Staff Report of the 

CALIFORNIA ENVIRONMENTAL PROTECTION AGENCY

REGIONAL WATER QUALITY CONTROL BOARD

CENTRAL VALLEY REGION

Selenium TMDL for Grasslands Marshes 

STATE OF CALIFORNIA

REGIONAL WATER QUALITY CONTROL

BOARD

★

★

CENTRAL

VALLEY

REGION

April 2000
Selenium TMDL for Grasslands Marshes 

Table of Contents 

List of Figures................................................................................................................................2 

List of Tables.................................................................................................................................2 

List of Attachments........................................................................................................................2 

Summary of TMDL Action ...........................................................................................................3 

Problem Statement.........................................................................................................................3 

Numeric Target ..............................................................................................................................7 

Source Analysis .............................................................................................................................7 

Implementation Plan ......................................................................................................................8 

Allocations.....................................................................................................................................8 

Performance Measures and Feedback............................................................................................8 

Margin of Safety ..........................................................................................................................12 

Public Participation......................................................................................................................13 

References....................................................................................................................................13 

List of Figures 

Figure 1. Location Map .................................................................................................................4 

Figure 2. Wetland Water Supply Schematic Before Grassland Bypass Project............................5 

Figure 3. Wetland Water Supply Schematic After Grassland Bypass Project ..............................6 

Figure 4. Mean Monthly Selenium in Santa Fe Canal..................................................................9 

Figure 5. Mean Monthly Selenium in San Luis Canal ..................................................................9 

Figure 6. Mean Monthly Selenium in Camp 13 Canal................................................................10 

Figure 7. Mean Monthly Selenium in Agatha Canal...................................................................10 

List of Tables 

Table 1. Annual Median Selenium Concentrations.....................................................................11 

List of Attachments 

1. Grassland Watershed Wetland Channels for Which Beneficial Uses Have Been Identified 

2. Regional Water Quality Control Board, Central Valley Region, 1996 Basin Plan 

Amendments for the Control of Agricultural Subsurface Drainage Discharges, Resolution 

96-147, Administrative Record Index 

3. Regional Water Quality Control Board, Central Valley Region, 1996 Basin Plan 

Amendments for the Control of Agricultural Subsurface Drainage Discharges, Letters 

Received 

4. Regional Water Quality Control Board, Central Valley Region, 1996 Basin Plan 

Amendments for the Control of Agricultural Subsurface Drainage Discharges, Response 

to Comments

2 
Summary of TMDL Action 

Following are the waste load allocations and load allocations for the Grassland Marshes 

selenium TMDL: 

TMDL (Loading Capacity) 2 ppb Selenium as a monthly mean 

Load Allocation 

Subsurface Drainage from Drainage Problem Area 

Background 

2 ppb Selenium as a monthly mean 

2 ppb Selenium as a monthly mean 

Waste Load Allocation 

(no NPDES sources) 

0 lbs Selenium

Problem Statement 

The Grassland Marshes are 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 8,224 

acres in 1988 as part of the water quality assessment and 303(d) listing process. The original 

basis for determining the extent of impairment is not available. As part of its 1996 Basin Plan 

Amendment, the Regional Board re-evaluated the miles of wetland channels and the extent of 

wetland acreage impaired or threatened by selenium contamination. The Regional Board 

determined that approximately 75 miles of wetland supply channels and 61,810 acres of wetland 

marshes were impaired or threatened by elevated selenium concentrations in agricultural 

subsurface drainage water (California Regional Water Quality Control Board, Central Valley 

Region, 1998b, Appendix 40). The Regional Board has not updated its 305(b) report or 303(d) 

list to reflect the more recent evaluation. The TMDL described below is based on the more 

recent information available regarding the extent of impairment. 

Soils in the Grassland Watershed (Figure 1) 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 wetlands. Water supplied to the 61,810 acres of wetland marshes through supply channels 

that, prior to completion of the Grassland Bypass Project in September 1996, also conveyed 

agricultural drainage water (California Regional Water Quality Control Board, Central Valley 

Region, 1996). Prior to completion of the Grassland Bypass Project, these supply channels 

alternately conveyed fresh water supplies and agricultural drainage water from 97,000 acres of 

tile drained farmland. Subsurface tile drainage water from these 97,000 acres is the primary 

source of selenium in the Grassland Watershed. The result of this combined use was that the 

wetland water supply channels and the wetlands, periodically had elevated selenium

concentrations. There are no NPDES permitted sources that drain to the wetland channels that 

convey water to the Grassland marshes. 

Dry conditions make irrigation necessary for nearly all crops grown commercially in the 

watershed. Irrigation of soils derived from marine sediments leaches selenium into the shallow 

groundwater. Subsurface drainage is produced when farmers drain the salty groundwater from

the root zone to protect their crops, and a portion of the Grassland Watershed that generates 

subsurface drainage has been designated as the Drainage Project Area (DPA). The discharge of 

subsurface drainage from that area resulted in elevated selenium concentrations in the wetland 

supply channels and other water bodies within the watershed and downstream. Selenium is a 

3 
highly bioaccumulative trace element which, under certain conditions, can be mobilized through 

the food chain and cause both acute and chronic toxicity to fish and wildlife. Deformities and 

deaths of waterfowl have been linked to toxic concentrations of selenium. There was concern 

that elevated selenium concentrations in subsurface drainage would cause problems for the 

aquatic birds and wildlife that use the Grassland marshes. The Grassland marshes were placed 

on the Section 303(d) list in 1988 because water in the wetland supply channels routinely 

exceeded 2 μg/L. At the time of the 1988 listing, 2 μg/L was the United States Fish and Wildlife 

Serevice recommended selenium criteria to protect waterfowl and other wildlife uses. 

The Grassland Watershed has undergone dramatic changes in hydrology and water quality due to 

agricultural development over the years. Prior to September 1996, subsurface drainage from the 

DPA flowed through the Grassland wetlands on its way to the San Joaquin River (figure 2). 

Starting in September 1996, this subsurface drainage was collected and conveyed in a single 

channel, the Grassland Bypass, to the northern reach of the San Luis Drain. The San Luis Drain 

discharges into Mud Slough (north) nine miles upstream of its confluence with the San Joaquin 

River. The effect of this Grassland Bypass Project was removal of most of the selenium load 

from wetland supply channels and therefore the wetlands themselves (Figure 3). 















 

Salt Slough

Mud Slough

Mendota Pool

SJR near Vernalis

Stanislaus River

Tuolumne River

Merced River

Grasslands Watershed

(370,000 acres)

Drainage Project Area

(97,000 acres)

North Grassland Water District

South Grassland Water District

Figure 1. Location Map 

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)

San Luis Drain

• •

CCID Main Canal

•

Figure 2. Wetland Water Supply Schematic Before Grassland Bypass Project

5 
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

Grassland Bypass

Figure 3. Wetland Water Supply Schematic After Grassland Bypass Project

6 
Numeric Target 

In 1996, the Regional Board adopted a Basin Plan Amendment for the Regulation of Agricultural 

Subsurface Drainage. The amendment contained a selenium water quality objective for wetland 

water supply channels and Salt Slough. This objective, which was approved by the State Board 

and the Office of Administrative Law, is a monthly mean concentration of 2 μg/L. The objective 

for the supply channels was made more stringent than the selenium objective for downstream

waterbodies to offer added protection to the waterfowl using the wetlands. Based on a review of 

the available scientific literature, the Regional Board determined that a 2 μg/L monthly mean 

selenium objective would be protective of waterfowl . This 2 μg/L monthly mean selenium

objective incorporates a margin of safety because it is based upon threshold water borne 

concentrations of 2.3 to 2.5 μgL correlated with selenium tissue concentrations in aquatic birds 

that have shown impaired hatchability of eggs and susceptibility to disease (California Regional 

Water Quality Control Board, Central Valley Region; 1996; pg. 61). 

Consideration was given to translating the selenium water quality objective into a load limit, but 

water quality data collected in wetland water delivery channels in the late 1980’s through early 

1990’s showed little change in concentration even in response to significant load reductions 

(California Regional Water Quality Control Board, Central Valley Region; 1995; pp. 5-7). 

Based on this information, the Regional Board concluded that removal of untreated subsurface 

agricultural drainage was required to meet water quality objectives (California Regional Water 

Quality Control Board, Central Valley Region; 1996; pp. 67-68). Therefore, a concentration 

based objective was determined to be the best measure of success for protecting beneficial uses 

and achieving water quality improvements. The numeric target for wetland water supply 

channels and the Grassland Marshes TMDL is the adopted Basin Plan selenium water quality 

objective of 2 μg/L (monthly mean). 

Source Analysis 

Although selenium exists naturally in the soils of this watershed, some land use practices 

accelerate its movement to ground water and surface water. Prior to the Grassland Bypass 

Project, water supply for the Grassland Marshes shared conveyance channels with subsurface 

and surface drainage from the DPA. Subsurface drainage, specifically from the tile drains in the 

DPA, is the most significant source of selenium in the Grassland Watershed. A survey of tile 

drainage in the San Joaquin River Basin (Chilcott et al., 1988) found the highest concentrations 

of selenium in the Grassland Watershed. Eighty-two percent of the samples collected at 173 tile 

drainage sites in the Grassland Watershed had selenium concentrations ranging from 11 to 500 

μg/L. The Regional Board has conducted water quality sampling in wetland water supply 

channels since 1985. Some of these channels, such CCID Main Canal at Russel Blvd., are 

upstream of the tile drainage discharges from the DPA. This site represents background 

selenium concentrations in supply water delivered to the wetland channels. The source of water 

in CCID Main Canal at Russel Blvd. includes deliveries from the Delta Mendota Canal, Mendota 

Pool, and agricultural return flows from outside the DPA. The median value of selenium was 1.6 

μg/L and the mean was 2.2 μg/L for over 200 samples collected (California Regional Water 

Quality Control Board, Central Valley Region; February, 1998a; pg. 178). 

Tile drainage from the Drainage Project Area is the primary source of selenium in the Grassland 

Watershed. There are no municipal or industrial sources. Selenium is a naturally occurring 

7 
element in sediments of the Grassland Watershed. Selenium can therefore be found in surface 

runoff and groundwater throughout the watershed. 

Implementation Plan 

In 1996, the Regional Board amended its Basin Plan for control of agricultural subsurface 

drainage discharges. This Basin Plan Amendment prohibits discharge of subsurface drainage 

water to Grassland Watershed wetland supply channels if the discharge results in concentrations 

exceeding the water quality objective. Removal of selenium from wetland supply channels will 

remove the source of selenium loading to the Grassland Marshes. This prohibition has 

eliminated the largest loading of selenium to the wetland supply channels. Since September 

1996, the Grasslands Bypass Project has isolated and rerouted tile drainage from the DPA away 

from wetland supply channels by using a portion of the former San Luis Drain to convey tile 

drainage directly to Mud Slough. The San Luis Drain discharges to Mud Slough approximately 

nine miles upstream of the San Joaquin River confluence (figure 3). 

Other sources of water in the wetland supply channels are deliveries from the Delta Mendota 

Canal and Mendota Pool via the Main Canal, wetland discharges, overland flows from the DPA 

during storm events, surface agricultural return flows, and groundwater accretions. Information 

available prior to 1996 indicated that selenium concentrations of those sources commonly fell 

below 2 μg/L. On this basis, no other implementation provisions appeared necessary, nor were 

included, in the 1996 Basin Plan Amendment for the Control of Agricultural Subsurface

Drainage Discharges (California Regional Water Quality Control Board, Central Valley Region; 

1996). 

Allocations 

Subsurface drainage is prohibited from discharge into Grassland wetland supply channels if the 

discharge results in concentrations exceeding the water quality objective; therefore, the 

subsurface drainage allocation is expressed as the water quality concentration of 2 μg/L as a 

monthly mean. As discussed in the Source Analysis section above, load allocations for the 

surface agricultural drainage and wetlands discharges are not necessary since they are not 

significant sources. Regional Board monitoring data shows that surface agricultural drainage 

and wetland discharges typically have selenium concentrations of less than 2 μg/L. Background 

sources such as groundwater and surface runoff are given a load allocation expressed as a 

monthly mean water quality concentration of 2 μg/L. 

Performance Measures and Feedback 

Water quality monitoring conducted after the start of the Grassland Bypass Project in September, 

1996 indicates that overall selenium concentrations in wetland supply channels have decreased 

dramatically, although the mean monthly objective is still being exceeded. The 2 μg/L objective 

has been exceeded in ten out of 24 months in the Santa Fe Canal (figure 4) and eleven out of 24 

months in the San Luis Canal (figure 5). The 2 μg/L objective has been exceeded in 10 out of 24 

months in the Camp 13 canal (figure 6) and 5 out of 24 months in the Agatha Canal (figure 7). 

These four channels are representative of supply channels that deliver water to the Grassland 

Marshes. 

8 
0

2 5

5 0

7 5

1 0 0

S e p -9 2 S e p -9 3 S e p -9 4 S e p -9 5 S e p -9 6 S e p -9 7 S e p -9 8

September 1992 to September 1998

Selenium (μg/L)

August 1996 to September 1998

0

2

4

6

8

1 0

Au g -9 6 F e b -9 7 Au g -9 7 F e b -9 8 Au g -9 8

August 1996 to September 1998

Selenium (μg/L)

Figure 4. Mean Monthly Selenium in Santa Fe Canal 

0

2 5

5 0

7 5

1 0 0

S e p -9 2 S e p -9 3 S e p -9 4 S e p -9 5 S e p -9 6 S e p -9 7 S e p -9 8

September 1992 to September 1998

Selenium (μg/L)

August 1996 to September 1998

0

2

4

6

8

1 0

Aug-9 6 F eb-9 7 Aug-9 7 F eb-9 8 Aug-9 8

August 1996 to September 1998

Selenium (μg/L)

Figure 5. Mean Monthly Selenium in San Luis Canal 

9 
0

2 5

5 0

7 5

100

S ep-9 2 S ep-9 3 S ep-9 4 S ep-9 5 S ep-9 6 S ep-9 7 S ep-9 8

September 1992 to September 1998

Selenium (μg/L)

August 1996 to September 1998

0

2

4

6

8

1 0

Aug-9 6 F eb-9 7 Aug-9 7 F eb-9 8 Aug-9 8

August 1996 to September 1998

Selenium (μg/L)

Figure 6. Mean Monthly Selenium in Camp 13 Canal 

0

2 5

5 0

7 5

1 0 0

S e p -9 2 S e p -9 3 S e p -9 4 S e p -9 5 S e p -9 6 S e p -9 7 S e p -9 8

September 1992 to September 1998

Selenium (μg/L)

August 1996 to September 1998

0

2

4

6

8

1 0

Aug-9 6 F eb-9 7 Aug-9 7 F eb-9 8 Aug-9 8

August 1996 to September 1998

Selenium (μg/L)

Figure 7. Mean Monthly Selenium in Agatha Canal 

10 
Most elevated selenium concentrations occurred during and immediately following storm events 

when surface runoff from the DPA that exceeded the capacity of the GBP was diverted into the 

wetland supply channels (Chilcott, 2000). There are some minor exceedances throughout the 

year. The median annual selenium concentration was less than or equal to 2.0 μg/L for all four 

sites in water years 1997 and 1998 except for the Santa Fe Canal which had a median 

concentration of 2.1 μg/L in water year 1997 (table 2). These median concentrations are much 

lower than the concentrations observed prior to use of the Grassland Bypass when median annual 

selenium concentrations sometimes exceeded 50 μg/L in these channels. This data suggests that 

with the control program already in place, most of the selenium has been diverted from the 

wetland supply channels. Annual median selenium concentrations were near or below 2 μg/L, 

indicating that exceedances of the objective are generally minor compared with concentrations 

observed prior to use of the Grassland Bypass. 

 

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

Agatha Canal 44 38 39 2.9 26 53 31 23 14 4.4 3.6 1.2 1.2

Camp 13 Slough 43 43 43 59 54 55 64 56 58 32 57 1.6 1.6

CCID Main Canal @ 

Russel Blvd.

1.3 2.2 1.7 1.7 2.3 1.5 2 1.4 1.7 1.4 0.9 - 1.1

Santa Fe Canal @ Henry

Miller Road

25 30 - - - - - 5.3 1.8 1.7 1.8 2.1 1.5

San Luis Canal @ Henry

Miller Road

- - - - - - - 12 2.5 2.2 1.8 2 1.8

Table 1. Annual Median Selenium Concentrations 

A review of potential causes for the continued exceedances of the 2 μg/L objective is currently 

underway. Preliminary findings from this review suggest several possible causes for the 

elevated selenium concentrations, including: releases from the DPA during flooding, seepage 

from DPA gates and canals, elevated selenium concentrations in supply water, surface and 

subsurface agricultural drainage from areas outside of the DPA, and groundwater accretions 

(Chilcott, 2000). Most exceedances of the 2 μg/L objectives have been associated with flood 

flows, seepage from the DPA, subsurface agricultural drainage from outside the DPA, and 

supply water. 

Several efforts are currently underway in response to these findings. A stormwater management 

plan has been put in place by local agencies to reduce selenium loading during and following 

storm events and to increase monitoring during storm events. Other recent efforts have focused 

on further controlling seepage from the DPA and consolidating and rerouting agricultural 

discharges from outside the DPA. Continued monitoring will be used to assess the effectiveness 

of these actions. Regional Board staff will review this monitoring data and will assess other 

sources, including supply water and groundwater, if selenium objectives are still being exceeded. 

At this time, Regional Board staff believes that corrective action taken to minimize stormwater 

flow, to control subsurface drainage outside the DPA, and to prevent seepage from the DPA, will 

eliminate the largest exceedances. Further action may be needed to eliminate all exceedances, 

particularly if these exceedances are associated with elevated selenium concentrations in water 

supplied to the wetland supply channels from the Mendota Pool, the Delta Mendota Canal, and 

11 
other sources. Appropriate actions will be evaluated subsequent to the corrective actions 

currently underway. A load allocation for these possible sources is unnecessary at this time 

because the prohibition of subsurface drainage is sufficient to fully implement the TMDL and 

meet the objective. Should further corrective actions be necessary to reduce concentrations in 

the supply water, a TMDL will be established for the sources of this supply water. 

Margin of Safety 

The Clean Water Act requires that a margin of safety be included with TMDL development. 

Sources of uncertainty in this analysis include the following three assumptions: 

• there will be no future discharges of tile drainage to wetland channels 

• complete removal of tile drainage alone will result in the attainment of established water 

quality objectives 

• the numeric objective is fully protective of beneficial uses 

Load reductions needed to meet water quality objectives for this TMDL are achieved through the 

complete prohibition of discharge of tile drainage to wetland water supply channels unless the 2 

μg/L objective is being met. This prohibition has, in practice, resulted in a selenium load 

allocation of zero for tile drainage. As described in the Implementation Plan section, all tile 

drainage in the DPA is now discharged to a portion of the San Luis Drain. The mean annual 

selenium concentration of tile drainage discharged to the San Luis Drain was 62 μg/L in water 

year 1997, and 67 μg/L in 1998 (Chilcott et al, 2000). No future discharges of this tile drainage 

to wetland supply channels will be possible without removal of over 95 percent of the selenium

load. This level of selenium load reduction is not likely in the foreseeable future. An additional 

implicit margin of safety is provided with the 2 μg/L mean monthly selenium objective. As 

explained in the Numeric Target section above, this objective is fully protective of waterfowl. 

Complete removal of selenium load attributable to the major source (tile drainage) provides the 

maximum possible margin of safety. Revision of this TMDL or the margin of safety may be 

necessary if ongoing monitoring suggests that current and subsequent control measures are 

insufficient to reduce selenium concentrations in the wetland supply channels below 2 μg/L. 

Seasonal Variation 

The load allocation for subsurface drainage, expressed as a mean monthly water quality 

concentration of 2 μg/L, applies year round. As discussed in the Implementation Plan section, 

all tile drainage in the DPA is now discharged to a portion of the San Luis Drain. Discharge of

tile drainage into wetland supply channels has been eliminated during all seasons of the year 

including periods of low flow. As discussed in the Numeric Target section above, the 2 μg/L 

mean monthly selenium objective is fully protective of waterfowl during all seasons. 

Prior to the 1996 amendments to the Basin Plan, wetland water supplies had generally been 

protected seasonally during the fall, when seasonal wetlands that had been dry during the 

summer months were then filled.. Subsequent to this Basin Plan amendment, wetland water 

supplies may be delivered to wildlife refuges using the wetland water supply channels at any 

time during the year. A seasonal adjustment in the numeric target (the water quality objective) is 

therefore not needed. 

12 
Public Participation 

The Regional Board held workshops and public hearings for the 1996 Basin Plan Amendments 

for the Control of Agricultural Subsurface Drainage Discharges. The State Board also held 

approval hearings. Adoption of the Basin Plan Amendment in 1996 enabled implementation of 

the Grasslands Marshes TMDL; therefore, the public hearings held for the Amendment will be 

used to fulfill the public participation requirements of this TMDL. The administrative record for 

the workshops and public hearings held for the Amendment are on file at the Regional Board in 

five 3.5 inch binders. The index for the administrative record is included as Attachment 2. 

Letters received during the comment periods are included in Attachment 3 and responses to these 

letters and the comments made during the workshops are included in Attachment 4. 

This TMDL will be incorporated into the Regional Board’s Water Quality Control Plan during 

the next Basin Plan Update. The Grasslands Marshes will be taken off the Section 303(d) list 

during the next Section 303(d) update, pending full compliance with established selenium water 

quality objectives. 

References 

California Regional Water Quality Control Board, Central Valley Region, 1995, Staff Report on 

the Beneficial Uses Designations and Water Quality Criteria to be Use(d) for the Regulation of 

Agricultural Subsurface Drainage Discharges in the San Joaquin Basin (5c); June, 1995. 

California Regional Water Quality Control Board, Central Valley Region, 1996, Amendments to 

the Water Quality Control Plan for the Sacramento River and San Joaquin River Basins for the 

Control of Agricultural Subsurface Drainage Discharges; Staff Report; March, 1996. 

California Regional Water Quality Control Board, Central Valley Region, 1998a, Compilation of 

Electrical Conductivity, Boron, and Selenium Water Quality Data for the Grassland Watershed 

and San Joaquin River; May 1985-September 1995; February, 1998. 

California Regional Water Quality Control Board, Central Valley Region, 1998b, Fourth Edition 

of the Water Quality Control Plan (Basin Plan) for the Sacramento River and San Joaquin River 

Basins; September, 1998. 

Chilcott, J.E.,1988, Water Quality Survey of Tile Drainage Discharges in the San Joaquin River 

Basin, Regional Water Quality Control Board, Central Valley Region, Staff Report. ,October, 

1988. 

Chilcott, J.E., 2000, Review of Selenium Concentrations in Wetland Water Supply Channels in 

the Grassland Watershed, Regional Water Quality Control Board, Central Valley Region, Draft 

Staff Report. 

Chilcott, J.E., Grober, L., Vargas, A, Eppinger, J., 2000, Agricultural Drainage Contribution to 

Water Quality in the Grassland Watershed of Western Merced County, California: October1997 

to September 1998 (Water Year 1998), Draft Staff Report. 

13 
Attachment Note 

Attachments 1 through 4 are available upon request. Please contact Jennifer Heyd at (916) 464 – 

4735 or at jheyd@waterboards.ca.gov to request copies. 

14