Selenium TMDL for Salt Slough 

Summary ofTMDL Action 

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

Load Allocation Subsurface Drainage 2 ppb Selenium as a monthly mean 

from the Drainage Problem Area 

Waste Load Allocation 0 lbs Selenium 

(no NPDES sources) 

Problem Description 

Salt Slough is listed in accordance with Section 303(d) of the Clean Water Act for 

exceeding selenium water quality objectives. It is one of the principal drainage arteries 

for the Grassland Watershed in the Western portion of the San Joaquin River Basin 

(Attachment 1 ). The soils in the watershed are derived from the marine sediments of the 

Coast Range, which are high in salts and selenium. Major land uses in the watershed 

include agriculture and wildlife refuge wetlands. There are no NPDES permitted sources 

that discharge to Salt Slough. 

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 ofthe Grassland 

Watershed that generates subsurface drainage has been designated as the Drainage Project 

Area (DP A). The discharge of subsurface drainage from that area resulted in violations 

of selenium water quality objectives in Salt Slough and other water bodies within the 

watershed and downstream. Selenium is a bioaccumulative trace element that, under 

certain conditions, can be mobilized through the food chain and cause both acute and 

chronic toxicity to fish and wildlife. Defmmities and deaths of aquatic birds have been 

linked to toxic concentrations of selenium. 

Salt Slough discharges to the San Joaquin River upstream of the Merced River inflow 

near the northern boundary of the Grassland Watershed. Salt Slough has undergone 

dramatic changes in hydrology and water quality due to agricultural and wetland 

development. Prior to September 1996, subsurface drainage from the DPA flowed 

through the Grassland wetlands and Salt Slough on its way to the San Joaquin River 

(Attachment 2). There was concern that the elevated selenium concentrations in the 

subsurface drainage would cause problems for the aquatic birds and wildlife that utilize 

the Grassland wetlands. Salt Slough was placed on the Clean Water Act Section 303(d) 

list in 1990 for exceeding the selenium water quality objective established to protect 

waterfowl and other wildlife uses. 

The Clean Water Act mandates that States establish Total Maximum Daily Loads 

(TMDL) for water bodies on the Section 303(d) list. The remaining sections of this 
Salt Slough TMDL Page2 

report describe the required TMDL elements developed for Salt Slough by the California 

Regional Water Quality Control Board, Central Valley Region (Regional Board). 

Numeric Target 

In 1996, the Regional Board adopted an amendment to the Water Quality Control Plan for 

the San Joaquin River Basin (Basin Plan) 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 of2 ppb. 

It was made more stringent than the selenium objective for other water bodies to offer 

added protection to the waterfowl using the wetlands. Based on a review ofthe available 

scientific literature, the Regional Board determined that a 2 ppb monthly mean selenium 

objective would be protective of waterfowl (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 Salt Slough 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 

(Callfornia 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 at protecting beneficial uses and achieving water quality improvements. The 

numeric target for the Salt Slough TMDL is the adopted Basin Plan selenium water 

quality objective of a monthly mean of2 ppb. 

Source Analysis 

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

accelerate its movement to ground and surface waters. The major components of the 

historical flow in Salt Slough are subsurface and surface drainage from the DP A and 

wetlands discharge. Subsurface drainage, specifically from the tile drains in the DPA, is 

the most significant source of selenium to Salt Slough. Selenium concentrations in tile 

drainage ranged from 25 to 500 ppb, far above that for the other two components of flow 

in the Slough. The Regional Board has conducted over a decade of water quality 

sampling at a site on Salt Slough upstream of historical inputs from the DP A. This site 

represents background contributions to Salt Slough (i.e. including wetland drainage flows 

and agricultural return flows outside of the DPA). The median value of selenium was 0.9 

ppb and the mean was 1.1 ppb for over 200 samples collected (California Regional Water 

Quality Control Board, Central Valley Region; February, 1998; pg. 171). Recent data 

also shows (attachment 4) that in the absence of agricultural subsurface drainage water 

from the DP A, concentrations in Salt Slough are less than 2 ppb. This data confirms 

that "background" sources of selenium in Salt Slough are not significant. 
Salt Slough TMDL Page3 

Implementation Plan 

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

drainage discharges. Tbis Basin Plan Amendment prohibits discharge of subsurface 

drainage water to Salt Slough and the Grassland wetlands if it results in concentrations 

exceeding the water quality objective, and therefore eliminates the largest loading of 

selenium to Salt Slough. Since September 1996, tile drainage from the DPA has been 

rerouted through the Grasslands Bypass Structure, which is a portion of the former San 

Luis Drain and away from the Grassland wetlands on its way to the San Joaquin River 

(Attachment 3). 

The other sources of water to Salt Slough are the wetlands discharge, surface drainage 

and groundwater accretions. The selenium concentrations of those sources are commonly 

less than 2 ppb, as discussed above; therefore, no implementation provisions are 

necessary to ensure sources, other than agricultural subsurface drainage from the DP A, 

remain below the numeric target. 

Allocations 

Subsurface drainage is prohibited from discharge into Salt Slough if it results in 

concentrations exceeding the water quality objective; therefore, the subsurface drainage 

allocation is expressed as the water quality concentration of 2 ppb as a monthly mean. 

As discussed in the "Source Analysis" section above, load allocations for the surface 

drainage, wetlands discharge and groundwater accretions are not necessary since they are 

not significant sources and are consistently found to be less than 2 ppb. 

Performance Measures & Feedback 

Monitoring conducted since the use of the Grasslands Bypass Project was initiated 

indicates that the diversion of the tile drainage away from the Grassland wetlands and 

Salt Slough has enabled Salt Slough to attain the selenium water quality objective except 

during the recent El Nino storm events (Attachment 4). In January 1997, there was one 

sample with a selenium concentration above 2 ppb, but the monthly mean water quality 

objective was met. During the El Nino storms in February and March of 1998, the water 

quality objective was exceeded. During this period, the San Luis Delta-Mendota Water 

Authority was not able to contain the flood flows and violated the Basin Plan by 

discharging subsurface drainage into the Grassland wetlands. The Water Authority 

through development of a stormwater management plan has addressed these violations of 

the Basin Plan. 

The Regional Board has monitored selenium levels in waters of the Grassland Watershed 

since 1985. One monitoring station is located in Salt Sough at Lander Avenue. Water 

quality data including selenjum concentration is collected weekly at this station. 

Monitoring reports are published monthly and available on the Intemet for public review 

as part of the Grassland Bypass Project (www.mp.usbr.gov/mp400/irrdrn/grasslnd). 
Salt Slough TMDL Page4 

Regional Board staff will review the monitoring data and consider revising the TMDL or 

taking other appropriate action ifthe numeric target is not met. 

Margin of Safety and Seasonal Variation 

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

development. This TMDL incorporates a margin of safety by prohibiting the discharge of 

subsurface drainage into Salt Slough if it results in selenium concentrations exceeding the 

water quality objective. The removal of agricultural subsurface drainage from Salt 

Slough (see discussion in Performance Measures and Feedback) provides the necessary 

margin of safety to ensure that the numeric target is consistently met. In addition, the 

removal of agricultural subsurface drainage originating from the DP A should result in 

average conditions in Salt Slough that are well below the numeric target (see discussion 

under Source Analysis). 

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

been protected seasonally during the fall flood-up. The availability of more water for 

wetland uses meant that such limited, seasonal protection was no longer protective of 

beneficial uses (California Regional Water Quality Control Board, Central Valley 

Region; 1996; pp. 9-ll). Since waterfowl are most sensitive to selenium and wetland 

water supplies may now be delivered from Salt Slough to wildlife refuges at any time 

during the year, there is no seasonal adjustment in the numeric target (which is the water 

quality objective). 

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. The adoption of the Basin Plan Amendment in 1996 

enabled the implementation of the Salt Slough TMDL; therefore, the public hearings held 

for the Amendment fulfill the public participation requirements of this TMDL. The 

administrative record for the workshops and public hearings held for the Amendment are 

on ftle at the Regional Board in five 3.5-inch binders. The index for the administrative 

record is included as Attachment 5. The letters received during the comment periods are 

included as Attachment 6; the responses to the letters and the comments made during the 

workshops are included as Attachment 7. 

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

during the next Basin Plan Update, and Salt Slough will be taken off the Section 303(d) 

list during the next Section 303(d) update following incorporation of the TMDL into the 

Basin Plan. 
Salt Slough TMDL Page5 

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; 1998; 

Compilation of Electrical Conductivity, Boron, and Selenium Water Quality Data for the 

Grassland Watershed and San Joaquin River; May 1985-September 1995; February, 

1998. 
Attachment 1: Grassland Watershe

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Attachment 3: Use of Grasslands Bypass to Divert Subsurfa

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Tuolumne River 

Merced River 

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Attachment 4 

lough Selenium Data 

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August 1996 to October 1998 

Grassland Bypass went into use in September 1996 
Attachment Note 

Attachments 5 through 7 are available upon request. Please contact Jennifer Heyd at 

(916) 464 - 4735 or at jheyd@waterboards.ca.gov to request copies.