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Marine sedimentary rocks of the Coast Ranges contribute selenium 

to soil, surface water, and ground water in the western San Joaquin 

Valley, California. Irrigation funnels selenium into a network of subsurface drains and canals. Proposals to build a master drain (i.e., San Luis 

Drain) to discharge into the San Francisco Bay-Delta Estuary remain as 

controversial today as they were in the 1950s, when drainage outside 

the San Joaquin Valley was first considered. An existing 85-mile portion 

of the San Luis Drain was closed in 1986 after fish mortality and deformities in ducks, grebes and coots were discovered at Kesterson National 

Wildlife Refuge, the temporary terminus of the drain. A 28-mile portion 

of the drain now conveys drainage from 100,000 acres into the San 

Joaquin River and eventually into the Bay-Delta. If the San Luis Drain 

is extended directly to the Bay-Delta, as is now being proposed as an 

alternative to sustain agriculture, it could receive drainage from an estimated one-million acres of farmland affected by rising water tables and 

increasing salinity. In addition to agricultural sources, oil refineries also 

discharge selenium to the Bay-Delta, although those discharges have 

declined in recent years. To understand the effects of changing selenium 

inputs, scientists have developed the Bay-Delta Selenium Model.

U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2004-3091

August 2004

Linking Selenium Sources to Ecosystems: 

San Francisco Bay-Delta Model

The Bay-Delta Selenium Model is a systematic linked approach for 

conducting forecasts of selenium (Se) 

effects on aquatic food webs including 

higher trophic level animals such as birds 

and fish (Luoma and Presser, 2000). The 

methodology is presented as a new tool 

to predict ecological effects based on the 

major processes leading from loading 

through consumer organisms to predators. The approach is illustrated here and 

can be used with any set of explicitly 

stated conditions. Forecasts obtained 

from the Bay-Delta Selenium Model consider (1) loads, (2) water column concentrations, (3) speciation, (4) transformation to particulate forms, (5) particulate 

concentrations, (6) bioaccumulation, and 

(7) trophic transfer to predators, in addition to traditional considerations of water 

supply and drainage demand. 

Major inputs used to determine a 

composite input load are (1) agricultural drainage via direct discharge to the 

Bay-Delta; (2) effluents from the North 

Bay oil refineries; (3) San Joaquin River 

inflows which include agricultural drainage; and (4) Sacramento River inflows. 

Historical analyses of drainage needs 

were used to identify the most likely Se 

loads that would be carried outside the 

San Joaquin Valley via a conveyance 

discharging a constant load and conveyance via the San Joaquin River. Selenium 

concentrations and forms in the BayDelta are forecast, then those concentrations are used to model bioaccumulation 

in invertebrates, like clams. Transfer 

from clams to predators is estimated from 

field data, and Se effects on predators are 

then forecast from data in the existing 

literature. Data gathered during the years 

prior to refinery cleanup helped check the 

model and provide a baseline for determining site-specific effects. 

The Se load delivered to the Bay also 

depends on the amount of flow from the 

San Joaquin River that passes through 

the Delta and the amount recycled south 
through the Delta and Tracy pumping 

stations. The protocol for linking Se load 

and Se concentration under assigned 

hydraulic conditions and time duration is: 

composite freshwater endmember concentration 

= composite input load/composite input volume

The projections or outputs of the 

model are presented by season, where a 

season is defined as six months of predominantly high river inflows (December 

through May) or six months of predominantly low river inflows (June through 

November). Riverine influences also 

depend upon water year type. In combination with flow seasons, forecasts are 

made for critically dry years or for wet 

years. A wide range of agricultural Se 

input loads is possible, depending upon 

which management strategies are chosen. 

Potential ranges of annual input loads 

were derived assuming Se discharge was 

continuous and are presented here as 

discharged load per six months (i.e. onehalf the annual load under a constant rate 

of loading). 

The model allows consideration of 

many different drainage options (Luoma 

and Presser, 2000). In general, most 

options that meet existing demand for 

drainage appear to pose strong risks to 

the reproduction and survival of sensitive 

birds and fish. Threats to reproduction and 

survival of birds and fish are particularly 

severe during periods of low river flow. 

Vulnerable species include diving ducks, 

white sturgeon and Sacramento splittail.

Example Selenium Forecast for the 

San Francisco Bay-Delta

An example forecast is shown (opposite page) for a dry year during the low 

flow season and with conveyance through 

a San Luis Drain extension directly to the 

Bay-Delta. The dry years and low flow 

seasons will be the ecological bottleneck (the times that will drive impacts) 

with regard to Se. Surf scoter, greater 

and lesser scaup, and white sturgeon are 

present in the estuary during the low flow 

season and leave before high flows subside. Animals preparing for reproduction, 

or for which early life stages develop 

in September through March, will be 

vulnerable. 

The example forecast shows Se 

concentrations for each media forecast 

(water, particulate, invertebrate, predator), along with guidelines or concentrations where biotic effects are expected 

(Luoma and Presser, 2000). The forecasts show conditions at the head of 

the estuary for a range of inputs (6,800; 

18,700; or 44,880 pounds Se released 

per six months) from the San Luis Drain 

and for a small amount of San Joaquin 

River inflow to the Bay. The input from 

oil refineries is assumed constant at 680 

pounds Se per six months. We assume a 

partitioning coefficient (Kd) of 3 x 103

typical of Bay-Delta shallow sediment 

conditions and a generic bivalve assimilation efficiency (AE) of 0.55 to reflect 

particulate transformation and bioaccumulation potential from a sediment with a 

mixture of forms. 

In general, the lowest guideline values 

for waterborne, particulate, dietary, and 

predator tissue Se are exceeded in every 

forecast considered in the figure where 

the input is from a proposed San Luis 

Drain extension. The highest guidelines from the literature are exceeded in 

all forecasts except that for the lowest 

load considered (6,800 pounds per six 

months) where exceedance does occur for 

particulates, white sturgeon, and greater 

and lesser scaup liver. If a San Luis Drain 

extension is constructed and if it discharges the quantities of Se predicted in 

our simulation scenarios, during low flow 

seasons, a high hazard seems likely, with 

threats to fish and bird species under the 

load scenarios tested here. 

Forecast simulations also were conducted for loading via the San Joaquin 

River (Luoma and Presser, 2000). If 

careful management of an out-of-valley 

resolution to the drainage problem results 

in discharges of Se via the San Joaquin 

River to the Bay-Delta (for example at 

3,500 pounds per six months), the risks 

are less than those forecast for a San Luis 

Drain extension. Under the low flow 

season of a dry year scenario, the Se concentrations forecast in prey and predators 

are similar to Se concentrations observed 

during conditions in the Bay-Delta prior 

to refinery cleanup. Selenium contamination documented from 1986 to 1996 

was sufficient to threaten reproduction in 

key species within the Bay-Delta estuary 

ecosystems and resulted in human health 

advisories being posted for consumption 

of those species. 

The San Luis Drain transports selenium-laden agricltural drainage from the western San Joaquin 

Valley. Agricultural drainage waterways are posted with a state fish and waterfowl consumption 

advisory because of selenium.
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The Bay-Delta is probably best 

suited for site-specific Se guidelines and 

the Bay-Delta Selenium Model could 

provide a framework for developing 

new protective criteria. If water quality 

criteria are to be employed in managing 

Se inputs, then consideration should be 

given to the elevated Se concentrations 

currently occurring in clams and fish of 

the Bay-Delta, even though waterborne 

Se concentrations in the Bay-Delta are 

less than recommended criteria (Luoma 

and Presser, 2000).

Monitoring Recommendations

A long-term monitoring program is 

crucial to understanding the fate and 

impact of management changes for 

protection of ecosystems receiving Se 

discharges. Monitoring, as conceptualized below, would sample critical 

environmental components at a frequency 

relevant to each process to determine 

trends in Se contamination or changes in 

processes that determine fate and effects 

of Se (Luoma and Presser, 2000).

 A linked or combined approach 

would include all considerations that 

cause systems to respond differently to Se 

contamination. 

• In any site-specific analysis of Se 

impacts, it is important that “site” be 

defined by all hydrologically relevant 

components. Hydrologic models would 

serve as a basis for developing this 

infrastructure. Specifically, the Bay-Delta 

ecosystem is connected to the San Joaquin River ecosystem. The Delta is the 

transition zone between the Bay and the 

largest potential source of Se (i.e., agricultural drainage from the San Joaquin 

Valley via either a dedicated drain or the 

San Joaquin River). 

 • The vulnerability of downstream 

water bodies should be considered when 

evaluating upstream source waters. Toxicity problems may not appear equally 

in all “site” components because some 

components may be more sensitive than 

others. For example, the San Joaquin 

River, as a flowing water system may be 

less sensitive to Se effects (especially if 

selenate dominates inputs) than adjacent 

wetlands, the Delta or the Bay, where residence times and biogeochemical transformations of selenate are more likely. 

• Any analysis of Se effects must 

take into account the influences of variable river inflows. Selenium impacts in 

the Bay-Delta could increase if water 

diversions increase or if San Joaquin 

River inflows increase with concomitant increases in Se loading (i.e. the Se 

issue and the water management issues 

are tightly linked). The most significant 

impacts of irrigation drainage disposal 

into the Bay-Delta will occur during low 

flow seasons and especially during lowriver flow conditions in dry or critically 

dry years. Dry or critically dry years 

have occurred in 31 of the past 92 years, 

with critically dry years comprising 15 of 

those years. 

• Establishing a mass balance or 

budget of Se through the estuary is 

crucial because internal (oil refinery) and 

external (agricultural drainage) sources 

of Se are changing as a result of management. At a minimum, a mechanism for 

tracking Se loading via oil refineries and 

the San Joaquin River is needed based on 

San Joaquin River, Sacramento River, and 

Bay-Delta hydrodynamics. Monitoring 

programs need to measure the on-going 

status of the system in terms of inputs, 

storage in sediment, through-put south via 

the Delta-Mendota Canal and California 

Aqueduct, and through-put north to the 

Bay. 

• Storms and high-flow years will be 

times of increased regional discharge of 

San Joaquin Valley drainage containing 

high concentrations and loads of Se. Simulations predict if the precipitation-dependence of agricultural Se inflows is not 

recognized, violations of upstream water 

quality criteria and load targets could 

result on a recurring basis. The long-term 

effects of such occurrences on wetlands, 

wetland channels, the Delta and the Bay 

need to be better understood. The possibilities of long-term storage after such 

conditions and the efficiency of bioaccumulation during varying conditions of 

flow should be studied. 

• Multiple-media guidelines, in combination, provide a feasible reference point 

for monitoring. The critical media defined 

here are water, particulate material, and 

prey and predator tissue. Monitoring plan 

components necessary for a mass balance 

approach include source loads; concentrations of dissolved Se and suspended 
Se; Se speciation in water and sediment; 

assimilation capacities of indicator food 

chain organisms; and Se concentrations 

in tissues of prey and predator species. 

• Determination of transformation 

efficiency and processes that determine 

Kds (distribution or partitioning coefficients) of Se in the Bay-Delta and San 

Joaquin River are crucial to relate loads 

to bioaccumulation, rates of transfer, and 

effects. Trace elements sequestered in 

bed sediments and in algal mats would 

be a part of recommended mass balance 

considerations. 

• Invertebrates may be the optimal 

indicator to use in monitoring Se because 

they are practical to sample and are 

most closely linked to predator exposure. Knowledge of optimal indicators 

in the Bay-Delta and San Joaquin River 

are necessary to fully explore feeding 

relations. Resultant correlations with Se 

bioaccumulation in food webs are a part 

of this process. 

• Determination of food web interrelations would help identify the most 

vulnerable species. Specific protocols 

that include life cycles of vulnerable 

predators including migratory and mobile 

species would then document Se effects 

for the species most threatened.

• If management and regulatory 

measures to restore the San Joaquin River 

ecological resources to their former level 

of abundance are to be effective, then 

the biogeochemistry of Se, ecological 

processes, and hydrodynamics in this 

system must be further investigated and 

understood. Adaptive management and 

monitoring for the San Joaquin River 

should be based on the biotransfer of Se 

and consideration of the environmental 

stresses imposed by present degraded 

conditions. Current discharge of agricultural drainage to the San Joaquin River 

via a 28-mile section of the San Luis 

Drain is under monthly and yearly load 

limitations. To determine whether load 

manipulation actually protects vulnerable 

predators, the following monitoring plan 

components are needed:

 1. Identification of vulnerable food 

webs

 2. Identification of sites most at risk 

from impacts of agricultural drainage

 3. Analysis of effects on predators that 

includes food web components

 4. Identification of elevated risk periods for effects based on hydrodynamics 

 5. Calculation of protective loads/concentrations based on bioaccumulation 

in prey

• In view of the analysis of the existing 

Se reservoir in the San Joaquin Valley, consideration of the degradation of groundwater aquifers needs to be a factor in 

management scenarios. Short-term management that results in more storage than 

leaching will result in more degradation 

of aquifers. Mass balance considerations 

should include a “storage” term, not only 

input and output terms. Monitoring and 

assessment of storage may help determine 

if treating discharge on an annual basis 

will suffice to manage the current regional 

imbalance of water, salt, and Se. 

• Treatment may also be important in 

determining source load impacts. Treatment technologies applied to source waters 

may affect both the concentration and 

speciation of the effluent. For example, a 

treatment process could decrease the concentration of Se in the influent, but result 

in enhanced Se food chain concentrations 

if speciation in the effluent changes to 

increase the efficiency of uptake. 

Theresa S. Presser and Samuel N. Luoma

 National Research Program

 Water Resources Division

 Menlo Park, CA 94025

Summary of Selenium Issues in California

• Accurate forecasting of the environmental fate of selenium (Se) in the San 

Francisco Bay-Delta Estuary is crucial because of the element’s effect on 

reproduction in aquatic birds and fish. 

• Internal and external sources of Se to the estuary are changing due to 

water management changes related to the restoration of the San Joaquin 

River and Bay-Delta. 

• Current projects allow discharge to the estuary of saline subsurface 

waters from the western San Joaquin Valley via the San Joaquin River. 

Direct conveyance of agricultural drainage to the estuary could occur if an 

extension of the San Luis Drain is built and discharge permits approved. 

• The U.S. Environmental Protection Agency is re-evaluating Se standards 

for the protection of fish and wildlife. The U.S. Fish and Wildlife Service 

and the National Marine Fisheries Service through the California Toxics 

Rule are asking for more stringent Se criteria. 

• Selenium concentrations were less than water quality guidelines in both 

the Delta and the Bay in the latest surveys in 1996. Nevertheless, Se in the 

food web was sufficient to be a threat to some species and a concern to 

human health if those species were consumed.

Cooperators:

1. U.S. Environmental Protection Agency 

 (Region 9, Water Division)

2. Contra Costa County 

3. Contra Costa Water District

Reference and for additional information:

Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of A 

Proposed San Luis Drain Extension, by Samuel 

N. Luoma and Theresa S. Presser, U.S. Geological 

Survey Open-File Report 00-416.

http://water.usgs.gov/pubs/ofr00-416/

or contact: tpresser@usgs.gov

 snluoma@usgs.gov

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