Section 319
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Grasslands Bypass Project Reduces Selenium in the San Joaquin Basin
\ a i , i i- i i Farmland irrigation contributed to selenium exceedances in sub-
Waterbodies Improved Sllrface drainage in the Grasslands Watershed, located in the san
Joaquin River (SJR) Basin. As a result, the Grasslands Watershed marshes and a portion of the SJR
were placed on California's Clean Water Act (CWA) section 303(d) list of impaired waters in 1988. The
listing of two local tributaries, Mud Slough (northern reach) and Salt Slough, followed in 1990. The
Grasslands Bypass Project implemented agricultural best management practices (BMPs) and areawide
measures to reroute drainage and reduce the total selenium loading. These efforts led to significant
selenium load reductions, which in turn resulted in the de-listing of Salt Slough (10 miles) in 2008 and
three segments of the SJR (totaling 40.4 miles) in 2010.
Problem
Bordering the SJR in California's Central Valley,
the 370,000-acre Grasslands Watershed (Figure 1)
contains the largest freshwater wetland ecosystem
in California. The watershed also includes approxi-
mately 97,000 acres of irrigated farmland. Irrigating
the area's selenium- and salt-rich soils allowed sele-
nium to leach into shallow groundwater. To protect
their crops from this salty groundwater, farmers
installed tile drain systems to lower the water table
below the root zone. Subsurface drainage from this
agricultural area increased selenium concentrations
in wetland supply channels and other downstream
water bodies.
Selenium is a highly bioaccumulative trace ele-
ment that, under certain conditions, can move
through the food chain and cause acute and chronic
toxicity to fish and wildlife. In 1988, 8,224 acres
of Grasslands marshes were listed on California's
CWA section 303(d) list of impaired waters because
water samples routinely exceeded the U.S. Fish
and Wildlife Service's (USFWS) recommended
selenium criterion of 2.0 micrograms per liter (/jg/L)
to protect waterfowl and other wildlife uses. The
lower SJR downstream from the subsurface drain-
age was also included on the state's 1988 CWA
section 303(d) list because water samples rou-
tinely exceeded the U.S. Environmental Protection
Agency's (USEPA) total selenium criterion of 5.0
/jg/L. Salt Slough and Mud Slough were placed on
the 1990 CWA section 303(d) list for exceeding the
selenium water quality objective established to
protect waterfowl and other wildlife uses. In 1999
and 2000, respectively, selenium total maximum
daily loads (TMDLs) for Salt Slough and Grasslands
Watershed marshes were set at a monthly mean of
2.0 /Jg/L to protect waterfowl and other wildlife. In
San Joaquin River
near Vernalis and
the Delta
Stanislaus River
Tuolumne River
Merced River
Grasslands
Watershed
Mud Slough
Salt Slough
Drainage Project
Area
Mendota
Figure 1. The Grasslands Watershed is in the San Joaquin Basin.
2001 selenium TMDLs for the lower SJR and Mud
Slough were set at a four-day average of 5.0/jg/L.
Project Highlights
In 1996 the Central Valley Regional Water Quality
Control Board (Regional Water Board) adopted an
amendment to the Central Valley Quality Control
Plan for the Control of Subsurface Agricultural
Drainage, which emphasized managing irrigation
in the Grasslands Watershed agricultural area. The
amendment included the Grasslands Bypass Project
(GBP), which was designed to:
Reroute agricultural subsurface drainage water
around wetlands to the SJR via the San Luis
Drain, a concrete-lined bypass, and a six-mile
segment of Mud Slough to attain water quality
objectives in the wetland supply channels
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Improve management practices to achieve
selenium objectives in the mainstem of the SJR
below the Merced River
Achieve short-term load reductions by October
2010, and prohibit discharges not meeting
objectives by 2019, to bring Mud Slough and a
lower flow portion of the SJR (above the Merced
confluence) into compliance.
The U.S. Bureau of Reclamation (USBR) and the San
Luis and Delta-Mendota Water Authority developed
a use agreement that states that the San Luis Drain
will be closed if annual load targets are exceeded
by more than 20 percent and no acceptable expla-
nation is provided. The Regional Water Board
adopted the three selenium TMDLs, developed a
Waste Discharge Requirement permit that required
Grasslands area farmers (known as the GAF) to
reduce the discharge of selenium below pre-GBP
levels, and established a plan to guide coordinated
implementation of these requirements.
California's Nonpoint Source Program provided
funding to develop a selenium trading program,
which established collective load limits for selenium
discharge at the San Luis Drain outlet and fees for
exceeding the limits. Over the past 15 years, the
GAF have implemented various BMPs to meet the
selenium targets, including changing crops, improv-
ing irrigation efficiency, reusing water and control-
ling discharge timing.
Results
Between 1998 and 2009, BMPs implemented by the
GAF prevented more than 22,300 pounds of sele-
nium and 80,735 acre-feet of drainage from discharg-
ing to waters. These load reductions brought Salt
Slough into compliance with the 2.0/Jg/L selenium
monthly mean objective (Figure 2), and reduced
selenium loading in the lower SJR below the four-day
average of 5.0 jug/L. As a result, California removed
several water bodies from its impaired waters list,
including Salt Slough (10 miles) in 2008 and three
segments (a combined 40.4 miles) of the SJR
Merced River to Tuolumne River (29 miles), Tuolumne
River to Stanislaus River (8.4 miles), and Stanislaus
River to the Delta Boundary (3 miles)in 2010.
Although the GBP has made significant progress,
additional work is required to achieve the ultimate
project goal of zero discharge. As scientific under-
standing of selenium problems improves, selenium
water quality standards are being revised to better
support beneficial uses.
Se Concentration at Site F (ng/L)
- 2 ng/L Monthly Mean Objective
Grasslands Bypass Project
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