Selenium TMDL for Salt Slough

Summary ofTMDL Action TMDL (Loading Capacity) 2 ppb Selenium as a monthlymean 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) ofthe Clean Water Actfor exceeding selenium water quality objectives. Itis one ofthe principal drainage arteries for the Grassland Watershed in the Western portion ofthe San JoaquinRiver Basin (Attachment 1 ). The soils in the watershed are derived from the marine sediments ofthe 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 irrigationnecessary for nearly all crops grown commercially in the watershed. Irrigation ofsoils derived from marine sediments leaches selenium into the shallow groundwater. Subsurface drainage isproduced 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 (DPA). The discharge ofsubsurface drainage from that area resulted in violations ofselenium 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 bemobilized through the food chain and causeboth acute and chronic toxicity to fish and wildlife. Defmmities and deaths ofaquatic birds have been linked to toxic concentrations ofselenium. Salt Slough discharges to the San Joaquin River upstream ofthe Merced Riverinflow near the northern boundary ofthe 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 JoaquinRiver (Attachment 2). There was concern that the elevated selenium concentrations in the subsurface drainage would causeproblems for the aquatic birds and wildlife that utilize the Grassland wetlands. Salt Sloughwas placed on the Clean Water Act Section303(d) list in 1990 for exceeding the selenium water quality objective established to protect waterfowl and otherwildlife uses. The Clean Water Act mandates that States establishTotal Maximum Daily Loads (TMDL) for water bodies on the Section 303(d) list. The remaining sections ofthis

### SaltSlough 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 ofAgricultural Subsurface Drainage. The amendment contained a selenium water quality objective for wetland water supply channels and Salt Slough. This objective, which was approved bythe State Board and the Office ofAdministrative 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 ofwaterfowl (California Regional Water Quality Control Board, Central ValleyRegion; 1996; pg. 61). Considerationwas given to translating the seleniumwater quality objective into a load limit, butwater quality datacollectedin Salt Slough in the late 1980's through early 1990's showed little change in concentration even inresponse to significant load reductions (California Regional Water Quality Control Board, Central ValleyRegion; 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 (CallforniaRegional 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 ofa monthly mean of2ppb. 

### Source Analysis Although selenium exists naturally in the soils ofthis watershed, some land use practices accelerate its movement to ground and surface waters
. The major components ofthe 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 ofselenium to Salt Slough. Selenium concentrations in tile drainage ranged from 25 to 500ppb, far above that for the other two components offlow in the Slough. TheRegional Board has conducted over a decade ofwater quality sampling at a site on Salt Slough upstream ofhistorical inputs from the DP A. This site represents background contributions to Salt Slough (i.e. including wetland drainage flows and agricultural return flows outside ofthe DPA). The median value ofselenium was 0.9 ppb and the mean was 1.1 ppb for over 200 samples collected (California Regional Water Quality Control Board, CentralValleyRegion ;February, 1998; pg. 171). Recent data also shows (attachment 4) that in the absence ofagricultural subsurface drainage water from the DPA, concentrations in Salt Slough are less than 2 ppb. This data confirms that "background" sources ofselenium in Salt Slough are not significant.

### SaltSlough TMDL Page3 Implementation 

### Plan In 1996, the Regional Board amended its BasinPlan for control ofagricultural subsurface drainage discharges. Tbis BasinPlan Amendmentprohibits discharge ofsubsurface drainage waterto 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 ofthe former San Luis Drainand awayfrom the Grassland wetlands on its way to the SanJoaquin River (Attachment 3). The other sources ofwater to Salt Slough are the wetlands discharge, surface drainage and groundwater accretions

. The selenium concentrations ofthose 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 DPA, remainbelow the numeric target. 

### Allocations Subsurface drainage is prohibited from discharge into Salt Sloughifit results in concentrations exceeding the water quality objective; therefore, the subsurface drainage allocation is expressed asthe water quality concentration of2 ppb as a monthlymean. As discussed inthe "Source Analysis" section above, load allocations for the surface drainage, wetlands discharge and groundwater accretions are notnecessary since they are not significant sources and are consistently found to be less than 2 ppb. 

### Performance Measures & 

### Feedback Monitoring conducted since the use ofthe Grasslands Bypass Project was initiated indicates that the diversion ofthe 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, butthe monthlymean water quality objective was met. During the El Nino storms inFebruary 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 BasinPlanby discharging subsurface drainage into the Grassland wetlands. The Water Authority through development ofa stormwatermanagementplanhas addressed these violations of the Basin Plan. The Regional Board has monitored selenium levels in waters ofthe Grassland Watershed since 1985. One monitoring stationis located in Salt Sough at Lander Avenue. Water quality data including selenjumconcentration is collected weekly at this station. Monitoring reports are published monthly and available on the Intemet for public review as part ofthe Grassland Bypass Project (www

.mp.usbr.gov/mp400/irrdrn/grasslnd).

### Salt Slough TMDL Page4 Regional Board staffwill review the monitoring data and considerrevising the TMDL or taking other appropriate action ifthe numeric target is notmet. Margin ofSafety and Seasonal Variation The CleanWater Act requires that a margin ofsafety beincluded with TMDL development. This TMDL incorporates a margin ofsafetybyprohibiting the discharge of subsurface drainage into Salt Slough ifit results in selenium concentrations exceeding the water quality objective. The removal ofagricultural subsurface drainage from Salt Slough (see discussion in Performance Measures and Feedback) provides the necessary margin ofsafety to ensure that thenumeric target is consistentlymet. In addition, the removal ofagricultural subsurface drainage originating from theDP 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 ofmore water for wetlanduses meant that such limited, seasonal protection was no longer protective of beneficial uses (California Regional Water Quality ControlBoard, 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 wildliferefuges 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 andpublic hearings for the 1996 Basin Plan Amendments for the Control ofAgricultural SubsurfaceDrainageDischarges. The State Board also held approval hearings. The adoption ofthe Basin Plan Amendment in 1996 enabled the implementation ofthe Salt Slough TMDL; therefore, the public hearings held for the Amendment fulfill the public participation requirements ofthis 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 Attachment7. This TMDLwill be incorporatedinto the Regional Board'sWater Quality Control Plan duringthe next Basin Plan Update, and Salt Slough will be taken offthe Section 303(d) list during the next Section 303(d) update following incorporation ofthe TMDL into the Basin Plan.SaltSlough 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. CaliforniaRegional Water Quality Control Board, Central ValleyRegion; 1996; Amendments to the Water Quality Control Plan for theSacramento River andSan Joaquin RiverBasins for the Control of Agricultural Subsurface Drainage Discharges; Staff Report; March, 1996. CaliforniaRegional Water Quality Control Boar d, CentralValleyRegion; 1998; Compilation of Electrical Conductivity, Boron, andSelenium Water Qualit y Data for the Grassland Watershed andSan Joaquin River; May 1985

-September 1995; February, 1998.Attachment 1: Grassland Watershed

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2: Drainage Project Area . . .. . . . . . . . . . .
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..Attachment 3: Use of Grasslands Bypass to Divert Subsurface Drainage

Delta Mud Slough Stanislaus River Tuolumne River Merced River **sc1~J** J, **~qf)ltjll** h.

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.({JJ:.>eJ · Nort iP' ' Grassland South Grassland Salt Slough Drainage Project Area Before September 1996 **I ~**  **~ ~**  **~ ~**  """ 0 Stanislaus River Tuolumne Uiver Merced River TG;

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4 Salt Slough Selenium Data

1 8 16 14 i 12 a 10 El · a 8 .. **~** 6 August 1996 to October 1998 Grassland Bypass went into use in September 1996Attachment Note Attachments 5 through 7 are available uponrequest. Please contact Jennifer Heyd at (916) 464

- 4735 or atjheyd@waterboards.ca.gov to request copies.