STATE OF CALIFORNIA

REGIONAL WATER QUALITY CONTROL

BOARD

★

★

CENTRAL

VALLEY

REGION

Staff Report of the 

CALIFORNIA ENVIRONMENTAL PROTECTION AGENCY

REGIONAL WATER QUALITY CONTROL BOARD

CENTRAL VALLEY REGION

TOTAL MAXIMUM DAILY LOAD

FOR SELENIUM IN THE

LOWER SAN JOAQUIN RIVER

August 2001
State 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 

Sacramento, 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 

CALIFORNIA ENVIRONMENTAL PROTECTION AGENCY

REGIONAL WATER QUALITY CONTROL BOARD

CENTRAL VALLEY REGION

TOTAL MAXIMUM DAILY LOAD

FOR SELENIUM IN THE

LOWER SAN JOAQUIN RIVER

August 2001

REPORT PREPARED BY: 

Matthew J. McCarthy, Land and Water Use Analyst 

Leslie F. Grober, Senior Land and Water Use Analyst 

San Joaquin River TMDL Unit 
Table of Contents 

Executive Summary................................................................................................................. iv

TMDL Summary....................................................................................................................... v

Problem Statement.................................................................................................................... 1

Environmental Setting and TMDL Scope............................................................................... 1

Regulatory History.................................................................................................................. 2

Target Analysis.......................................................................................................................... 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

Selenium Loading................................................................................................................ 8

Selenium Concentration.................................................................................................... 12

Load Allocations...................................................................................................................... 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................................................................................................................ 21

Load Allocation................................................................................................................. 21

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 Water Quality Objectives1

 (in bold) and Performance Goals (in italics) ........ 6 

Table 2. Annual discharge1

 (thousand acre-ft) of three locations in the lower San Joaquin River 

Basin ....................................................................................................................................... 9 

Table 3. Annual selenium loading1

 (pounds) at three locations in the lower San Joaquin River 

Basin ....................................................................................................................................... 9 

Table 4. Differences in selenium loading1

 (pounds) between three locations in the lower San 

Joaquin River Basin .............................................................................................................. 10 

Table 5. Percent difference in selenium loading1 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 

River Basin............................................................................................................................ 12 

Table 7. Unmeasured selenium concentrations1

 (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 number 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 ....................................................................................................... 20 

Table 10. Annual values for the calculation of load allocations for four water year types......... 21 

Table 11. Calculation of load allocation for each month and year type ...................................... 22 

Table 12. Stepwise calculation of load allocation, including design flow, TMML, background 

load and margin of safety...................................................................................................... 23 

Table 13. Annual load allocations from this TMDL and 2001 Tentative Waste Discharge 

Requirements (WDR) (CRWQCB-CVR, 2001)................................................................... 26 

ii
List of Figures 

Figure 1. Location map of the lower San Joaquin River Basin ...................................................... 2 

Figure 2. Wetland water supply schematic before Grassland Bypass Project................................ 4 

Figure 3. Wetland water supply schematic after Grassland Bypass Project................................... 5 

Figure 4. Annual selenium loading from four locations 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. Comparison of monthly historical concentration, 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 compliance dates for the Grassland Bypass Project (GBP) as 

outlined in the 2001 Draft Use Agreement for the San Luis Drain (USBR-SLDMWA, 2001) 

and 2001 Tentative Waste Discharge Requirements (CRWQCB-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 selected 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 Agreement for Use of the San Luis Drain 

Appendix H. 2001 Draft Agreement for Use of the San Luis Drain 

Appendix I. 1998 Waste Discharge Requirements for the Grassland Bypass Project 

Appendix J. 2001 Tentative Waste Discharge Requirements for the Grassland Bypass Project 

and 15 August 2001 Revisions 

Appendix K. Regional Board 1996 Basin Plan Amendment for the Control of Agricultural 

Subsurface Drainage Discharges, Comment Letters Received 

Appendix L. Regional Board 1996 Basin Plan Amendment for the Control of Agricultural 

Subsurface Drainage Discharges, Response to Comments 

Appendix M. Regional Board 1996 Basin Plan Amendment for the Control of Agricultural 

Subsurface Drainage Discharges, Administrative Record 

Appendix N. 2001 EIS/EIR for the Grassland Bypass Project, Public Hearing Dates and List of 

Commenters

Appendix O. 2001 EIS/EIR for the Grassland Bypass Project, Response to Comments 

Appendix P. Selenium Total Maximum Daily Load Workshop held on 16 May 2001 

Appendix Q. 2001 Waste Discharge Requirements for the Grassland Bypass Project, Regional 

Board Meeting Agenda Item, 6-7 September 2001 

Appendix R. 2001 Waste Discharge Requirements for the Grassland Bypass Project, Letter to 

Regional Board 

iii
Executive Summary 

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

impaired for selenium, which is toxic to waterfowl at high levels. The impairment extends from

the Salt Slough confluence to the Airport Way Bridge near Vernalis. The 303(d) listing requires 

development of a Total Maximum Daily Load (TMDL) for selenium in the lower SJR. The 

major 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 

specify how much selenium can be discharged while still maintaining a healthy ecosystem. 

Based on these load allocations, waste discharge requirements are assigned to the DPA’s 

drainage system, the Grassland Bypass Project (GBP). This report outlines the development of a 

TMDL for the lower SJR to reduce the selenium impairment in the river and outlines load 

allocations that will be implemented for the GBP. 

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

levels. Death and deformities of waterfowl at Kesterson Wildlife Refuge in 1983 first focused 

attention on agricultural drainage and selenium. The Central Valley Regional Water Quality 

Control Board (Regional Board) has adopted the U.S. Environmental Protection Agency aquatic 

life criterion for total selenium of 5 μg/L four-day average as the selenium water quality 

objective for the lower SJR. While 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 Watershed. Subsurface agricultural drainage discharges from

this area are the major 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 

methods used in the 1994 report; they are designed to meet selenium water quality objectives 

downstream of the Merced River confluence. The methods group a thirty year historical flow 

record by water year type and season, resulting in monthly load allocations for the DPA as 

displayed in the TMDL Summary section. A linkage analysis was developed as a check of the 

load allocation methods. This linkage analysis considers historical discharges, background 

selenium loads, and estimated load allocations. The analysis confirmed the ability of the load 

allocations for meeting monthly selenium water quality objectives. 

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

Amendment for the Control of Agricultural Subsurface Drainage Discharges. Included in this 

program is a compliance time schedule for meeting the four-day average and monthly mean 

water quality objectives for selenium. Landowners within the DPA formed a group called the 

Grassland Area Farmers 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 requirements to the GBP in 1998 that require the 

Grassland Area Farmers to reduce the discharge of selenium from pre-GBP load levels. The 

waste discharge requirements 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 

Water body: San Joaquin River 

Total Size: 330 miles 

Impaired: 50 miles from the Salt Slough confluence to the Airport Way Bridge near 

Vernalis 

Pollutant: Selenium

Source: Major: Subsurface agricultural return flows (tile drainage) from the 

97,000-acre Drainage Project Area of the Grassland Watershed (88% of 

total load) 

 

Minor: Distributed inputs throughout the San Joaquin River Basin 

Schedule: Level 1 (three year timeframe) 

Priority: High 

Report Date: August 2001 

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

four-day average water quality objective for the lower San Joaquin River. There is no waste load 

allocation for this Total Maximum Daily Load. 

Drainage Project Area Monthly Load Limits (pounds) 

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

Critical 151 93 92 101 105 69 70 75 57 55 55 152

Dry/Below Normal 319 185 184 193 197 130 131 137 235 233 233 319

Above Normal 398 472 472 490 497 212 214 225 264 260 260 398

Wet 211 488 488 506 512 354 356 366 332 328 328 211

v
Problem Statement 

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

Water Act for exceeding selenium water quality objectives. Areal extent of the impairment was 

listed as 50 river miles from the Salt Slough confluence to the Airport Way Bridge near Vernalis. 

This water quality limited segment was listed in 1988 as part of the water quality assessment and 

303(d) listing process. 

Environmental Setting and TMDL Scope

The southern part of the Central Valley of California is comprised of two hydrologic basins: the 

SJR and the Tulare Lake Basins. The SJR Basin (Figure 1) is drained by the SJR, which 

discharges to the Sacramento-San Joaquin Delta. The Tulare Lake Basin is for the most part an 

internal drainage basin that occasionally overflows into the SJR Basin during extremely 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 Sacramento River in the Sacramento-San Joaquin Delta. The main stem of the SJR is 

about 300 miles long and drains approximately 13,500 square miles. The geographic scope of 

this TMDL is 50 miles of the lower SJR from the Salt Slough confluence to the Airport Way 

Bridge near Vernalis. This reach of the SJR drains an area of approximately 2.9 million acres. 

Mud Slough and Salt Slough are tributaries to the SJR that drain the 370,000-acre Grassland 

Watershed. These sloughs contain a mix of agricultural return flows, runoff from managed 

wetlands, rainfall runoff, and flood flows. Mud Slough discharges to the SJR approximately two 

miles upstream of the confluence between the SJR and the Merced River. Salt Slough flows into 

the SJR approximately 6 miles upstream of the Mud Slough confluence. Flow in the lower SJR 

is limited 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 marine origin in the Coast 

Range that are high in selenium and salts. Major land uses in the watershed include agriculture 

and managed wetlands. Dry conditions make irrigation necessary for nearly all crops grown 

commercially in the watershed. Irrigation of the soils derived from these marine sediments 

leaches selenium and salt into the shallow groundwater. Subsurface drainage is produced when 

farmers 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 most recently, the Drainage Project Area (DPA). 

Selenium is a highly bioaccumulative trace element, which, under certain conditions, can be 

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

1
Deformities and deaths of waterfowl 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. Environmental Protection Agency’s (U.S. EPA) criteria for total selenium of 5 μg/L. The 

effects of selenium on waterfowl are the driving force behind current criteria. Subsurface 

agricultural drainage is the primary source of selenium in the lower SJR Basin although selenium

sources at low concentrations (less than 2 μg/L) are widespread. 

Stanislaus River

Tuolumne River

Merced River

SJR near

Vernalis

SJR at Lander

SJR near Patterson

Orestimba Creek

San Joaquin River

Grassland Watershed

Del Puerto

Ho

Creek

spital Creek

Ingram Creek

Mud

Slough

Salt

Slough

Mendota Dam

Sack Dam

Drainage Project Area

(370,000 acres)

(97,000 acres)

SJR at Crows Landing

Sierra Nevada

Coast Range

N

Figure 1. Location map of the lower San Joaquin River Basin 

Regulatory History

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

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

Westlands Water District in the Tulare Lake Basin to Kesterson Reservoir via the partially 

completed San Luis Drain. Discovery of the adverse impacts 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 Westlands Water District. Westlands Water District is just 

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

2
quality. Subsurface agricultural drainage water in the Grassland Watershed has historically 

drained to the SJR via a network of constructed and natural channels. These same channels are 

also used to convey fresh water supplies for managed wetlands. 

Regional Board staff commenced a program of monitoring and assessment of waterbodies in the 

Grassland Watershed in 1985. A 1988 Regional Board Basin Plan Amendment for the Control 

of Agricultural Subsurface Drainage Discharges identified water conservation measures as a 

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

From 1985 to 1996, channels in the Grassland Water District were used to alternately convey 

agricultural drainage water and freshwater (Figure 2). An agreement between Grassland Water 

District and agricultural districts in the DPA allowed use of a series of wetland supply channels 

to convey drainage through the north and south portions of the Grassland Water 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 

demand for freshwater supplies, and continued environmental concern with this arrangement, led 

to development of the Grassland Bypass Project (GBP) and the Regional Board’s 1996 Basin 

Plan Amendment for the Control of Subsurface Agricultural Drainage (1996 Basin Plan 

Amendment). 

The GBP was implemented in September 1996 to divert agricultural drainage water from the 

DPA out of the Grassland Water District water supply channels (Figure 3). This diversion 

allows refuge managers greater control over their supply and release operations, so they can 

receive and apply all of their fresh water allocations according to optimum habitat management 

schedules. Diversion of agricultural drainage water away from the Grassland Water District 

channels reduces the selenium exposure to fish, wildlife, and humans in the wetland channels 

and Salt Slough. Other pollutants of concern in the drainage water, such as salt and boron, may 

also be reduced. Combining agricultural drainage flows into a single concrete-lined structure, 

the San Luis Drain, allows for better monitoring, potentially leading to a more detailed 

evaluation as well as effective control of selenium and agricultural drainage. The establishment 

of an accountable drainage entity has provided the framework necessary for responsible 

watershed management in the Grassland Watershed. 

Total Maximum Daily Load (TMDL) reports have been completed for selenium in Salt Slough 

and the Grassland Marshes (CRWQCB-CVR, 1999 and 2000). These TMDLs have been 

implemented through the Regional Board’s 1996 Basin Plan Amendment. In accordance with 

the 1996 Basin Plan Amendment, Waste Discharge Requirements for discharges from the GBP 

were issued in July 1998. 

 

Target Analysis 

Water quality objectives were adopted in the Regional Board’s 1996 Basin Plan Amendment. 

The amendment contained selenium water quality objectives for Mud Slough (north), Salt 

Slough and wetland supply channels in the Grassland Watershed and for the main 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 Water Resources Control 

Board and the Office 

3
Santa Fe

Canal

Drainage Project Area

Agatha Canal Camp 13

Canal

•

North 

Grassland

Water

District

South 

Grassland

Water

District

San Luis Canal •

Salt Slough

San Joaquin River

Mud Slough

(north)

San Luis Drain

• •

CCID Main Canal

•

Blake-Porter

Bypass

San Luis Canal

Fremont Canal

Santa Fe

Canal

Figure 2. Wetland water supply schematic before Grassland Bypass Project

4
Santa Fe

Canal

Drainage Project Area

Agatha Canal Camp 13

Canal

•

North 

Grassland

Water

District

South 

Grassland

Water

District

San Luis Canal •

Salt Slough

San Joaquin River

Mud Slough

(north)

• •

CCID Main Canal

•

San Luis Drain

Blake-Porter

Bypass

San Luis Canal

Fremont Canal

Santa Fe

Canal

Grassland Bypass

Figure 3. Wetland water supply schematic after Grassland Bypass Project

of Administrative Law, is a four-day average concentration of 5 μg/L (CRWQCB-CVR, 1998a). 

This TMDL uses the four-day average 5 μg/L objective as the numeric target. Targets adopted 

5
for other impaired waterbodies in the SJR Basin include 2 μg/L monthly mean for the Grassland 

wetland supply channels, 2 μg/L monthly mean for Salt Slough, and 5 μg/L four-day average for 

Mud Slough. Selenium water quality objectives and performance goals are shown in Table 1. 

Table 1. Selenium Water Quality Objectives1 (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 

monthly mean

5 μg/L 

four-day

average

San Joaquin River below the 

Merced River; Critical, Dry and 

Below Normal Water Year 

types 

8 μg/L 

monthly mean

5 μg/L 

monthly mean

5 μg/L 

four-day

average

Mud Slough (north) and the 

San Joaquin River from Sack 

Dam to the Merced River 

5 μg/L 

four-day

average

1

Copy of table found in the Water Quality Control Plan for the Sacramento and San Joaquin Rivers (CRWQCB-CVR, 1998a)

Source Analysis 

Subsurface agricultural return flows from the DPA in the Grassland Watershed are the primary 

source of selenium in the lower SJR Basin. There are no municipal or industrial sources. 

Selenium is a naturally occurring element found in sediments of the Coast Ranges on the west 

side of the lower SJR Basin. Selenium can therefore 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, some land use practices may accelerate its movement 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 maintain agricultural productivity. Tile drains are installed in areas 

of high groundwater to lower the water table below the root zone. The lower SJR Basin has 

many areas with high groundwater levels due to poorly drained soils and application of irrigation 

water. Tile drainage may have high selenium concentrations, especially in the Grassland 

Watershed. Drainage from tile drains in the DPA is the primary source of selenium in the 

Grassland Watershed and the SJR. A survey of tile drainage in the lower SJR Basin (Chilcott et 

al., 1988) found the highest concentrations of selenium in the Grassland Watershed. Eighty-two 

6
percent of the samples collected at 173 tile drainage sites in the Grassland Watershed had 

selenium concentrations ranging from 11 to 500 μg/L. Six percent of the samples 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 Watershed has selenium concentrations 

significantly lower than the Grassland Watershed and the DPA. A survey of agricultural 

drainage found that the range of selenium concentrations 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 median of 2.2 μg/L (Westcot 

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 

same 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 (Westcot et al., 1989) found the mean selenium concentration 

of surface return flows, with source water from a mix 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. With use of the GBP, Salt 

Slough no longer received subsurface agricultural return 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 comprised mostly 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 Watershed, is generally a gaining stream. The U.S. 

Geological Survey (USGS) investigated the quality and quantity of groundwater inflow to the 

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

cfs/mile, with a range of 1.1 to 3.2 cfs/mile. This flow translates to about 1,500 acre-ft/mile 

annually and 75,000 acre-ft for the impaired 50 mile stretch of the SJR. The concentration of 

selenium in the groundwater was estimated to be 0.9 μg/L. Assuming a mean groundwater 

inflow of 2.0 cfs/mile at a selenium concentration of 0.9 μg/L, groundwater contributes 

approximately 200 pounds of selenium per year along the impaired 50-mile stretch of the SJR. 

Tributary Inflows 

A survey of the water quality of ephemeral west side SJR tributaries between 1984 and 1988 

(Westcot et al., 1991) found median selenium concentrations generally less than or equal to 1.0 

μg/L for Del Puerto, Orestimba and Hospital Creeks. Ingram Creek had a median selenium

concentration of 4.3 μg/L. The maximum annual load contributed to the SJR by these and 36 

other ephemeral streams was estimated to be approximately 600 pounds per year. Little data is 

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

the samples collected from these rivers between 1985 and 1988 (USGS, 1988 and USGS, 1991) 

had selenium concentrations below the detection limit of 1.0 μg/L but some samples from each 

7
tributary had concentrations at the detection limit. 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 contribute selenium to the lower SJR at concentrations 

well below the water quality objective of 5 μg/L. The load they contribute may be highest 

during periods of high discharge when extremely low concentrations may still account for 

significant loads. For example, a discharge of 100,000 acre-ft per month at a selenium

concentration of 0.2 μg/L would account for a monthly selenium load of 54 pounds. During wet 

years, flow from east side tributaries can be in excess of 200,000 acre-ft per month. Such a flow 

may account for 108 pounds of selenium per month. 

San Joaquin River Selenium Loads

The Regional Board has conducted water quality sampling at numerous sites in the Grassland 

Watershed and the lower SJR since 1985. Results from the first ten water years of this sampling 

program, 1985 through 1995, are summarized in two Regional Board staff reports (Steensen et 

al, 1998 and Grober et al, 1998). Results for water years 1996 through 1998 are summarized in 

Chilcott et al, 1998 and Chilcott et al, 2000. These reports include monthly and annual flow and 

selenium load information for discharges from the DPA, the Grassland Watershed, the SJR near 

Patterson, and the SJR near Vernalis. The reports demonstrate that the DPA accounts for, on 

average, 88% of the selenium load in the lower SJR. 

Discharge 

Water discharges from the DPA account for a small percentage of the total flow volume in the 

lower SJR (Table 2). The mean annual discharge from the DPA from 1986 through 1998 was 48 

thousand acre-feet (taf) per year. The mean annual discharge from the Grassland Watershed 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 volume in the SJR near Vernalis. The 

range of discharge is most pronounced in the SJR near Vernalis, with a low of 657 taf in 1991 to 

a high of 8,489 taf in 1998. Grassland Watershed 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 Watershed is much more highly variable 

than discharge from the DPA. 

Selenium Loading 

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

mean annual selenium load in the SJR near Vernalis during this same period was 9,788 pounds 

(Table 3). The mean annual difference of 1,128 pounds (Table 4) is attributable to distributed 

sources of selenium throughout the lower SJR Basin. Distributed sources are primarily from

background sources and include all non-DPA sources of selenium. On average, the DPA has 

accounted for 88 percent of the mean 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 approximately 1,670 pounds in 1988 to a gain of 5,077 

pounds in 1986. In other words, DPA loads have accounted for 120 percent (Water Year 1988) 

to 65 percent (Water 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 measurement and calculation 

error although no consistent source of error has been identified (Grober et al, 1998). Losses are 

8
also attributable to water diversions from the SJR. 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 discharge1 (thousand acre-ft) of three 

locations in the lower San Joaquin River Basin 

Water 

Year 

Drainage Project 

Area 

Grassland 

Watershed 

SJR near 

Vernalis 

1986 67 284 5,226

1987 75 234 1,813 

1988 65 230 1,168

1989 54 211 1,059 

1990 42 195 916

1991 29 102 657 

1992 25 85 700

1993 41 168 1,702 

1994 39 184 1,219

1995 58 264 6,299 

1996 50 270 3,950

1997 40 290 6,770 

1998 46 378 8,489

average 48 223 3,075 1

Data from Steensen et al., 1998 

Table 3. Annual selenium loading1

 (pounds) at three 

locations in the lower San Joaquin River Basin 

Water 

Year 

Drainage Project 

Area 

Grassland 

Watershed 

SJR near 

Vernalis 

1986 9,524 6,643 14,601

1987 10,959 7,641 8,502 

1988 10,097 8,132 8,427

1989 8,718 8,099 8,741 

1990 7,393 7,719 7,472

1991 5,858 3,899 3,611 

1992 5,083 2,919 3,558

1993 8,856 6,871 8,905 

1994 8,468 7,980 7,760

1995 11,875 10,694 17,238 

1996 10,034 9,491 11,431

1997 6,959 7,722 11,190 

1998 8,760 9,630 15,810

average 8,660 7,495 9,788 1

Data from Steensen et al., 1998

9
Table 4. Differences in selenium loading1

 (pounds) between 

three locations in the lower San Joaquin River Basin 

This site: 

Grassland 

Watershed SJR near Vernalis 

Minus this 

site: 

Drainage 

Project Area 

Drainage 

Project Area 

Grassland 

Watershed 

1986 -2,881 5,077 7,958

1987 -3,318 -2,457 861 

1988 -1,965 -1,670 295

1989 -619 23 642 

1990 326 79 -247

1991 -1,959 -2,247 -288 

1992 -2,164 -1,525 639

1993 -1,985 49 2,034 

1994 -488 -708 -220

1995 -1,181 5,363 6,544 

1996 -543 1,397 1,940

1997 763 4,231 3,468 

1998 870 7,050 6,180

Water Year 

average -1,165 1,128 2,293 1

Data from Steensen et al., 1998

Table 5. Percent difference in selenium loading1 between 

three locations in the lower San Joaquin River Basin 

Difference 

between: 

Grassland 

Watershed SJR near Vernalis 

and: 

Drainage 

Project Area 

Drainage 

Project Area 

Grassland 

Watershed 

1986 143% 65% 45%

1987 143% 129% 90% 

1988 124% 120% 96%

1989 108% 100% 93% 

1990 96% 99% 103%

1991 150% 162% 108% 

1992 174% 143% 82%

1993 129% 99% 77% 

1994 106% 109% 103%

1995 111% 69% 62% 

1996 106% 88% 83%

1997 90% 62% 69% 

1998 91% 55% 61%

Water Year 

average 116% 88% 77% 1

Data from Steensen et al., 1998

10




























































 









 



















































0

8000600040002000

1800016000140001200010000

1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998

Water Year

Selenium Load (pounds)

Drain

age Project Area/Grasslan

d Byp

ass Project

  

Gr

assland W

atershe

d

SJR ne

ar P

atterson/Crows L

anding

SJR near Vernalis 

11 

Figure 4. Annual selenium loading from four locations in the low

er San Joaquin Riv

er Basin
Selenium Concentration 

Discharges from the DPA are the most concentrated source of selenium in the lower SJR. The 

mean annual selenium concentration for discharge from the DPA from 1986 through 1998 was 

68 μg/L (Table 6). The mean annual selenium concentration for the SJR near Patterson and SJR 

near Vernalis was 3.8 and 1.8 μg/L respectively. The time series of mean monthly selenium

concentrations for the DPA and the SJR near Vernalis is shown in Figure 5. As already 

indicated, the high selenium concentration discharges from the DPA account for most of the 

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

be used to estimate the selenium concentration for unmeasured, distributed sources of selenium

in the lower SJR Basin. 

Table 6. Annual selenium concentrations 

(μg/L) from three locations in the lower 

San Joaquin River Basin 

Water 

Year 

Drainage 

Project 

Area 

SJR near 

Patterson1

SJR near 

Vernalis 

1986 52 1.5 1.0

1987 54 4.9 1.8 

1988 57 6.2 2.7

1989 59 6.3 3.0 

1990 65 5.6 3.0

1991 74 5.4 2.0 

1992 76 4.4 1.9

1993 79 3.7 1.9 

1994 81 5.4 2.3

1995 76 1.5 1.0 

1996 70 2.7 1.1

1997 68 0.8 0.6 

1998 70 1.1 0.7

average 68 3.8 1.8 1

Data for water years 1996 to 1998 is based 

on SJR at Crows Landing 

The concentration of the unmeasured selenium sources can be estimated by calculating a 

concentration from the unmeasured 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 most 

are less than 0.5 μg/L. The average concentration of these sources of selenium for water years 

1986 through 1998 was approximately 0.3 μg/L. This data shows that the DPA is the primary 

source of selenium in the Grassland Watershed and in the lower SJR Basin. 

12
0

80604020

140120100

1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998

Water Year

Monthly Selenium Concentration (μg/L)

Drainage Project Area/Grassland Bypass ProjectSJR near Vernalis

13 

Figure 5. Monthly selenium concentrations for the Drainage Project Area and the San Joaquin River near Vernalis 
Table 7. Unmeasured selenium 

concentrations1

 (μg/L) from three locations 

in the lower San Joaquin River Basin 

Water 

Year 

SJR near 

Patterson2

SJR near 

Vernalis 

1986 0.72 0.48

1987 1.04 -0.11 

1988 1.38 -0.54

1989 -1.01 0.75 

1990 -2.80 0.97

1991 -0.68 0.06 

1992 0.24 0.46

1993 0.77 0.24 

1994 -0.69 0.27

1995 0.41 0.39 

1996 0.37 0.11

1997 0.09 0.36 

1998 0.35 0.21

average 0.32 0.28 1

Data from Steensen et al., 1998 

2

Data for water years 1996 to 1998 is based 

on SJR at Crows Landing

Load Allocations 

Load allocations for discharges from the DPA 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 Maximum Monthly Load (TMML) model and the 

methods used in the model to calculate selenium load allocations. This TMML model is a simple 

spreadsheet model that calculates monthly 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 for meeting the selenium water 

quality objective in the SJR downstream of the Merced River confluence. There would be 

effectively no allocation of selenium load in the absence of Merced River dilution flows. The 

source analysis has shown that subsurface agricultural return flows form the DPA are the 

primary source of selenium load in the lower SJR Basin. The source analysis has shown that the 

selenium concentration of all other SJR inflows is much lower than the water quality objective. 

The selenium water quality objective for the entire SJR downstream of the Merced River will 

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

the Merced River confluence. 

The schedule for compliance with selenium water quality objectives in the SJR (Table 1) shows 

that the 5 μg/L objective must be met for the SJR from Sack Dam to the Merced River 

confluence starting in October 2010. Prior to this date, selenium loads from the DPA may 

continue to be discharged to the SJR upstream of the Merced River confluence. Attainment of 

the selenium water quality objective upstream of the Merced River confluence may require 

significant changes to the DPA discharge, including the relocation of the discharge point. 

14 
Through September 2010, the SJR at Crows Landing is the water quality compliance point of the 

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

used as the compliance point because the dominant 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 monitored 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 model uses historical flow records, grouped by season and water year type, to 

calculate critical flow or design flow conditions. Design flows are multiplied by the water 

quality objective to calculate the TMML or assimilative capacity. A monthly load limit is 

established, rather than a daily limit, since most agricultural water districts lack the facilities 

needed to manage drainage on a daily basis. 

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

similar to the present and future hydrology. Completion 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 impact on both the Merced River and 

SJR, only the hydrology subsequent to dam filling and completion in 1969 is used in the 

calculation of design flows. 

Data Sources

The SJR at Crows Landing is the compliance point for 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 must be reconstructed based 

on SJR near Patterson flow data that is available from 1969 through 1999. Reconstruction of the 

flow record at Crows Landing was done using Patterson flow data and the mass balance model 

SJRIO-2. SJRIO-2 can be used to do a mass balance accounting of monthly flow and water 

quality (Kratzer, 1987) for water years 1977 through 1996. When run in calibration mode, the 

model provides a monthly 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: 

Pat, Model

Crows, Model Pat, Hist

Crows,Calc

Q

Q Q Q ⋅ (1) = 

where 

QCrows, Calc = calculated streamflow at Crows Landing 

QCrows, Model = SJRIO2 model calculated streamflow at Crows Landing 

QPat, Hist = historical measured streamflow at Patterson 

QPat, Model = SJRIO2 model calculated streamflow 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 

15 
1999 was presented in the U.S. Bureau of Reclamation (USBR) update to the model (USBR, 

2000). This combined dataset, using a combination 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 Regimes

The model develops flow regimes by categorizing flow data based on water year type and 

season. Water year type is based on the SJR Index of unimpaired flows (CDWR, 2000). This 

water year classification scheme identifies water years as Critical (C), Dry (D), Below Normal 

(BN), Above Normal (AN), or Wet (W). The SJR Index is composed of the unimpaired runoff 

from the four major rivers in the Basin: 

Stanislaus River inflow into Melones Reservoir 

Tuolumne River inflow into Don Pedro Reservoir 

Merced River inflow into Exchequer Reservoir 

San Joaquin River inflow into Millerton Reservoir 

The index is determined as follows: 

60% current year April to July runoff 

20% current year October to March runoff 

20% of the previous year index, not exceeding 0.9 million acre-ft 

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

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

 Year Type Threshold (million acre-feet)

 Critical C < 2.1 

 Dry 2.1 ≤ D < 2.5 

 Below Normal 2.5 ≤ BN < 3.1 

 Above Normal3.1 ≤ AN < 3.8 

 Wet 3.8 ≤ W 

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

AN/W. The seasonal grouping divides the year into four seasons, with months grouped by time 

of year. The four seasonal groupings are September through November, December and January, 

February through May, and June through August. The seasonal grouping represents the distinct 

seasonality of flow in the SJR and DPA drainage flows. High drainage flows occur from

February through August and high river flows occur from December through May. The seasonal 

groupings divide the water years into seasons that cover the combinations of high and low river 

flows and high and low drainage flows. This seasonal grouping allows the discharger to make 

the necessary adjustments to meet the load allocation for the particular season. The three water 

year groupings and four seasonal groupings are combined into 12 flow regimes. The current 

update to the model increased the number of water year groupings from three to four, resulting in 

16 
16 flow regimes instead of 12. The new groupings are C, D/BN, AN, and W. The increased 

number of groupings maximizes flexibility to dischargers in the DPA by accounting for 

increased temporal variations of flow. 

Violation Rate and Design Flow

After assigning the flow data into appropriate flow regimes, 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 more than 

once every three years on average. The compliance point for this TMDL is the SJR at Crows 

Landing, which has an incomplete 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 available for the years 1973-1995. The model SJRIO-2 was 

used to calculate monthly 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 similar 

flow patterns and a daily flow record must be used. A coefficient must be developed for the 

similar flow site to convert monthly 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 month is: 

4 (3) 

3

0

∑

= =

−

i

Qn i

 Four - Day Average Flow 

The lowest four-day average flow for the month 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 

mean monthly flow for the site was found: 

Pat, mean Monthly

Pat, Four - day,low

Pat

Q

Q (4) C =

where 

CPat = monthly to daily coefficient at Patterson 

QPat, Four-day, low = four-day average low streamflow at Patterson 

QPat, mean Monthly = mean monthly streamflow at Patterson 

This coefficient was multiplied by QCrows, Calc (from equation 1) to determine the monthly 

equivalent of the four-day average low flow at Crows Landing: 

(5) QCrows,Four - day,low = CPat ( ) QCrows,Calc

where 

17 
CPat = monthly to daily coefficient at Patterson 

QCrows, Four-day, low = four-day average low streamflow at Crows Landing 

QCrows,Calc = monthly calculated streamflow at Crows Landing 

The allowable number of violations is calculated based upon an average exceedance rate of once 

every three years. This calculation involves multiplying the period of record by the allowable 

frequency of violations. 

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

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

flow record under consideration. These violations may be distributed between the various flow 

regimes. 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 some of 

the driest water years on record in the SJR Basin (CDWR, 2000) The low flow condition, or 

design flows are calculated for each flow regime by rank ordering the historical flows. 

For each flow regime, the flows are rank-ordered from the lowest to highest observed flow. A 

user-defined percentile is then assigned to each rank-ordered flow regime. Selection of the 0th

percentile means the lowest observed flow is selected as a design flow. Selection of the 100th

percentile means the highest flow is selected. The Microsoft ExcelTM percentile function 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 most of 

the flow regimes is based on the 0th percentile or the lowest observed flow. If the lowest flow 

for any flow regime is lower than the C year design flow, the C year design flow is used for that 

flow regime. 

For the 1994 selenium TMML for the lower SJR, all violations were grouped in the C water year 

groupings with the assumption that dischargers would have the most difficulty in meeting water 

quality objectives during C water years. Experience of the drainers in the DPA with operating 

the GBP has identified difficulty also in meeting load limits during wet periods. As a result, 

some violations have now been assigned to AN and W water years as well as C water years by 

selecting a user-defined percentile for these flow regimes (Table 8). A 0th percentile (lowest 

observed flow) is used for all other flow regimes. 

Calculating the TMML

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

assimilative capacity of the water body. The assimilative capacity is calculated by multiplying 

the design flow (QDF) by the water quality objective (WQO) and applying a conversion factor. 

(7) TMML (pounds) = QDF(acre - ft) × WQO(μg/L) × 0.0027 (conversion factor)

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

and the number of violations over a 30 year period for the San 

Joaquin River at Crows Landing 

Year Type Grouping Percentile Rank Design Flow Number of Violations 

 acre-ft 

C Sep-Nov 0.07 5,016 2

D/BN Sep-Nov 0 20,298 0

AN Sep-Nov 0 22,667 0

W Sep-Nov 0 27,850 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 Feb-May 0.03 9,308 2

D/BN Feb-May 0 17,132 0

AN Feb-May 0.05 43,155 1

W Feb-May 0.02 45,623 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 assimilative capacity, or TMML, must be distributed between a waste load allocation 

(WLA) for point sources, a load allocation (LA) for non-point sources, a margin of safety 

(MOS), and a background load (BL). 

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

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

municipal wastewater treatment plant. There are no point sources of selenium in the lower SJR 

Basin, so there is no waste load allocation. The DPA is the only non-point source in this TMML.

 With no waste load allocation component, the load allocation for the DPA can be calculated 

using: 

(9) LA = TMML - BL - MOS

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 must be calculated for 

the three main 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 (column a) and grouping (column b) which are combined to 

provide sixteen flow regimes. For each flow regime, a design flow for the SJR at Crows 

Landing (column c) has already been determined based on historical Crows Landing flows 

(Appendix A). The historical Crows Landing flow (column d) that is closest to the design flow 

(column c) is determined. The month and year of the historical Crows Landing flow (column e) 

is used to select monthly flows for the Merced River (column f) and the SJR at Lander (column 

19
g). The historical Merced River and SJR at Lander Avenue flows are given in Appendix B. The 

four-day average low flow equivalent to monthly average coefficient (column h) is used to 

convert monthly flows for both the Merced River and the SJR at Lander Avenue to the four-day 

average equivalent. This is the same coefficient used to convert from a monthly 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 monthly average flows are multiplied by the four-day average 

low flow equivalent to monthly average coefficient to obtain the four-day low flow average for 

the Merced River (column i) and the SJR at Lander Avenue (column j). 

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

San Joaquin River Basin 

SJR @

Crows 

SJR @

Crows Merced SJR @

Lander 

Four-day 

average 

Merced SJR @

Lander 

Design Historical Historical Historical low flow Four-day Four-day

Four-day Four-day Similar Monthly Monthly equivalent average average

Year Seasonal average average Flow flow3 flow3 to Monthly low flow low flow 

Type Grouping low flow1 low flow2 Month flow equivalent5 equivalent

5

ac-ft ac-ft ac-ft ac-ft coefficient4 ac-ft ac-ft

a b c d e f g h i j

C Sep-Nov 5,016 5,345 Nov-77 7,220 269 0.45 3,242 121

D/BN Sep-Nov 20,298 20,298 Sep-72 54,860 4,580 0.29 16,085 1,343

AN Sep-Nov 22,667 22,667 Oct-70 13,430 2,188 0.80 10,719 1,746

W Sep-Nov 27,850 27,850 Sep-97 5,470 389 0.93 5,109 364

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 Feb-May 9,308 9,272 May-77 4,000 519 0.57 2,291 297

D/BN Feb-May 17,132 17,132 Apr-72 12,250 1,401 0.62 7,640 874

AN Feb-May 43,155 43,931 Apr-70 16,730 6,248 0.92 15,376 5,742

W Feb-May 45,623 46,101 Feb-93 21,166 39,330 0.48 10,065 18,702

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 multiplying historical flow (column f,g) by a coefficient (column h) 

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

the Merced River is 0.2 μg/L (Westcot et al., 1990) and the SJR at Lander is 0.5 μg/L (Chilcott 

et al., 2000). Wetland flow data was obtained from a USBR analysis of wetland discharges in an 

assessment of water quality impacts of the GBP (Swain and Quinn, 1991). Wetland water 

quality is 1.0 μg/L, based on improvements in wetland supply water quality in the Grassland 

Watershed. With 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 

20
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). 

Margin of Safety 

No consistent errors have been identified in the flow and selenium water quality information 

used to generate this TMML. An explicit ten percent MOS is applied to account for errors in 

flow measurements and selenium concentrations and uncertainty in the TMML analyses. The 

same ten percent MOS was used in the 1994 TMML (Karkoski, 1994). The ten percent MOS is 

applied to the calculated assimilative capacity or TMML: 

(10) MOS = 0.10 × TMML

Load Allocation 

After accounting for the margin of safety and background loads, the remaining 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 determine 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 assimilative capacity in the SJR. Calculation of 

background load, margin of safety and load allocation is displayed in Table 10 on an annual 

basis and Table 11 on a monthly basis. A detailed look at calculation of monthly values for 

TMML, background load, margin of safety, and load allocation is displayed in Table 12. 

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

 Total Total Total 

 SJR @ Total SJR @ Total Total Margin Total 

 Crows Landing Total Merced Lander Wetland Background of Load 

Time Year Design Flow TMML Flow Flow Flow Load Safety Allocation 

Period Type acre-ft pounds acre-ft acre-ft acre-ft pounds pounds pounds

Oct-Sept C 97,214 1,320 37,489 3,301 33,300 115 132 1,073

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

Oct-Sept AN 367,846 4,996 132,784 61,605 65,400 333 500 4,163

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 numeric targets, identified 

sources, and the total assimilative capacity (loading capacity) of the waterbody. The linkage 

analysis for this TMDL was used to determine if numeric targets would have been met 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 compiled and 

calculated for the SJR at Lander Avenue, Merced River, Mud Slough, and Salt Slough 

(Appendix C). Monthly flows are based on daily USGS flow measurements. Selenium

concentrations for the SJR at Lander Avenue and the Merced River are assumed to be 0.5 and 

0.2 μg/L respectively. Selenium concentration in Mud Slough and Salt Slough is assumed to be 

21
Table 11. Calculation of load allocation for each month and year type

Month Year Type Design Flow TMML Background Load Margin of Safety Load Allocation

acre-ft

Sep C 5,016 68 5 7 57

Sep D/BN 20,298 276 13 28 235

Sep AN 22,667 308 13 31 264

Sep W 27,850 378 8 38 332

Oct C 5,016 68 7 7 55

Oct D/BN 20,298 276 15 28 233

Oct AN 22,667 308 17 31 260

Oct W 27,850 378 12 38 328

Nov C 5,016 68 7 7 55

Nov D/BN 20,298 276 15 28 233

Nov AN 22,667 308 17 31 260

Nov W 27,850 378 12 38 328

Dec C 13,187 179 10 18 152

Dec D/BN 27,263 370 14 37 319

Dec AN 35,297 479 33 48 398

Dec W 19,260 262 24 26 211

Jan C 13,187 179 10 18 151

Jan D/BN 27,263 370 15 37 319

Jan AN 35,297 479 34 48 398

Jan W 19,260 262 25 26 211

Feb C 9,308 126 21 13 93

Feb D/BN 17,132 233 25 23 185

Feb AN 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 AN 43,155 586 55 59 472

Mar W 45,623 620 70 62 488

Apr C 9,308 126 13 13 101

Apr D/BN 17,132 233 16 23 193

Apr AN 43,155 586 37 59 490

Apr W 45,623 620 52 62 506

May C 9,308 126 9 13 105

May D/BN 17,132 233 13 23 197

May AN 43,155 586 31 59 497

May W 45,623 620 45 62 512

Jun C 6,188 84 7 8 69

Jun D/BN 11,402 155 9 15 130

Jun AN 18,877 256 18 26 212

Jun W 30,191 410 15 41 354

Jul C 6,188 84 6 8 70

Jul D/BN 11,402 155 8 15 131

Jul AN 18,877 256 16 26 214

Jul W 30,191 410 14 41 356

Aug C 6,188 84 1 8 75

Aug D/BN 11,402 155 3 15 137

Aug AN 18,877 256 6 26 225

Aug W 30,191 410 3 41 366

--------------------------------- pounds -------------------------------------------

22
Table 12. Stepwise calculation of load allocation, including design flow, TMML, background load and margin of safety

Background M argin

W ater SJR @ SJR @ SJR @ Load of Load

Q uality C rows Landing T M M L3 M erced M erced Lander Lander W etland W etland 4 x 5 + 6 x 7 Safety7 Allocation

O bjective1 D esign Flow2 1 x 2 Flow C onc.4 Flow C onc.4 Flow5 C onc.6 + 8 x 9 3 x 10% 3 - 10 - 11

Tim e Year μg/L acre-ft pounds acre-ft μg/L acre-ft μg/L acre-ft μg/L pounds pounds pounds

Period Type 1 2 3 4 5 6 7 8 9 10 11 12

Sep C 5 5,016 68 3,242 0.2 121 0.5 1,000 1 5 7 57Sep D /BN 5 20,298 276 16,085 0.2 1,343 0.5 1,000 1 13 28 235Sep AN 5 22,667 308 10,719 0.2 1,746 0.5 1,900 1 13 31 264Sep W 5 27,850 378 5,109 0.2 364 0.5 1,900 1 8 38 332

O ct C 5 5,016 68 3,242 0.2 121 0.5 1,700 1 7 7 55O ct D /BN 5 20,298 276 16,085 0.2 1,343 0.5 1,700 1 15 28 233O ct AN 5 22,667 308 10,719 0.2 1,746 0.5 3,300 1 17 31 260O ct W 5 27,850 378 5,109 0.2 364 0.5 3,300 1 12 38 328

N ov C 5 5,016 68 3,242 0.2 121 0.5 1,700 1 7 7 55N ov D /BN 5 20,298 276 16,085 0.2 1,343 0.5 1,700 1 15 28 233N ov AN 5 22,667 308 10,719 0.2 1,746 0.5 3,300 1 17 31 260N ov W 5 27,850 378 5,109 0.2 364 0.5 3,300 1 12 38 328

D ec C 5 13,187 179 8,630 0.2 472 0.5 1,600 1 10 18 152D ec D /BN 5 27,263 370 14,374 0.2 1,702 0.5 1,600 1 14 37 319D ec AN 5 35,297 479 8,531 0.2 14,710 0.5 3,200 1 33 48 398D ec W 5 19,260 262 4,981 0.2 9,616 0.5 3,200 1 24 26 211

Jan C 5 13,187 179 8,630 0.2 472 0.5 1,700 1 10 18 151Jan D /BN 5 27,263 370 14,374 0.2 1,702 0.5 1,700 1 15 37 319Jan AN 5 35,297 479 8,531 0.2 14,710 0.5 3,300 1 34 48 398Jan W 5 19,260 262 4,981 0.2 9,616 0.5 3,300 1 25 26 211

Feb C 5 9,308 126 2,291 0.2 297 0.5 7,200 1 21 13 93Feb D /BN 5 17,132 233 7,640 0.2 874 0.5 7,200 1 25 23 185Feb AN 5 43,155 586 15,376 0.2 5,742 0.5 14,400 1 55 59 472Feb W 5 45,623 620 10,065 0.2 18,702 0.5 14,400 1 70 62 488M ar C 5 9,308 126 2,291 0.2 297 0.5 7,300 1 21 13 92M ar D /BN 5 17,132 233 7,640 0.2 874 0.5 7,300 1 25 23 184M ar AN 5 43,155 586 15,376 0.2 5,742 0.5 14,400 1 55 59 472M ar W 5 45,623 620 10,065 0.2 18,702 0.5 14,400 1 70 62 488

Apr C 5 9,308 126 2,291 0.2 297 0.5 4,000 1 13 13 101Apr D /BN 5 17,132 233 7,640 0.2 874 0.5 4,000 1 16 23 193Apr AN 5 43,155 586 15,376 0.2 5,742 0.5 7,800 1 37 59 490Apr W 5 45,623 620 10,065 0.2 18,702 0.5 7,800 1 52 62 506

M ay C 5 9,308 126 2,291 0.2 297 0.5 2,700 1 9 13 105M ay D /BN 5 17,132 233 7,640 0.2 874 0.5 2,700 1 13 23 197M ay AN 5 43,155 586 15,376 0.2 5,742 0.5 5,300 1 31 59 497M ay W 5 45,623 620 10,065 0.2 18,702 0.5 5,300 1 45 62 512

Jun C 5 6,188 84 446 0.2 269 0.5 2,400 1 7 8 69Jun D /BN 5 11,402 155 4,433 0.2 294 0.5 2,400 1 9 15 130Jun AN 5 18,877 256 7,354 0.2 1,326 0.5 4,600 1 18 26 212Jun W 5 30,191 410 3,149 0.2 914 0.5 4,600 1 15 41 354

Jul C 5 6,188 84 446 0.2 269 0.5 2,000 1 6 8 70Jul D /BN 5 11,402 155 4,433 0.2 294 0.5 2,000 1 8 15 131Jul AN 5 18,877 256 7,354 0.2 1,326 0.5 3,900 1 16 26 214Jul W 5 30,191 410 3,149 0.2 914 0.5 3,900 1 14 41 356

Aug C 5 6,188 84 446 0.2 269 0.5 0 1 1 8 75Aug D /BN 5 11,402 155 4,433 0.2 294 0.5 0 1 3 15 137Aug AN 5 18,877 256 7,354 0.2 1,326 0.5 0 1 6 26 225Aug W 5 30,191 410 3,149 0.2 914 0.5 0 1 3 41 366

1 1 in 3 year exceedance rate of a 4-day standard2 Flow record W Y 1970-W Y 19993 C onversion Acre-ft x μg/L to lbs. = 0.00274 C oncentration for M erced R iver is from W estcot et al., 1990 and for SJR at Lander is from C hilcott et al., 20005 Flow for G rassland wetlands is from Table 2C in Appendix 4 of C RW Q C B-C VR , 19966 C oncentration for G rassland wetlands is from C hilcott et al., 20007 M argin of Safety (M O S) is 10% from Karkosk i, 1994

23 
8

6420

1210

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

Month

Selenium Concentration (μg/L)

Linkage AnalysisHistorical

5 ug/Lobjective

Figure 6. Comparison of monthly historical concentration, linkage analysis concentration and the water quality objective from water

year 1986 through water year 1999 for the SJR at Crows Landing

24 
25

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 monthly 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 described 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 water 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 and 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 five 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 Number 98-171 (CRWQCB, 

1998b) (Appendix I). In the absence of new load limits from a new Use Agreement or TMDL

for the period after September 2001, these 1998 Waste Discharge Requirements establish 

monthly and annual selenium load limits based upon the draft TMML presented in the 1996 

Basin Plan Amendment. 

The USBR has drafted a new use agreement, Agreement for Use of the San Luis Drain (2001 Use

Agreement) (USBR-SLDMWA, 2001) (Appendix H) that, if approved by the USBR and 

SLDMWA, will permit the SLDMWA to implement the GBP through December 2009 (Table 

13). This draft 2001 Use Agreement establishes monthly and annual load limits that continue the

ve percent per year reduction in load limits through water year 2004. Starting in water year 

on water year type, as shown in Figure 7 (USBR-SLDMWA, 

05, the load limits specified in the use agreement are based, in 

e of 5 

ter

fi

2005, load limits diverge based

2001). Starting in water year 20

part, on load limits in this TMDL. The Basin Plan specifies that the water quality objectiv

μg/L must be met in the SJR downstream of the Merced River in AN and W water years starting 

in water year 2006. The draft 2001 Use Agreement contains load limits calculated in this TMDL

to meet water quality objectives in AN and W water years starting in water year 2005. The wa

quality objective for D/BN and C water years must be met starting in water year 2011. The draft 

2001 Use Agreement contains load limits calculated in this TMDL to meet water quality 

objectives in D/BN and C water years starting in water year 2011. The draft 2001 Use 

Agreement load limits 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) Fresno and Merced Counties

(CRWQCB-CVR, 2001) (Appendix J). 

Table 13. Annual load allocations from this TMDL and 2001 Tentative 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 methods used by the 

Grassland Area Farmers. The Grassland Area Farmers is a consortium of water and irrigatio

districts responsible for agricultural subsurface drainage collected and discharged to the San Luis

Drain as part of the GBP. The Grassland Area Farmers have a comprehensive program in place 

that evaluates and implements a variety of regional, district-level, and farm-level activities to 

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

n

26
ement 

2012

Figure 7. Load allocations and compliance dates for the Grassland Byfor the San Luis Dr MWA, 2001)

pass Project (GBP) as outlined in the 2001 Draft Use Agre

e Waste Discharge Requirements (CRWQCB-CVR, 2001)

2006 2007 2008 2009 2010

Calendar Year

WetAbove NormalDry/Below NormalCritical

Meets Basin Plan selenium objectives for Dry/Below Normal and Critical water years

****

ain (USBR-SLD

2001

Meets Basin

2009 in the currenimplemented TMD

and 2001 Tentativ

2004 2005 2011

m ctives

e absen f a new

y.

27 

0

600050004000300020001000

2000 2002 2003

GBP Selenium Loading (lbs) Plan seleniu obje Wet and Above Normal water years

se

lo

A

a

gr

d li

eem

Use Agreement or waste discharge requirements, the fully 

mits

ent

wi

. In th

ll appl

for

ce o

* No load limits are currently specified beyond December 

t U

L
28

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. 
prepared for the continued use of the GBP. Appendix N contains a list of meeting dates and list 

of com o included (Appendix 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 announcement, a list of 

attendees at this workshop, a copy of the material presented, and a copy of the mailing list used 

notify interested parties. Load allocations in this report and the methods used to calculate 

staff workshop.

The a a-Mendota Water Authority and

United States Department of the Interior Bureau of Reclamation Grassland Bypass Project 

(Ph e ounties are being considered as an agenda item (Appendix Q) 

for ional Board meeting. Stakeholders including Environmental 

Defense, San Luis & Delta-Mendota Water Authority, Contra Costa County, Panoche Drainage 

Dis t ict, and Camp 13 Drainage District are supportive of these 

Wa e TMDL load limits as indicated by their 22 August 2001 

lett

menters. The response to comments section is als

to

them were presented at this

W ste Discharge Requirements for San Luis and Delt

as II) Fresno and Merced

the 6-7 September 2001 Reg

C

tric , Contra Costa Water Distr

ste Discharge Requirements and th

er of support (Appendix R).

29
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ca.

trol Plan for the Sacramento River and SJR Basins

r the Control of Agricultural Subsurface Drainage Discharges; Staff Report. 

.

r

Interior Bureau of Reclamation Grassland Bypass Channel

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CRWQCB-CVR (California Regional Water Quality Control Board, Central Valley Region). 

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CRWQCB-CVR (California Regional Water Quality Control Board, Central Valley Region). 

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he Great Basin from Walker River to Truckee

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Grober, L.F., J. Karkoski, and L. Dinkler. 1998. Loads of Salt, Boron, and Selenium in the 

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I:

Karkoski, J. 1994. A Total Maximum Monthly Load Model for the San Joaquin River. 

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Steensen, R.A., J.E. Chilcott, and T. Burns. 1996. Agricultural Drain

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r

Use of the San Luis Drain.

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