Open File Report 00-416

By Samuel N. Luoma and Theresa S. Presser


Note: This report has been superseded by USGS Professional Paper 1646

The full report is available in pdf.  Links to the pdf.




Generic Selenium Issues

Selenium Issues in the Bay-Delta




Inputs of Selenium from Agriculture in the Western San Joaquin Valley

The problem

Prediction of long-term reservoir: how sustainable is discharge?

Selenium concentrations in source waters

Drainage management

Forecasting loads of selenium: general consideratons

How to determine load

Characteristics of agricultural subareas

Development of forecasts

Forecasting selenium loadings using the sum of data from all subareas

Forecasting selenium loadings using data from individual subareas

Loading scenarios

Scenarios based on the capacity of an extension of the San Luis Drain

The San Joaquin River as a conveyance facility, a de facto drain


Inputs of Selenium from Oil Refineries

Inputs of Selenium from the Sacramento River




Interpreting Effects of Source Water Se Loads on Receiving Water Se Concentrations

Existing Concentrations in the Bay-Delta

Regional baseline

Concentrations observed in the Bay-Delta



Processes Affecting Particulate Selenium



Range of distribution coefficients (Kd’s)

Sources of Particulate Selenium in the Bay-Delta

Particulate selenium in the San Joaquin River

Particulate selenium in the Delta

Particulate selenium in existing portion of the San Luis Drain

Sedimentary selenium in Suisun Bay and San Pablo Bay

Suspended particulate selenium in Suisun Bay and San Pablo Bay




Selenium in Invertebrates from the Bay-Delta

Summary of Selenium in Invertebrates from the Bay-Delta

Modeling Selenium Bioaccumulation in the Bay-Delta: DynBaM


Dietary Exposure

Existing Selenium Concentrations in Tissues of Birds and Fish in the Bay-Delta


Relating Selenium Concentrations in Food (Prey) to Effects in Predators



Relating Selenium Concentrations in Tissue to Effects in Predators



Comparison to Selenium Hazard Index


Forecasts of Composite Input Loads and Volumes to the Bay-Delta

Forecasts of Waterborne Selenium Concentrations

Calculating composite selenium input (or freshwater endmember) concentrations

Comparing forecasted selenium concentrations to observed conditions prior to refinery cleanup

Forecasting influence of a San Luis Drain extension: seasonal waterborne selenium concentrations

Forecasting influence of selenium release via the San Joaquin River: seasonal waterborne selenium concentrations

Monthly waterborne selenium concentrations

Summary of forecasts

Forecasts of Speciation and Transformation

Defining speciation, transformation, and bioavailability

Comparison to Bay-Delta conditions prior to refinery cleanup

Forecasts of Particulate Selenium Concentrations

Sediment quality guidelines

Particulate selenium concentrations (all concentrations are in µg Se/g dry weight, dw)

Cumulative summary

Other possible scenarios

Forecasts of Bioaccumulation in Consumer Organisms

Calculating bioaccumulation in a generic bivalve (modeling)

Comparing model predictions to Bay-Delta conditions prior to refinery cleanup

Bivalves as food for predators

Generic bivalve selenium concentrations (i.e., contamination of prey)

Effects on predators based on selenium concentrations in food

Forecast of Selenium Concentrations in Tissues of Predators

Choice of predators

Relation of selenium concentrations in bivalves to selenium concentrations in predators

Selenium concentrations in predators


Cumulative Impacts on the Bay-Delta

Extent and Sustainability of Agricultural Discharge from the San Joaquin Valley

Implications and Monitoring Needs






During the next few years, federal and state agencies may be required to evaluate proposals and discharge permits that could significantly change selenium (Se) inputs to the San Francisco Bay-Delta Estuary (Bay-Delta), particularly in the North Bay (i.e., Suisun Bay and San Pablo Bay). These decisions may include discharge requirements for an extension of the San Luis Drain (SLD) to the estuary to convey subsurface agricultural drainage from the western San Joaquin Valley (SJV), a renewal of an agreement to allow the existing portion of the SLD to convey subsurface agricultural drainage to a tributary of the San Joaquin River (SJR) (coincident with changes in flow patterns of the lower SJR), and refinements to promulgated Se criteria for the protection of aquatic life for the estuary.

Understanding the biotransfer of Se is essential to evaluating the fate and impact of proposed changes in Se discharges to the Bay-Delta. However, past monitoring programs have not addressed the specific protocols necessary for an element that bioaccumulates. Confusion about Se threats in the past have stemmed from failure to consider the full complexity of the processes that result in Se toxicity. Past studies show that predators are more at risk from Se contamination than their prey, making it difficult to use traditional methods to predict risk from environmental concentrations alone. In this report, we employ a novel procedure to model the fate of Se under different, potentially realistic load scenarios from the SJV. For each potential load, we progressively forecast the resulting environmental concentrations, speciation, transformation to particulate form, bioaccumulation by invertebrates, trophic transfer to predators, and effects in those predators. Enough is known to establish a first order understanding of effects should Se be discharged directly into the North Bay via a conveyance such as the SLD.

Our approach uses 1) existing knowledge concerning the biogeochemical reactions of Se (e.g., speciation, partitioning between dissolved and particulate forms, and bivalve assimilation efficiency) and 2) site-specific data mainly from 1986 to 1996 on clams and bottom-feeding fish and birds. Forecasts of Se loading from oil refineries and agricultural drainage from the SJV enable the calculation of a composite freshwater endmember Se concentration at the head of the estuary and at Carquinez Strait as a foundation for modeling. Our analysis of effects also takes into account the mode of conveyance for agricultural drainage (i.e., the SLD or SJR). The effects of variable flows on a seasonal or monthly basis from the Sacramento River and SJR are also considered.

The results of our forecasts for external SJV watershed sources of Se mirror predictions made since 1955 of a worsening salt (and by inference, Se) buildup exacerbated by the arid climate and irrigation for agricultural use. We show that the reservoir of Se in the SJV is sufficient to provide loading at an annual rate of approximately 42,500 pounds (lbs) of Se to a Bay-Delta disposal point for 63 to 304 years at the lower range of our projections, even if influx of Se from the California Coast Ranges could be curtailed. Disposal of wastewaters on an annual basis outside of the SJV may slow the degradation of valley resources, but drainage alone cannot alleviate the salt and Se buildup in the SJV, at least within a century.

Our forecasts show the different proportions of Se loading to the Bay-Delta. Oil refinery loads from 1986 to 1992 ranged from 11 to 15 lbs Se per day; with treatment and cleanup, loads decreased to 3 lbs Se per day in 1999. In contrast, SJV agricultural drainage loads could range from of 45 to 117 lbs Se per day across a set of reasonable conditions. Components of this valley-wide load include five source subareas (i.e., Grassland, Westlands, Tulare, Kern, and Northern) based on water and drainage management. Loads vary per subarea mainly because of proximity of the subarea to geologic sources and irrigation history. Loads from the Sacramento River, depending on flow conditions, range from 0.8 to 10 lbs Se per day.

A consistent picture of ecological risk emerges for the Bay-Delta based on concurrent lines of evidence. The threat to the estuary is greatest during low flows and dry years. Where Se undergoes reactions typical of low flow or longer residence time, highly problematic bioaccumulation in prey (food) is forecast to result. The Bay-Delta predators—surf scoter, greater and lesser scaup, and white sturgeon—appear to be most at risk because they feed on filter-feeding bivalves. Recent findings add Sacramento splittail to that list. During the low flow season of dry years, the lower range of proposed protective guidelines for waterborne, particulate, dietary, and predator tissue Se is exceeded under the most likely forecast of Se inputs from a proposed SLD extension. Also under low flow conditions, the upper range of guidelines (i.e., high certainty of adverse effects) is exceeded in all instances except at the lowest load considered. High flows afford some protection in the forecast SJR scenarios under certain conditions. However, meeting a combined goal of releasing a specific load during maximum flows and keeping Se concentrations below a certain objective to protect against bioaccumulation may not always be attainable. Management of the SJR on a constant concentration basis could also create problematic bioaccumulation during a wet year, especially during the low flow season, because high flows translate to high loads that are not always offset by seasonal inflows.

Prior to refinery cleanup, Se contamination was sufficient to threaten reproduction in key species within the Bay-Delta ecosystems and human health advisories were posted based on Se concentrations in livers of diving ducks. During this time, Se concentrations in the Bay-Delta were well below the most stringent water quality criteria. Enhanced biogeochemical transformations to bioavailable particulate Se and efficient uptake by bivalves and then predators characterized the system. If these biogeochemical conditions continue to prevail, the forecasts suggest the risk of adverse effects will be difficult to eliminate under an out-of-valley resolution to the Se problem.

The forecasts for Se loading present a new tool to evaluate ecological effects based upon the major processes leading from loads through consumer organisms to predators. It is a feasible approach for site-specific analysis and could provide a framework for developing new protective criteria. We conclude that credible protective criteria should be based on 1) contaminant concentrations in sources, such as particulate material, that most influence bioavailability and 2) concentrations in media and organisms relevant to vulnerable food webs. Existing criteria for water, particulate material, and tissue of prey and predators should be used in combination to evaluate risk or hazard. Bivalves appear to be the most sensitive indicator of Se contamination in the Bay-Delta.

The text and graphics are presented here in pdf format (print quality): The full report is 6MB.


For faster downloading:

Main Report (784 KB)

Figures and Tables (1.1 MB)

Appendices A-F (2 MB)


If you have Adobe Acrobat Reader installed on your computer, you may view and/or print the PDF version of this report. If you do not have Acrobat Reader, you may download it here.


Users with visual disabilities can visit this site for conversion tools and information to help make PDF files accessible.


Samuel N. Luoma
Theresa S. Presser
U.S. Geological Survey
345 Middlefield Road, MS 439
Menlo Park, CA 94025
Copies of this report may be purchased from:
U.S. Geological Survey
Information Services
Box 25286 Federal Center
Denver, CO 80225
Or call: 1-888-ASK-USGS

(updated 3/27/2007 by Mike Diggles)

U.S. Department of the Interior, U.S. Geological Survey
Persistent URL:
Page Contact Information: Contact USGS
Last modified: Wednesday, December 07 2016, 06:07:31 PM
FirstGov button  Take Pride in America button