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Toxic Substances Hydrology Program

U.S. Geological Survey

Professional Paper 1646

By Theresa S. Presser and Samuel N. Luoma

2006

This work was performed with the support of a U.S.

Environmental Protection Agency interagency funding

agreement (EPA/IAG DW 14955347-01-0, Region 9) and

cooperative funding agreements with Contra Costa County

and Contra Costa Water District.

This is a revision of and supersedes U.S. Geological Survey

Open-File Report 00-416 (Luoma, S.N. and Presser, T.S.,

2000, Forecasting Selenium Discharges to the San Francisco

Bay-Delta Estuary: Ecological Effects of a Proposed San Luis

Drain Extension, 358 p.).

This report is available online in Portable Document Format (PDF). If

you do not have Adobe PDF Reader, it is available for free

download from Adobe Systems Incorporated.

Download the report (pp1646.pdf, 5.3 MB)

Abstract

Selenium discharges to the San Francisco Bay-Delta Estuary (Bay-Delta) could change significantly if

federal and state agencies (1) approve an extension of the San Luis Drain to convey agricultural drainage

from the western San Joaquin Valley to the North Bay (Suisun Bay, Carquinez Strait, and San Pablo Bay);

(2) allow changes in flow patterns of the lower San Joaquin River and Bay-Delta while using an existing

portion of the San Luis Drain to convey agricultural drainage to a tributary of the San Joaquin River; or (3)

revise selenium criteria for the protection of aquatic life or issue criteria for the protection of wildlife.

Understanding the biotransfer of selenium is essential to evaluating effects of selenium on Bay-Delta

ecosystems. Confusion about selenium threats to fish and wildlife stem from (1) monitoring programs that

do not address specific protocols necessary for an element that bioaccumulates; and (2) failure to consider

the full complexity of the processes that result in selenium toxicity. Past studies show that predators are

more at risk from selenium contamination than their prey, making it difficult to use traditional methods to

predict risk from environmental concentrations alone. This report presents an approach to conceptualize

and model the fate and effects of selenium under various load scenarios from the San Joaquin Valley. For

each potential load, progressive forecasts show resulting (1) water-column concentration; (2) speciation;

(3) transformation to particulate form; (4) particulate concentration; (5) bioaccumulation by

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invertebrates; (6) trophic transfer to predators; and (7) effects on those predators. Enough is known to

establish a first-order understanding of relevant conditions, biological response, and ecological risks should

selenium be discharged directly into the North Bay through a conveyance such as a proposed extension of

the San Luis Drain.

The approach presented here, the Bay-Delta selenium model, determines the mass, fate, and effects of

selenium released to the Bay-Delta through use of (1) historical land-use, drainage, alluvial-fill, and runoff

databases; (2) existing knowledge concerning biogeochemical reactions and physiological parameters of

selenium (e.g., speciation, partitioning between dissolved and particulate forms, and bivalve assimilation

efficiency); and (3) site-specific data mainly from 1986 to 1996 for clams and bottom-feeding fish and

birds. Selenium load scenarios consider effluents from North Bay oil refineries and discharges of

agricultural drainage from the San Joaquin Valley to enable calculation of (a) a composite freshwater

endmember selenium concentration at the head of the estuary; and (b) a selenium concentration at a

selected seawater location (Carquinez Strait) as a foundation for modeling. Analysis of selenium effects

also takes into account the mode of conveyance for agricultural drainage (i.e., the San Luis Drain or San

Joaquin River); and flows of the Sacramento River and San Joaquin River on a seasonal or monthly basis.

Load scenarios for San Joaquin Valley mirror predictions made since 1955 of a worsening salt (and by

inference, selenium) build-up exacerbated by an arid climate and massive irrigation. The reservoir of

selenium in the San Joaquin Valley is sufficient to provide loading at an annual rate of approximately

42,500 pounds of selenium to a Bay-Delta disposal point for 63 to 304 years at the lower range of

projections presented here, even if influx of selenium from the California Coast Ranges could be curtailed.

Disposal of wastewaters on an annual basis outside of the San Joaquin Valley may slow the degradation of

valley resources, but drainage alone cannot alleviate the salt and selenium build-up in the San Joaquin

Valley, at least within a century.

Load scenarios also show the different proportions of selenium loading to the Bay-Delta. Oil refinery loads

from 1986 to 1992 ranged from 8.5 to 20 pounds of selenium per day; with treatment and cleanup, loads

decreased to 3.0 pounds of selenium per day in 1999. In contrast, San Joaquin Valley agricultural drainage

loads disposed of in a San Luis Drain extension could range from 45 to 117 pounds of selenium per day

across a set of historical and future conditions. Components of this valley-wide load include five source

subareas (i.e., Grassland, Westlands, Tulare, Kern, and Northern) defined by water and drainage

management. Loads vary per subarea mainly because of proximity of the subarea to geologic sources of

selenium and irrigation history. Loads from the Sacramento River, depending on flow conditions, range

from 0.8 to 10 pounds of selenium per day. Loads from the San Joaquin River vary depending on

restoration and flow conditions, which are considered.

A consistent picture of ecological risk emerges under modeled selenium discharges from a proposed San

Luis Drain extension. The threat to the estuary is greatest during low flow seasons and critically dry years.

Where selenium undergoes reactions typical of low flow or longer residence time, highly problematic

bioaccumulation in prey (food) is forecast. Surf scoter, greater and lesser scaup, and white sturgeon

appear to be most at risk because these Bay-Delta predators feed on deposit and filter-feeding bivalves.

Recent findings add Sacramento splittail and Dungeness crab to that list. During the low flow season of

critically dry years, forecasted selenium concentrations in water, particulate matter, prey (diet), and

predator tissue exceed guidelines with a high certainty of producing adverse effects under the most likely

load scenario from a proposed San Luis Drain extension. High flows afford some protection under certain

conditions in modeled San Joaquin River scenarios. However, meeting a combined goal of releasing a

specific load during maximum flows and keeping selenium concentrations in the river below a certain

objective to protect against bioaccumulation may not always be attainable. Management of the San

Joaquin River on a constant concentration basis also could 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 river inflows.

Prior to refinery cleanup, selenium contamination was sufficient to threaten reproduction in key species

within the Bay-Delta ecosystems and human health advisories were posted based on selenium

concentrations in tissues of diving ducks. During this time, selenium concentrations in the Bay-Delta were

well below the most stringent recommended water quality criterion [1 microgram per liter (1 μg/L)].

Enhanced biogeochemical transformations to bioavailable particulate selenium and efficient

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bioaccumulation by bivalves characterized the system. If these biogeochemical conditions continue to

prevail and agricultural selenium sources replace or exceed refinery sources, ecological forecasts suggest

the risk of adverse effects will be difficult to eliminate under an out-of-valley resolution to the selenium

problem.

The Bay-Delta selenium model presented here is a systematic approach for conducting forecasts of the

ecological effects from selenium on aquatic food webs. It is a new tool that links and models the major

processes leading from loads through consumer organisms to predators. It also is a feasible approach for

site-specific analysis and could provide a framework for developing new protective selenium foodweb

guidelines and predator criteria. Model components that help ensure understanding ecosystems and the

basis of environmental protection are (1) contaminant concentrations and speciation in sources, such as

particulate material, that most influence bioavailability; (2) bioaccumulation models that calculate

concentrations in diet, specifically in bivalves of the Bay-Delta that act as sensitive indicators of selenium

contamination; (3) food-web type that determines what animals are threatened and when; and (4)

multiple media concentrations (water, particulate material, and tissue of prey and predators) that,

in-combination, determine risk or hazard.

Contents

Abstract

Introduction

Changing Selenium Issues

Approach to Understanding Changing Issues

Sources of Selenium in the Bay-Delta

Hydraulic Connections and Conveyance of Selenium to the Bay-Delta

Concentrations of Selenium in the Bay-Delta

Chemical Forms of Selenium (Speciation)

Particulate and Sediment-Associated Selenium

Bioaccumulation of Selenium by Invertebrates

Bioaccumulation of Selenium by Predators

Effects of Selenium on Predators

Scenarios and Forecasts

Ecological Risk

Conclusions

Appendix A. Export Drain Planning History and Geologic Inventory

Appendix B. San Joaquin Valley Agricultural Drainage Projections

Appendix C. Agricultural Drainage Discharge to the San Joaquin River

Appendix D. Temporal and Spatial Variability in Selenium Load

Appendix E. Sediment Quantity and Quality Tables

Appendix F. Supplemental Spreadsheets

Acknowledgments

References Cited (includes references for appendices)

This report is available online in Portable Document Format (PDF). If you do not have the Adobe Reader,

it is available for free download from Adobe Systems Incorporated.

Download the report (PDF; 5.3 MB)

Suggested citation:

Presser, T.S., and Luoma, S.N., 2006, Forecasting selenium discharges to the San Francisco Bay-Delta

Estuary; ecological effects of a proposed San Luis Drain extension: U.S. Geological Survey Professional

Paper 1646, 196 p. [http://pubs.usgs.gov/pp/p1646/].

Document Accessibility: Adobe Systems Incorporated has information about PDFs and the visually

impaired at Adobe Access.

Send questions or comments about this report to the authors, Theresa S. Presser, (650) 329-4512 or

Samuel N. Luoma, (650) 329-4481.

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