentrations at the detection lim it. Selenium concentrations for the SJR at Lander Avenue (upstream of discharges from the DPA) have ranged from 0.1 to 1.3 μg/L in water years 1993 through 1995 (Chilcott et al., 1995 and Steensen et al., 1996). The east side

tributaries and the SJR at Lander Avenue contribut e selenium to the lower SJR at concentrations well below the water quality objective of 5 μg/L. The load they contribute m a y be highest during periods of high discharge when extrem ely low concentrations m a y still account for significant loads. For exam ple, a discharge of 100,000 acre-ft per m onth at a selenium concentration of 0.2 μg/L would account for a m onthly selenium load of 54 pounds. During wet years, flow from east side tributaries can be in excess of 200,000 acre-ft per m onth. Such a flow

m a y account for 108 pounds of selenium per m onth.



### San Joaquin River Selenium Loads
The Regional Board has conducted water quality sam p ling at num erous sites in the Grassland

W a tershed and the lower SJR since 1985. Results from the first ten water years of this sam p ling

program , 1985 through 1995, are sum m a rized in two Re gional Board staff reports (Steensen et al, 1998 and Grober et al, 1998). Results for water years 1996 through 1998 are sum m a rized in Chilcott et al, 1998 and Chilcott et al, 2000. These reports include m onthly and annual flow and

selenium load inform ation for discharges from the DPA, the Grassland W a tershed, the SJR near Patterson, and the SJR near Vernalis. The reports dem onstrate that the DPA accounts for, on average, 88% of the selenium load in the lower SJR.

Discharge

W a ter discharges from the DPA account for a sm all percentage of the total flow volum e in the lower SJR (Table 2). The m ean annual discharge from the DPA from 1986 through 1998 was 48 thousand acre-feet (taf) per year. The m ean annual discharge from the Grassland W a tershed and in the SJR near Vernalis was 223 and 3,075 taf, respectively. Discharge from the DPA, on average, accounts for only two percent of the total flow volum e in the SJR near Vernalis. The range of discharge is m o st pronounced in the SJR near Vernalis, with a low of 657 taf in 1991 to a high of 8,489 taf in 1998. Grassland W a tershed discharges ranged from a low of 85 taf in 1992 to a high of 378 taf in 1998. DPA discharges varied from a low of 25 taf in 1992 to a high of 75 taf in 1987. Discharge in the SJR and the Grassland W a tershed is m u ch m o re highly variable than discharge from the DPA.

Selenium Loading

The m ean annual selenium load from the DPA from 1986 through 1998 was 8,660 pounds. The

m ean annual selenium load in the SJR near Vernalis during this sam e period was 9,788 pounds (Table 3). The m ean annual difference of 1,128 pounds (Table 4) is attributable to distributed

sources of selenium throughout the lower SJR Ba sin. Distributed sources are prim arily from background sources and include all non-DPA sources of selenium . On average, the DPA has accounted for 88 percent of the m ean annual selenium load in the SJR near Vernalis (Table 5). There is significant annual variability in the differences in loads between the DPA and the SJR near Vernalis, ranging from a loss of approxim a tely 1,670 pounds in 1988 to a gain of 5,077 pounds in 1986. In other words, DPA loads have accounted for 120 percent (W ater Year 1988) to 65 percent (W ater Year 1986) of the loads in the SJR near Vernalis. A portion of the positive (gain) and negative (loss) differences in loads can be attributed to m easurem ent and calculation error although no consistent source of error has been identified (Grober et al, 1998). Losses are

8also attributable to water diversions from the SJ R. Gains are attributable to distributed sources

of selenium throughout the basin. Variability in selenium loads is also shown in Figure 4. This

data shows lower loads from all sources during dry years and higher loads during wet years.

Table 2. Annual discharge 1 (thousand acre-ft) of three

locations in the low e r San Joaquin Riv e r Basin

Water

Year Drainage Project

Area Grassland

Watershed SJR near

Vernalis

1 9 8 6 6 7 2 8 4 5

, 2 2 6

1987 75 234 1,813

1 9 8 8 6 5 2 3 0 1

, 1 6 8

1989 54 211 1,059

1 9 9 0 4 2 1 9 5 9 1 6

1991 29 102 657

1 9 9 2 2 5 8 5 7 0 0

1993 41 168 1,702

1 9 9 4 3 9 1 8 4 1

, 2 1 9

1995 58 264 6,299

1 9 9 6 5 0 2 7 0 3

, 9 5 0

1997 40 290 6,770

1 9 9 8 4 6 3 7 8 8

, 4 8 9

a v e r a g e 4 8 2 2 3 3

, 0 7 5

1 Data from Steensen et al., 1998

Table 3. Annual selenium loading 1 (pounds) at three

locations in the low e r San Joaquin Riv e r Basin

Water

Year Drainage Project

Area Grassland

Watershed SJR near

Vernalis

1 9 8 6 9

, 5 2 4 6

, 6 4 3 1 4

, 6 0 1

1987 10,959 7,641 8,502

1 9 8 8 1 0

, 0 9 7 8

, 1 3 2 8

, 4 2 7

1989 8,718 8,099 8,741

1 9 9 0 7

, 3 9 3 7

, 7 1 9 7

, 4 7 2

1991 5,858 3,899 3,611

1 9 9 2 5

, 0 8 3 2

, 9 1 9 3

, 5 5 8

1993 8,856 6,871 8,905

1 9 9 4 8

, 4 6 8 7

, 9 8 0 7

, 7 6 0

1995 11,875 10,694 17,238

1 9 9 6 1 0

, 0 3 4 9

, 4 9 1 1 1

, 4 3 1

1997 6,959 7,722 11,190

1 9 9 8 8

, 7 6 0 9

, 6 3 0 1 5

, 8 1 0

a v e r a g e 8

, 6 6 0 7

, 4 9 5 9

, 7 8 8

1 Data from Steensen et al., 1998

9Table 4. Differences in selenium loading 1 (pounds) betw een three locations in the low e r San Joaquin Riv e r Basin

This s i te: Grassland

Watershed SJR near Vernalis

Minus this

s i te: Drainage Project Area Drainage Project Area Grassland

Watershed

1 9 8 6

- 2

, 8 8 1 5

, 0 7 7 7

, 9 5 8

1987 -3,318 -2,457 861

1 9 8 8

- 1

, 9 6 5

- 1

, 6 7 0 2 9 5

1989 -619 23 642

1 9 9 0 3 2 6 7 9

- 2 4 7

1991 -1,959 -2,247 -288

1 9 9 2

- 2

, 1 6 4

- 1

, 5 2 5 6 3 9

1993 -1,985 49 2,034

1 9 9 4

- 4 8 8

- 7 0 8

- 2 2 0

1995 -1,181 5,363 6,544

1 9 9 6

- 5 4 3 1

, 3 9 7 1

, 9 4 0

1997 763 4,231 3,468

1 9 9 8 8 7 0 7

, 0 5 0 6

, 1 8 0Water Year

a v e r a g e

- 1

, 1 6 5 1

, 1 2 8 2

, 2 9 3

1 Data from Steensen et al., 1998

Table 5. Percent difference in selenium loading 1 betw een three locations in the low e r San Joaquin Riv e r Basin

Difference

between: Grassland

Watershed SJR near Vernalis

and: Drainage Project Area Drainage Project Area Grassland

Watershed

1 9 8 6 1 4 3 % 6 5 % 4 5 %

1987 143% 129% 90%

1 9 8 8 1 2 4 % 1 2 0 % 9 6 %

1989 108% 100% 93%

1 9 9 0 9 6 % 9 9 % 1 0 3 %

1991 150% 162% 108%

1 9 9 2 1 7 4 % 1 4 3 % 8 2 %

1993 129% 99% 77%

1 9 9 4 1 0 6 % 1 0 9 % 1 0 3 %

1995 111% 69% 62%

1 9 9 6 1 0 6 % 8 8 % 8 3 %

1997 90% 62% 69%

1 9 9 8 9 1 % 5 5 % 6 1 %Water Year

a v e r a g e 1 1 6 % 8 8 % 7 7 %

1 Data from Steensen et al., 1998

10            

                          

                              0200040006000800010000120001400016000180001986198719881989199019911992199319941995199619971998Water Year

Selenium Load (pounds)Drainage Project Area/GrasslandBypass Project

   Grassland Watershed

SJRnearPatterson/Crows Landing

SJRnear Vernalis

11Figure 4. Annual selenium loading from four locations in the lower San Joaquin River BasinSelenium Concentration Discharges from the DPA are the m o st concentrated source of selenium in the lower SJR. The

m ean annual selenium concentration for discharge from the DPA from 1986 through 1998 was 68 μg/L (Table 6). The m ean annual selenium concentration for the SJR near Patterson and SJR near Vernalis was 3.8 and 1.8 μg/L respectively. The tim e series of m ean m onthly selenium concentrations for the DPA and the SJR near Vernalis is shown in Figure 5. As already indicated, the high selenium concentration disc harges from the DPA account for m o st of the

selenium load in the lower SJR. Discharge and selenium load inform ation already presented can

be used to estim ate the selenium concentration for unm easured, distributed sources of selenium

in the lower SJR Basin.

Table 6. Annual selenium concentrations (μg/L) from three locations in the low e r San Joaquin Riv e r Basin

Water

Year Drainage Project

Area SJR near

Patters on 1 SJR near

Vernalis

1 9 8 6 5 2 1

. 5 1

. 0

1987 54 4.9 1.8

1 9 8 8 5 7 6

. 2 2

. 7

1989 59 6.3 3.0

1 9 9 0 6 5 5

. 6 3

. 0

1991 74 5.4 2.0

1 9 9 2 7 6 4

. 4 1

. 9

1993 79 3.7 1.9

1 9 9 4 8 1 5

. 4 2

. 3

1995 76 1.5 1.0

1 9 9 6 7 0 2

. 7 1

. 1

1997 68 0.8 0.6

1 9 9 8 7 0 1

. 1 0

. 7

a v e r a g e 6 8 3

. 8 1

. 8

1 Data for w a ter y ears 1996 to 1998 is based

on SJR at Crow s Landing

The concentration of the unm easured selenium sources can be estim ated by calculating a

concentration from the unm easured selenium loads and flows (Table 7). Calculated concentrations for SJR near Patterson and SJR near Vernalis are all less than 1.4 μg/L and m o st are less than 0.5 μg/L. The average concentration of these sources of selenium for water years 1986 through 1998 was approxim a tely 0.3 μg/L. This data shows that the DPA is the prim ary source of selenium in the Grassland W a tershed and in the lower SJR Basin.

1202040608010012014019851986198719881989199019911992199319941995199619971998Water Year

Monthly Selenium Concentration (μg/L)DrainageProject Area/Grassland BypassProjectSJRnear Vernalis

13Figure 5. Monthlyselenium concentrations for the Drainage Project Area and the San Joaquin River near VernalisTable 7. Unmeasured selenium

concentrations 1 (μg/L) from three locations

in the low e r San Joaquin Riv e r Basin

Water

Year SJR near

Patters on 2 SJR near

Vernalis

1 9 8 6 0

. 7 2 0

. 4 8

1987 1.04 -0.11

1 9 8 8 1

. 3 8

- 0

. 5 4

1989 -1.01 0.75

1 9 9 0

- 2

. 8 0 0

. 9 7

1991 -0.68 0.06

1 9 9 2 0

. 2 4 0

. 4 6

1993 0.77 0.24

1 9 9 4

- 0

. 6 9 0

. 2 7

1995 0.41 0.39

1 9 9 6 0

. 3 7 0

. 1 1

1997 0.09 0.36

1 9 9 8 0

. 3 5 0

. 2 1

a v e r a g e 0

. 3 2 0

. 2 8

1 Data from Steensen et al., 1998

2 Data for w a ter y ears 1996 to 1998 is based

on SJR at Crow s Landing



## Load Allocations

Load allocations for discharges from the DP A were first developed in a 1994 Regional Board staff report, Total Maximum Monthly Load Model for the San Joaquin River (Karkoski, 1994). This report presented a description of a Total Maxim u m Monthly Load (TMML) m odel and the

m e thods used in the m odel to calculate selenium load allocations. This TMML m odel is a sim p le spreadsheet m odel that calculates m onthly selenium load allocations for the SJR based on critical flow conditions for the SJR at Crows Landing and an acceptable violation rate of the water quality objective. Load allocations in this TMDL are established f o r m eeting the selenium water quality objective in the SJR downstream of the Merced River conf luence. There would be effectively no allocation of selenium load in th e absence of Merced River dilution flows. The source analysis has shown that subsurface agricultural return flows form the DPA are the prim ary source of selenium load in the lower SJR Basin. The source analysis has shown that the

selenium concentration of all other SJR inf l ows is m u ch lower than the water quality objective.

The selenium water quality objective f o r the entire SJR downstream of the Merced River will

theref ore be attained when the water quality objective is attained at a point just downstream of

the Merced River confluence.

The schedule f o r com p liance with selenium water quality objectives in the SJR (Table 1) shows that the 5 μg/L objective m u st be m e t for the SJR from Sack Dam to the Merced River confluence starting in October 2010. Prior to this date, selenium loads from the DPA m a y continue to be discharged to the SJR upstream of the Merced River confluence. Attainm e nt of

the selenium water quality objective upstream of the Merced River conf luence m a y require significant changes to the DPA discharge, including the relocation of the discharge point.

14Through Septem ber 2010, the SJR at Crows Landing is the water quality com p liance point of the

selenium water quality objective in the SJR and is also used to calculate the TMDL. This site is

used as the com p liance point because the dom inant source of selenium in the lower SJR Basin is discharged to the river upstream of the Merced River confluence. The SJR at Crows Landing is the first easily m onitored site downstream of the Merced River confluence. The source analysis

has identified no additional concentrated sources of selenium downstream of the SJR at Crows Landing. The m odel uses historical flow record s, grouped by season and water year type, to

calculate critical f l ow or design f l ow conditions. Design f l ows are m u ltiplied by the water quality objective to calculate the TMML or assim ilative capacity. A m onthly load lim it is established, rather than a daily lim it, since m o st agricultural water districts lack the f acilities

needed to m a nage drainage on a daily basis.

Application of design flows to calculate load allocations requires use of a hydrology that is

sim ilar to the present and future hydrology. Com p letion of New Exchequer Dam on the Merced River caused a significant change in hydrology because of the increase of reservoir capacity from 281,000 to 1,024,000 acre-feet. Since this dam had an im pact on both the Merced River and SJR, only the hydrology subsequent to dam filling and com p letion in 1969 is used in the calculation of design flows.



### Data Sources
The SJR at Crows Landing is the com p liance point f o r selenium water quality objectives in the lower SJR but flow data for this site is only available for water years 1969 through 1972 and 1996 through 1999. Flow data for water years 1972 through 1995 m u st be reconstructed based

on SJR near Patterson flow data that is ava ilable from 1969 through 1999. Reconstruction of the flow record at Crows Landing was done using Patterson flow data and the m a ss balance m odel

SJRIO-2. SJRIO-2 can be used to do a m a ss balance accounting of m onthly flow and water quality (Kratzer, 1987) for water years 1977 through 1996. W h en run in calibration m ode, the

m odel provides a m onthly flow record for any site in the lower SJR from upstream of Salt Slough to Vernalis.

Crows Landing flow data for water years 1977 through 1995 was calculated using:

Model Pat, Hist Pat, Model Crows,
Calc Crows, Q Q Q Q ⋅

= (1)

where

Q Crows, Calc = calculated stream flow at Crows Landing Q Crows, Model = SJRIO2 m odel calculated stream flow at Crows Landing Q Pa t, Hist = historical m easured stream flow at Patterson Q Pat, Model = SJRIO2 m odel calculated stream flow at Patterson

SJR at Crows Landing flow data for 1970 through 1991 was presented in the Regional Board staff report describing the original selenium TMML (Karkoski, 1994). Flow for 1992 through

151999 was presented in the U.S. Bureau of Reclam ation (USBR) update to the m odel (USBR, 2000). This com b ined dataset, using a com b ination of historical (1970 through 1976 and 1996 through 1999) and calculated (1977 through 1995) hydrology, was used to calculate the design flows in this TMML. The flow data is presented in Appendix A.



### Seasonal Variations and Flow Regim es
The m odel develops flow regim e s by categorizi ng flow data based on water year type and

season. W a ter year type is based on the SJR Index of unim p aired flows (CDW R, 2000). This water year classification schem e identifies water years as Critical (C), Dry (D), Below Norm al (BN), Above Norm al (AN), or W e t (W ). The SJ R Index is com posed of the unim p aired runoff

from the four m a jor rivers in the Basin:

Stanislaus River inflow into Melones Reservoir

Tuolum ne River inflow into Don Pedro Reservoir Merced River inflow into Exchequer Reservoir San Joaquin River inf l ow into Millerton Reservoir

The index is determ ined as f o llows:

60% current year April to July runoff 20% current year October to March runoff 20% of the previous year index, not exceeding 0.9 m illion acre-ft

ndex) I SJR year (previous 0.2 runoff) Mar to (Oct 0.2 runoff) Jul to (Apr 0.6 Index SJR + + = (2)

The water year classifications are based on threshold values of the SJR Index:

Year Type Threshold (m illion acre-f eet)

Critical C < 2.1
Dry 2.1 ≤ D < 2.5

Below Norm al 2.5 ≤ BN < 3.1

Above Norm al 3.1 ≤ AN < 3.8

W e t 3.8 ≤ W

The three water year groupings used in the original selenium TMML m odel are C, D/BN and

AN/W

. The seasonal grouping divides the year into four seasons, with m onths grouped by tim e of year. The four seasonal groupings are Septem ber through Novem b er, Decem ber and January, February through May, and June through August. The seasonal grouping represents the distinct seasonality of f

l ow in the SJR and DPA drainage f l ows. High drainage f l ows occur f r om February through August and high river flows occur from Decem ber through May. The seasonal groupings divide the water years into seasons that cover the com b inations of high and low river flows and high and low drainage flows. This seasonal grouping allows the discharger to m a ke the necessary adjustm e nts to m eet the load allocation for the particular season. The three water year groupings and four seasonal groupings are com b ined into 12 flow regim e s. The current update to the m odel increased the num ber of water year groupings from three to four, resulting in

1616 flow regim e s instead of 12. The new groupings are C, D/BN, AN, and W

. The increased

num ber of groupings m a xim i zes flexibility to dischargers in the DPA by accounting for

increased tem poral variations of flow.



### Violation Rate and Design Flow
After assigning the flow data into appropriate fl ow regim e s, an acceptable violation rate of the objective was needed. The U.S. EPA criterion continuous concentration (chronic toxicity) is the four-day average concentration of a pollutant in water that should not be exceeded m o re than once every three years on average. The com p liance point for this TMDL is the SJR at Crows Landing, which has an incom p lete historical flow record. For the years 1969-1972 and 1996- 1999, flow data is available at Crows Landing, and a four-day average flow can be calculated. Daily flow at Crows Landing is not availabl e for the years 1973-1995. The m odel SJRIO-2 was

used to calculate m onthly flow data for Crows Landing for these years (see Data Sources ), but daily data is not available. In order to obtain a four-day average for this site, a site with sim ilar flow patterns and a daily flow record m u st be used. A coefficient m u st be developed for the

sim ilar flow site to convert m onthly data to four-day average data. The SJR at Patterson was used to develop these coefficients since it is selected as the closest site with daily data (Karkoski, 1994).

The equation for calculating the four-day average flow on “n”th day of the m onth is:

4 (3) 3

0 ∑

= = −
i i n Q

Flow Average Day

- Four

The lowest four-day average flow for the m onth was selected. In situations when data from the Patterson site was required, a coefficient from the ratio of the four-day average low flow to the

m ean m onthly flow for the site was found:

Monthly mean Pat, low day,

- Four Pat,

Pat Q Q C = (4)

where

C Pa t = m onthly to daily coefficient at Patterson Q P a t, F our- day, low = four-day average low stream flow at Patterson Q P a t, mean Monthly = m ean m onthly stream flow at Patterson

This coef f i cient was m u ltiplied by Q Crows, Calc (from equation 1) to determ ine the m onthly equivalent of the four-day average low flow at Crows Landing:



## ( ) Calc Crows, Pat low day,

- Four Crows, Q C Q = (5)

where

17C Pa t = m onthly to daily coefficient at Patterson Q Crows, F our- day, low = four-day average low stream flow at Crows Landing Q Crows,Calc = m onthly calculated stream flow at Crows Landing

The allowable num ber of violations is calculated based upon an average exceedance rate of once every three years. This calculation involves m u ltiplying the period of record by the allowable frequency of violations.

Violations of Frequency Allowable Record of Period Violations of Number Allowable × = (6)

There are 10 allowable violations for a one in three year violation frequency over the 30-year

flow record under consideration. These violations m a y be distributed between the various flow regim e s. Future rates of violation in this TMDL are based on the observed historical hydrology. This historical hydrology includes water years 1977, and 1987 through 1992, which are som e of the driest water years on record in the SJR Basin (CDW R, 2000) The low flow condition, or design flows are calculated for each flow regi m e by rank ordering the historical flows.

For each flow regim e , the flows are rank-ordered fr om the lowest to highest observed flow. A user-defined percentile is then assigned to each rank-ordered flow regim e . Selection of the 0 th
percentile m eans the lowest observed f l ow is selected as a design f l ow. Selection of the 100 th
percentile m eans the highest f l ow is selected. The Microsof t Excel TM percentile f unction is used to select a consistent position for the user-defined percentile within each flow distribution. This function interpolates, as necessary, between actual observed flows. The design flow for m o st of

the f l ow regim e s is based on the 0th percentile or the lowest observed f l ow. If the lowest f l ow for any flow regim e is lower than the C year desi gn flow, the C year design flow is used for that flow regim e

.

For the 1994 selenium TMML for the lower SJR, all violations were grouped in the C water year groupings with the assum p tion that dischargers w ould have the m o st difficulty in m eeting water quality objectives during C water years. Experience of the drainers in the DPA with operating

the GBP has identif ied dif f i culty also in m eeting load lim its during wet periods. As a result,

som e violations have now been assigned to AN and W water years as well as C water years by selecting a user-def ined percentile f o r these f l ow regim e s (Table 8). A 0 th percentile (lowest observed flow) is used for all other flow regim e s.



### Calculating the TMML

Calculation of a TMML follows the sam e steps required for a TMDL. The TMML is the full

assim ilative capacity of the water body. The assim ilative capacity is calculated by m u ltiplying the design flow (Q
DF ) by the water quality objective (W QO) and applying a conversion factor.

factor) n (conversio 0.0027 (μg/L) WQO ft)

- (acre Q (pounds) TMML DF × × = (7)

18Table 8. Year ty pe, seasonal grouping, percentile rank, design flow

and the number of v i olations ov er a 30 y ear period for the San Joaquin Riv e r at Crow s Landing
Year Type Grouping Percentile Rank De sign Flow Number of Violations

ac re-ft

C S e p

- N o v 0

. 0 7 5

, 0 1 6 2

D / B N S e p

- N o v 0 2 0

, 2 9 8 0

A N S e p

- N o v 0 2 2

, 6 6 7 0

W S e p

- N o v 0 2 7

, 8 5 0 0

C Dec-Jan 0.08 13,187 2

D/BN Dec-Jan 0 27,263 0

AN Dec-Jan 0 35,297 0

W Dec-Jan 0 19,260 0

C F e b

- M a y 0

. 0 3 9

, 3 0 8 2

D / B N F e b

- M a y 0 1 7

, 1 3 2 0

A N F e b

- M a y 0

. 0 5 4 3

, 1 5 5 1

W F e b

- M a y 0

. 0 2 4 5

, 6 2 3 1

C Jun-Aug 0.07 6,188 2

D/BN Jun-Aug 0 11,402 0

AN Jun-Aug 0 18,877 0

W Jun-Aug 0 30,191 0

The total assim ilative capacity, or TMML, m u st be distributed between a waste load allocation (W LA) for point sources, a load allocation (LA) for non-point sources, a m a rgin of safety (MOS), and a background load (BL).

MOS BL LA WLA TMML + + + = (8)

Point sources include any concentrated discharge that can be controlled at a point, such as a

m

unicipal wastewater treatm e nt plant. There ar e no point sources of selenium in the lower SJR Basin, so there is no waste load allocation. Th e DPA is the only non-point source in this TMML.

W ith no waste load allocation com ponent, the load allocation for the DPA can be calculated using:

MOS

- BL

- TMML LA = (9)

Background Load

Distributed selenium loads from low selenium concentration sources in the lower SJR are assigned to the background load of the TMML. Background load values m u st be calculated for

the three m a in sources of flow and selenium upstream of Crows Landing and exclusive of the DPA: the Merced River, the SJR at Lander Avenue, and the Grassland wetlands. Table 9

contains data used to calculate flow values from each source based on design flows. Design flows are calculated for year type (colum n a) and grouping (colum n b) which are com b ined to provide sixteen flow regim e s. For each flow regim e , a design flow for the SJR at Crows Landing (colum n c) has already been determ in ed based on historical Crows Landing flows (Appendix A). The historical Crows Landing flow (c olum n d) that is closest to the design flow (colum n c) is determ ined. The m onth and year of the historical Crows Landing flow (colum n e)

is used to select m onthly flows for the Merced River (colum n f) and the SJR at Lander (colum n

19g). The historical Merced River and SJR at La nder Avenue flows are given in Appendix B. The four-day average low flow equivalent to m onthl y average coefficient (colum n h) is used to

convert m onthly flows for both the Merced River and the SJR at Lander Avenue to the four-day average equivalent. This is the sam e coefficient used to convert from a m onthly average to a four-day average low flow for the SJR at Crows Landing, as explained in the Violation Rate and Design Flow section above. The m onthly average flows are m u ltiplied by the four-day average low flow equivalent to m onthly average coeffici ent to obtain the four-day low flow average for the Merced River (colum n i) and the SJR at Lander Avenue (colum n j).

Table 9. Flow from v a rious sources used to calculate background loads of selenium in the low e r San Joaquin Riv e r Basin

SJ R @

Crows SJ R @

Crows M e r c e d SJ R @

Lander Four-day

average Merced SJ R @

Lander

D e s i g n H i s t o r i c a l H i s t o r i c a l Hist o r i c a l l o w f l o w F o u r

- d a y F o u r

- d a y
F o u r

- d a y F o u r

- d a y S i m i l a r M o n t h l y M o n t h l y e q u i v a l e n t a v e r a g e a v e r a g e
Y e a r S e a s o n a l a v e r a g e a v e r a g e F l o w flow 3 f l o w 3 to Monthly low flow low flow

T y p e G r o u p i n g low flow 1 l o w flow 2 M o n t h f l o w equivalent 5 e q u i v a l e n t 5

ac

- f t ac

- f t ac

- f t ac

- f t c oeffic i ent 4 a c

- f t ac

- f t

a b c d e f g h i j

C S e p

- N o v 5

, 0 1 6 5

, 3 4 5 N o v

- 7 7 7

, 2 2 0 2 6 9 0

. 4 5 3

, 2 4 2 1 2 1

D / B N S e p

- N o v 2 0

, 2 9 8 2 0

, 2 9 8 S e p

- 7 2 5 4

, 8 6 0 4

, 5 8 0 0

. 2 9 1 6

, 0 8 5 1

, 3 4 3

A N S e p

- N o v 2 2

, 6 6 7 2 2

, 6 6 7 Oct- 7 0 1 3

, 4 3 0 2

, 1 8 8 0

. 8 0 1 0

, 7 1 9 1

, 7 4 6

W S e p

- N o v 2 7

, 8 5 0 2 7

, 8 5 0 S e p

- 9 7 5

, 4 7 0 3 8 9 0

. 9 3 5

, 1 0 9 3 6 4

C Dec-Jan 13,187 11,817 Dec-77 11,250 615 0.77 8,630 472

D/BN Dec-Jan 27,263 27,263 Dec-71 17,140 2,029 0.84 14,374 1,702

AN Dec-Jan 35,297 35,395 Jan-73 22,420 38,660 0.38 8,531 14,710

W Dec-Jan 19,260 19,260 Jan-78 21,410 41,330 0.23 4,981 9,616

C F e b

- M a y 9

, 3 0 8 9

, 2 7 2 M a y

- 7 7 4

, 0 0 0 5 1 9 0

. 5 7 2

, 2 9 1 2 9 7

D / B N F e b

- M a y 1 7

, 1 3 2 1 7

, 1 3 2 A p r

- 7 2 1 2

, 2 5 0 1

, 4 0 1 0

. 6 2 7

, 6 4 0 8 7 4

A N F e b

- M a y 4 3

, 1 5 5 4 3

, 9 3 1 A p r

- 7 0 1 6

, 7 3 0 6

, 2 4 8 0

. 9 2 1 5

, 3 7 6 5

, 7 4 2

W F e b

- M a y 4 5

, 6 2 3 4 6

, 1 0 1 F e b

- 9 3 2 1

, 1 6 6 3 9

, 3 3 0 0

. 4 8 1 0

, 0 6 5 1 8

, 7 0 2

C Jun-Aug 6,188 6,314 Aug-77 548 330 0.81 446 269

D/BN Jun-Aug 11,402 11,402 Jul-72 6,220 412 0.71 4,433 294

AN Jun-Aug 18,877 18,877 Jul-70 8,960 1,615 0.82 7,354 1,326

W Jun-Aug 30,191 30,191 Aug-97 3,925 1,139 0.80 3,149 914

1 Data from Table 8

2 Data from Appendix A

3 Data from Appendix B

4 Coefficient calculated using Equation 4

5 Results from multiply ing historical flow (column f,g) by a coe fficient (column h)

Concentration data for these background sources ar e based on fixed values. The concentration of

the Merced River is 0.2 μ g/L (W estcot et al., 1990) and the SJR at Lander is 0.5 μ g/L (Chilcott et al., 2000). W e tland flow data was obtained from a USBR analysis of wetland discharges in an

assessm ent of water quality im pacts of the GBP (Swain and Quinn, 1991). W e tland water quality is 1.0 μ g/L, based on im provem e nts in wetland supply water quality in the Grassland

W a tershed. W ith the operation of the GBP, Salt Slough and Mud Slough upstream of the San Luis Drain confluence no longer convey subsurface agricultural return flows; they convey only surface agricultural return flows and wetland discharges. Annual selenium concentration was 1

20μg/L for Salt Slough during water year 1997 (Chilcott et al., 1998). Annual selenium concentration was 1 μg/L for Salt Slough and 1 μg/L for Mud Slough upstream of the San Luis Drain during water year 1998 (Chilcott et al., 2000).

Margin of Safety

No consistent errors have been identif ied in the f l ow and selenium water quality inf o rm ation used to generate this TMML. An explicit ten percent MOS is applied to account for errors in

flow m easurem ents and selenium concentrations and uncertainty in the TMML analyses. The

sam e ten percent MOS was used in the 1994 TMML (Karkoski, 1994). The ten percent MOS is applied to the calculated assim ilative capacity or TMML:

TMML 0.10 MOS × = (10)

Load Allocation After accounting for the m a rgin of safety and background loads, the rem a ining load is assigned to the load allocation for the DPA. The TMML and background load vary according to season and water year type. Since the TMML and background load determ ine the load allocation, the load allocation varies according to season and water year type. Load allocations are higher during wet seasons and years due to higher assim ilative capacity in the SJR. Calculation of background load, m a rgin of safety and load allocation is displayed in Table 10 on an annual

basis and Table 11 on a m onthly basis. A deta iled look at calculation of m onthly values for TMML, background load, m a rgin of safety, and load allocation is displayed in Table 12.

Table 10. Annual v a lues for the calculation of load allocations for four w a ter y ear ty pes

Total Total Total

SJ R @ Total SJ R @ Total Total Margin Total Crows Landing Total Merced Lander Wetland Background of Load

Time Year Design Flow TMML Flow Flow Flow Load Safety Allocation

P e r i o d T y p e a c r e

- f t p o u n d s a c r e

- f t a c r e

- f t a c r e

- f t p o u n d s p o u n d s p o u n d s
O c t

- S e p t C 9 7

, 2 1 4 1

, 3 2 0 3 7

, 4 8 9 3

, 3 0 1 3 3

, 3 0 0 1 1 5 1 3 2 1

, 0 7 3 Oct-Sept D/BN 218,155 2,963 120,859 11,807 33,300 172 296 2,495

O c t

- S e p t A N 3 6 7

, 8 4 6 4

, 9 9 6 1 3 2

, 7 8 4 6 1

, 6 0 5 6 5

, 4 0 0 3 3 3 5 0 0 4

, 1 6 3 Oct-Sept W 395,136 5,367 74,994 97,872 65,400 351 537 4,479



## Linkage Analysis

A linkage analysis is used to describe the relationship between the num eric targets, identified sources, and the total assim ilative capacity (loading capacity) of the waterbody. The linkage analysis for this TMDL was used to determ ine if num eric targets would have been m e t if the proposed load allocations had been applied to historic flows and background loads from 1986 through 1999. Background flows and selenium loads for this historic period were com p iled and calculated for the SJR at Lander Avenue, Merced River, Mud Slough, and Salt Slough (Appendix C). Monthly flows are based on da ily USGS flow m easurem ents. Selenium

concentrations for the SJR at Lander Avenue and the Merced River are assum e d to be 0.5 and 0.2 μg/L respectively. Selenium concentration in Mud Slough and Salt Slough is assum e d to be

21Table 11. Calculation of load allocation for each month and y ear ty pe

Month Y ear T y pe Design Flow T MML B a c k gr ound Load Mar g in of S a f e ty Load A lloc a tion

a c re -f t

Se p C 5,016 68 5 7 57

Se p D / B N 20,298 276 13 28 235

Se p A N 22,667 308 13 31 264

Se p W 27,850 378 8 3 8 332

Oc t C 5,016 68 7 7 55

Oc t D / B N 20,298 276 15 28 233

Oc t A N 22,667 308 17 31 260

Oc t W 27,850 378 12 38 328

Nov C 5,016 68 7 7 55

Nov D /B N 20,298 276 15 28 233

Nov A N 22,667 308 17 31 260

Nov W 27,850 378 12 38 328

Dec C 13,187 179 10 18 152

Dec D /B N 27,263 370 14 37 319

Dec A N 35,297 479 33 48 398

Dec W 19,260 262 24 26 211

Ja n C 13,187 179 10 18 151

Ja n D / B N 27,263 370 15 37 319

Ja n A N 35,297 479 34 48 398

Ja n W 19,260 262 25 26 211

Feb C 9,308 126 21 13 93

Feb D /B N 17,132 233 25 23 185

Feb A N 43,155 586 55 59 472

Feb W 45,623 620 70 62 488

Mar C 9,308 126 21 13 92

Mar D /BN 17,132 233 25 23 184

Mar A N 43,155 586 55 59 472

Mar W 45,623 620 70 62 488
Ap r C 9,308 126 13 13 101
Ap r D / B N 17,132 233 16 23 193
Ap r A N 43,155 586 37 59 490
Ap r W 45,623 620 52 62 506
May C 9,308 126 9 1 3 105
May D /BN 17,132 233 13 23 197
May A N 43,155 586 31 59 497
May W 45,623 620 45 62 512

Ju n C 6,188 84 7 8 69

Ju n D / B N 11,402 155 9 1 5 130

Ju n A N 18,877 256 18 26 212

Ju n W 30,191 410 15 41 354

Ju l C 6,188 84 6 8 70

Ju l D / B N 11,402 155 8 1 5 131

Ju l A N 18,877 256 16 26 214

Ju l W 30,191 410 14 41 356

Au g C 6,188 84 1 8 75

Au g D / B N 11,402 155 3 1 5 137

Au g A N 18,877 256 6 2 6 225

Au g W 30,191 410 3 4 1 366 ---- -------- -------- -------- ----- pounds ------ ------- -------- -------- -------- ------

22Table 12. Stepwise calculation of load allocation, including design flow, TMML, background load and margin of safetyBackgroundMarginWaterSJR@SJR@SJR@LoadofLoadQualityCrowsLandingT MML3MercedMercedLanderLanderWetlandWetland4 x 5 + 6 x 7Safety7AllocationO bjective1Design Flow21 x 2FlowConc.4FlowConc.4Flow5Conc.6+ 8 x 93x 10%3 -10 -11TimeYearμg/Lacre-ftpoundsacre-ftμg/Lacre-ftμg/Lacre-ftμg/LpoundspoundspoundsPeriodType123456789101112SepC55,016683,2420.21210.51,00015757SepD/BN520,29827616,0850.21,3430.51,00011328235SepAN522,66730810,7190.21,7460.51,90011331264SepW527,8503785,1090.23640.51,9001838332OctC55,016683,2420.21210.51,70017755OctD/BN520,29827616,0850.21,3430.51,70011528233OctAN522,66730810,7190.21,7460.53,30011731260OctW527,8503785,1090.23640.53,30011238328NovC55,016683,2420.21210.51,70017755NovD/BN520,29827616,0850.21,3430.51,70011528233NovAN522,66730810,7190.21,7460.53,30011731260NovW527,8503785,1090.23640.53,30011238328DecC513,1871798,6300.24720.51,60011018152DecD/BN527,26337014,3740.21,7020.51,60011437319DecAN535,2974798,5310.214,7100.53,20013348398DecW519,2602624,9810.29,6160.53,20012426211JanC513,1871798,6300.24720.51,70011018151JanD/BN527,26337014,3740.21,7020.51,70011537319JanAN535,2974798,5310.214,7100.53,30013448398JanW519,2602624,9810.29,6160.53,30012526211FebC59,3081262,2910.22970.57,2001211393FebD/BN517,1322337,6400.28740.57,20012523185FebAN543,15558615,3760.25,7420.514,40015559472FebW545,62362010,0650.218,7020.514,40017062488MarC59,3081262,2910.22970.57,3001211392MarD/BN517,1322337,6400.28740.57,30012523184MarAN543,15558615,3760.25,7420.514,40015559472MarW545,62362010,0650.218,7020.514,40017062488AprC59,3081262,2910.22970.54,00011313101AprD/BN517,1322337,6400.28740.54,00011623193AprAN543,15558615,3760.25,7420.57,80013759490AprW545,62362010,0650.218,7020.57,80015262506MayC59,3081262,2910.22970.52,7001913105MayD/BN517,1322337,6400.28740.52,70011323197MayAN543,15558615,3760.25,7420.55,30013159497MayW545,62362010,0650.218,7020.55,30014562512JunC56,188844460.22690.52,40017869JunD/BN511,4021554,4330.22940.52,4001915130JunAN518,8772567,3540.21,3260.54,60011826212JunW530,1914103,1490.29140.54,60011541354JulC56,188844460.22690.52,00016870JulD/BN511,4021554,4330.22940.52,0001815131JulAN518,8772567,3540.21,3260.53,90011626214JulW530,1914103,1490.29140.53,90011441356AugC56,188844460.22690.5011875AugD/BN511,4021554,4330.22940.501315137AugAN518,8772567,3540.21,3260.501626225AugW530,1914103,1490.29140.50134136611 in3 yearexceedance rateofa 4-daystandard2FlowrecordWY1970-WY19993Conversion Acre-ftxμg/Ltolbs.= 0.00274Concentration forMerced RiverisfromWestcotetal.,1990 and forSJRatLanderisfromChilcottetal.,20005FlowforGrassland wetlandsisfromTable 2CinAppendix 4 ofCRWQCB-CVR,19966Concentration forGrassland wetlands isfromChilcottetal.,20007MarginofSafety(MOS)is10%fromKarkoski,1994

23024681012Jan-86Jan-88Jan-90Jan-92Jan-94Jan-96Jan-98Jan-00Month

Selenium Concentration (μg/L)LinkageAnalysisHistorical5 ug/LobjectiveFigure 6. Comparison of monthlyhistorical concentration, linkage analysis concentration and the water qualityobjective fromwateryear 1986 through water year 1999 for the SJR at Crows Landing

2425 1.0 μg/L. The sum of the monthly background load and the monthly TMML load allocation is divided by the total monthly flow to obtain a monthly selenium concentration (Appendix D). Based on these assumptions there would have been no violations of a 5 μg/L monthly selenium objective for this 14-year period. Historical m onthly selenium concentrations in the SJR were significantly higher than those that would have occurred if TMML load limits had been in place (Figure 6). A detailed look, using the methods desc ribed above, at daily concentrations for water years 1991 and 1997 shows that there would have been only 6 violations of the 5 μg/L four-day average (Appendix E and F). This rate of exceedance is in line with the allowable rate of violations (1 in 3 years for a total of 5 over 15 years) and validates use of the TMML m establish load limits that will achieve compliance with water quality objectives.



## Implementation Plan

The program to implement this TMDL and the selenium TMDLs for Salt Slough and the Grassland Marshes was adopted in the Regional Board’s 1996 Basin Plan Amendment. Included in this 1996 Basin Plan Amendment is a timetable for meeting selenium water quality objectives in the lower SJR (Table 1). The 5 μg/L four-day average water quality objective for the SJR

below the Merced River must be met in AN and W years starting in wate r year 2006. The 5 μg/L four-day average objective must be met for C, D and BN years starting in water year 2011. The 5 μg/L four-day average water quality objective must also be met for all year types in Mud Slough and the SJR from Sack Dam to the Merced River starting in water year 2011. Starting in water year 1997, this amendment also prohibited discharge of agricultural subsurface drainage to Grassland Watershed wetland supply channels and Salt Slough if the discharge results in concentrations exceeding the 2 μg/L water quality objective established for these channels.

Concurrent with development of the 1996 Basin Plan Amendment, the San Luis and Delta Mendota Water Authority (SLDMWA) and the USBR entered into an agreement to use a portion of the San Luis Drain to convey agricultural subsurface drainage directly to Mud Slough. This Agreement for Use of the San Luis Drain (1995 Use Agreement) (USBR-SLDMWA, 1995) (Appendix G) allowed use of a 28-mile segment of the San Luis Drain as part of the GBP for a five-year period starting in November 1995. The GBP commenced operation on Septem 1996. Since September 1996, the GBP has isolated a nd rerouted agricultural subsurface drainage from the DPA away from Salt Slough and the wetland supply channels by using a portion of the San Luis Drain to convey agricultural subsurface drainage directly to Mud Slough. The San Luis Drain discharges to Mud Slough approximately nine miles upstream of the SJR confluence.

Interim load limits were established for the first fi ve years of operation of the GBP as part of the 1995 Use Agreement. Load limits were agreed upon by consensus of the dischargers in the DPA, the U.S. EPA, the U.S. Fish and Wildlife Service and the USBR (CRWQCB-CVR, 1996). The annual load limit for the first two years of the project, water years 1997 and 1998, was set at 6,660 pounds per year. This annual load limit was reduced by five percent per year for the next three years. The 1995 Use Agreement was renewed in 1999 to extend use of the San Luis Drain for an additional two-year period that concludes September 30, 2001.

These consensus-based monthly and annual selenium load limits for August 1998 through September 2001, were incorporated into Waste Discharge Requirements for San Luis and DeltaMendota Water Authority and United Sates Department of the Interior Bureau of Reclamation odel to

ber 23,Grassland Bypass Project Fresno and Merced Counties , Order Num b er 98-171 (CRW QCB, 1998b) (Appendix I). In the absence of new load lim its from a new Use Agreem e n t o r T M D L for the period after Septem ber 2001, these 1998 W a ste Discharge Requirem e nts establish

m onthly and annual selenium load lim its based upon the draft TMML presented in the 1996

Basin Plan Am endm ent.

The USBR has drafted a new use agreem ent, Agreement for Use of the San Luis Drain ( 2 0 0 1 U s e Agreem ent) (USBR-SLDMW A , 2001) (Appendix H) that, if approved by the USBR and

SLDMW A , will perm it the SLDMW A to im plem ent the GBP through Decem ber 2009 (Table 13). This draft 2001 Use Agreem ent establishes m onthly and annual load lim i t s t h a t c o n t i n u e t h e

v e p e r c e n t p e r y e a r r e d u c t i o n i n l o a d l i m its through water year 2004. Starting in water year

o n w a t e r y e a r t y p e , a s s h o w n i n F i g u r e 7 ( U S B R

- S L D M W A

, 0 5

, t h e l o a d l i m its specified in the use agreem ent are based, in

e o f 5

t e r f i 2005, load lim i t s d i v e r g e b a s e d

2 0 0 1 )

. S t a r t i n g i n w a t e r y e a r 2 0 part, on load lim its in this TMDL. The Basin Plan specif i e s t h a t t h e w a t e r q u a l i t y o b j e c t i v

μ g/L m u st be m e t in the SJR downstream of the Merced River in AN and W water years starting in water year 2006. The draft 2001 Use Agreem ent contains load lim i t s c a l c u l a t e d i n t h i s T M D L

to m eet water quality objectives in AN and W w a t e r y e a r s s t a r t i n g i n w a t e r y e a r 2 0 0 5

. T h e w a quality objective for D/BN and C water years m u st be m e t starting in water year 2011. The draft 2001 Use Agreem ent contains load lim its calculated in this TMDL to m eet water quality objectives in D/BN and C water years starting in water year 2011. The draft 2001 Use Agreem ent load lim its are also incorporated in the Tentative Waste Discharge Requirements for San Luis and Delta-Mendota Water Authority and United States Department of the Interior Bureau of Reclamation Grassland Bypass Project (Phase II) F r e s n o a n d M e r c e d C o u n t i e s (CRW QCB-CVR, 2001) (Appendix J).

Table 13. Annual load allocations from th is TMDL and 2001 Tentativ e Waste Discharge Requirements (WDR) (CRWQCB-CVR, 2001)

Year Type 2001 TMDL

Load Allocation 2003 WDR

Load Allocation 2006 WDR

Load Allocation 2010 WDR

Load Allocation

C 1,073 4,995 3,853 1,073

D/BN 2,495 4,995 3,995 2,495

AN 4,163 4,995 4,163 4,163

W 4,479 4,995 4,479 4,479

Selenium load reduction is being achieved through a variety of control m e thods used by the

Grassland Area Farm ers. The Grassland Area Farm ers is a consortium o f w a t e r a n d i r r i g a t i o d i s t r i c t s r e s p o n s i b l e f o r a g r i c u l t u r a l s u b s u r f a c e d r a i n a g e c o l l e c t e d a n d d i s c h a r g e d t o t h e S a n L u i s Drain as part of the GBP. The Grassland Area Farm ers have a com p rehensive program in place

that evaluates and im plem ents a variety of regional, district-level, and f a rm -level activities to

reduce selenium discharge. Following is a partial listing of these activities: n

26ement2012Figure 7. Load allocations and compliance dates for the Grassland ByfortheSanLuisDrMWA,2001)pass Project (GBP) as outlined in the 2001 Draft Use Agree Waste Discharge Requirements (CRWQCB-CVR, 2001)20062007200820092010Calendar YearWetAbove NormalDry/BelowNormalCriticalMeets Basin Plan selenium objectives forDry/Below Normal and Critical water years****ain(USBR-SLD2001MeetsBasin2009inthecurrenimplementedTMDand2001Tentativ200420052011mctiveseabsenfanewy.

270100020003000400050006000200020022003

GBP Selenium Loading (lbs)PlanseleniuobjeWet and Above Normal water yearsseloaAgrdlieemUse Agreement or waste discharge requirements, the fullymitsentwi.Inthllapplforceo* No load limits are currently specified beyond DecembertUL28 Regional Components

• Regional Drainage Entity (Activity Agreement)

• Regional Drainage Coordinator

• Irrigation and Drainage Workshops

• Active Land Management Program

• Economic Incentives Program

District Level Components

• Low interest water conservation equipment loans

• Tiered water pricing

• Sprinkler pre-irrigations

• Tailwater recirculation

• Sump management

• Drainage water recycling

• Drainage water displacement

• Drainage water treatment

• Limited water transfers

Farm Level Components

• Improved irrigation methods

• Tailwater return ponds

• On-farm recycling

Full description of these activities is available in the 1998-1999 Annual Report of the Grassland Bypass Project (USBR, 1999).



## Performance Measures and Feedback

There has been on-going water quality monitoring of the GBP, conducted by several agencies, including the Regional Board and the Grassland Area Farmers, since September 1996. The monitoring plan is described in the 1998-1999 Annual Report of the Grassland Bypass Project (USBR, 1999). The purpose of monitoring is to verify compliance with selenium objectives in the Basin Plan. If monitoring demonstrates that the water quality objectives are not being m then additional load reductions or amendments to the TMDL will be required.



## Public Participation

The Regional Board held workshops and public hearings for the 1996 Basin Plan Amendm The State Water Resources Control Board also held approval hearings. Comment letters (Appendix K) and a response to comments (Appendix L) are included in this report. The administrative record (Appendix M) for the workshops and public hearings held for the 1996 Basin Plan Amendment are on file at the Regional Board in five 3.5 inch binders.

Additional meetings have been held as part of the Environmental Impact Statement and Environmental Impact Report for the Grassland Bypass Project (URS, 2001) that has been et,

ent.p r e p a r e d f o r t h e c o n t i n u e d u s e o f t h e G B P

. A p p e n d i x N c o n t a i n s a l i s t o f m eeting dates and list

of com o i n c l u d e d ( A p p e n d i x O )

.

A Regional Board staff workshop was held on 16 May 2001 that presented this TMDL to all interested parties. Appendix P contains a copy of the workshop announcem ent, a list of attendees at this workshop, a copy of the m a terial presented, and a copy of the m a iling list used

n o t i f y i n t e r e s t e d p a r t i e s

. L o a d a l l o c a t i o n s i n t h i s r e p o r t a n d t h e m e thods used to calculate

s t a f f w o r k s h o p

.

T h e a a

- M e n d o t a W a t e r A u t h o r i t y a n d United States Department of the Interior Bureau of Reclamation Grassland Bypass Project ( P h e o u n t i e s are being considered as an agenda item (Appendix Q)

f o r i o n a l B o a r d m eeting. Stakeholders including Environm ental Defense, San Luis & Delta-Mendota W a ter Aut hority, Contra Costa County, Panoche Drainage

D i s t i c t

, a n d C a m p 13 Drainage District are supportive of these

W a e T M D L l o a d l i m its as indicated by their 22 August 2001

l e t t m e nters. The response to com m e n t s s e c t i o n i s a l s

t o them w e r e p r e s e n t e d a t t h i s

W s t e D i s c h a r g e R e q u i r e m e n t s f o r S a n L u i s a n d D e l t

a s I I ) F r e s n o a n d M e r c e d

t h e 6

- 7 S e p t e m b e r 2 0 0 1 R e g C

t r i c , C o n t r a C o s t a W a t e r D i s t r ste Discharge Requirem e n t s a n d t h

e r o f s u p p o r t ( A p p e n d i x R )

.

29

## References

C D W R (California Departm e nt of W a ter Resour ces). 2000. Chronological Sacram ento and San

c a

.

t r o l P l a n f o r t h e S a c r a m e n t o R i v e r a n d S J

R B a s i n s

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