U.S. Department of the Interior

U.S. Geological Survey

Forecasting Selenium Discharges 

to the San Francisco Bay-Delta Estuary: 

Ecological Effects of a Proposed San Luis Drain Extension

Professional Paper 1646
COVER PHOTOGRAPHS

Sources

California Coast Ranges adjacent to the western San Joaquin Valley

Irrigated farm fields in the western San Joaquin Valley

A section of the San Luis Drain presently being used

Oil refinery adjacent to San Francisco Bay

Environment

Satellite view of San Francisco Bay-Delta Estuary with close-up of wetland environment

Physiology/Bioaccumulation

Mysid

Clam

Amphipod

Effects

Lesser scaup in flight
Forecasting Selenium Discharges to the San Francisco 

Bay-Delta Estuary: Ecological Effects of a Proposed 

San Luis Drain Extension

Theresa S. Presser and Samuel N. Luoma

Professional Paper 1646

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.).

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

Dirk Kempthorne, Secretary

U.S. Geological Survey

P. Patrick Leahy, Acting Director

U.S. Geological Survey, Reston, Virginia: 2006

For sale by U.S. Geological Survey Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

For product and ordering information:

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For more information on the USGS—the Federal source for science about the Earth,

its natural and living resources, natural hazards, and the environment:

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Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply 

endorsement of the U.S. Government.

Cataloging-in-publication data are on file with the Library of Congress (URL http://www.loc.gov/).
iii

Contents

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................2

Generic Selenium Issues.....................................................................................................................6

Selenium Issues in the Bay-Delta......................................................................................................7

Changing Selenium Issues.........................................................................................................................15

Approach to Understanding Changing Issues........................................................................................18

Sources of Selenium in the Bay-Delta .....................................................................................................19

Selenium from the Western San Joaquin Valley...........................................................................19

Selenium from Oil Refineries ............................................................................................................35

Selenium from the Sacramento River .............................................................................................36

Summary...............................................................................................................................................36

Hydraulic Connections and Conveyance of Selenium to the Bay-Delta ............................................36

Concentrations of Selenium in the Bay-Delta.........................................................................................38

Effects of Source Water Selenium Loads on Receiving Water Selenium Concentrations ....38

Existing Concentrations in the Bay-Delta.......................................................................................39

Chemical Forms of Selenium (Speciation)...............................................................................................40

Particulate and Sediment-Associated Selenium ...................................................................................41

Processes Affecting Particulate Selenium ....................................................................................41

Sources of Particulate Selenium in the Bay-Delta .........................................................................43

Bioaccumulation of Selenium by Invertebrates .....................................................................................46

Processes ............................................................................................................................................46

Selenium in Invertebrates from the Bay-Delta ..............................................................................47

Summary of Exposure ........................................................................................................................48

Modeling Selenium Bioaccumulation in the Bay-Delta: Dynamic Multi-Pathway 

Bioaccumulation (DYMBAM) Model .................................................................................49

Bioaccumulation of Selenium by Predators............................................................................................50

Dietary Exposure.................................................................................................................................50

Existing Selenium Concentrations in Tissues of Birds and Fish in the Bay-Delta ...................51

Effects of Selenium on Predators .............................................................................................................54

Relating Selenium Concentrations in Food (Prey) to Effects in Predators................................55

Relating Selenium Concentrations in Tissue to Effects in Predators.........................................57

Selenium Hazard Rating ....................................................................................................................59

Scenarios and Forecasts............................................................................................................................63

Scenarios of Composite Loads and Volumes to the Bay-Delta ..................................................63

Forecasts of Speciation and Transformation ................................................................................75

Forecasts of Particulate Selenium Concentrations ......................................................................77

Forecasts of Bioaccumulation in Consumer Organisms..............................................................82

Forecast of Selenium Concentrations in Tissues of Predators...................................................87

Ecological Risk .............................................................................................................................................90

Cumulative Effects on the Bay-Delta...............................................................................................90

Implications for Water Quality Criteria for the Protection of Aquatic Life................................94
iv

Conclusions...................................................................................................................................................94

Extent and Sustainability of Agricultural Discharge from the San Joaquin Valley..................94

Water Management Implications ....................................................................................................95

Indicators of Ecological Risk and Monitoring Needs ...................................................................95

Concluding Perspective.....................................................................................................................97

Appendix A. Export Drain Planning History and Geologic Inventory ................................................100

Envisioned Drainage Discharges and Salt Loads .......................................................................101

Geologic Inventory and Reservoir of Selenium in the San Joaquin Valley.............................107

Characteristics and Timing of Selenium Source Water Release as Drainage.......................110

Appendix B. San Joaquin Valley Agricultural Drainage Projections ................................................114

Projected Selenium Loads from Historic Data and Evidentiary Testimony.............................116

Projections from Drainage Program Management Options......................................................124

Projections from Currently Available Data...................................................................................124

Estimates of Capacity of Drainage Conveyance (proposed San Luis Drain extension) .......135

Total flux from Agricultural Drainage Discharge (lbs Selenium per day)................................135

Appendix C. Agricultural Drainage Discharge to the San Joaquin River.........................................137

Models of Discharge to the San Joaquin River ..........................................................................138

Appendix D. Temporal and Spatial Variability in Selenium Load .......................................................147

Introduction........................................................................................................................................149

Temporal Variability..........................................................................................................................149

Spatial Variability ..............................................................................................................................152

Prediction of Short-Term Selenium Reservoirs ...........................................................................155

Appendix E. Sediment Quantity and Quality Tables .............................................................................159

Appendix F. Supplemental Spreadsheets ..............................................................................................161

Acknowledgments.....................................................................................................................................175

References Cited (includes references for appendices)....................................................................177

Figures

Figure 1. Conceptual model of selenium pollution with examples of source deposits, 

anthropogenic activities, source waters, receiving waters, and biota at risk............... 3

Figure 2. Conceptual model (the Bay-Delta Selenium Model) describing linked factors 

that determine the effects of selenium on ecosystems ..................................................... 4

Figure 3. Map showing the San Francisco Bay-Delta Estuary and the San Joaquin Valley 

of California, with subareas for management of agricultural drainage highlighted. 

Insets show details of (a) the North Bay including locations of oil refineries; 

(b ) San Joaquin River riparian wetlands area including locations of the San Luis 

Drain, Kesterson National Wildlife Refuge, and Grassland wetland area...................... 5

Figure 4. Schematic showing detailed hydrologic connections of the San Francisco 

Bay-Delta Estuary with the San Joaquin Valley, California.................................................. 8

Figure 5. Schematic of selenium concentration in drainage (source waters) as a 

function of flow (water flux) and resultant selenium load illustrating the 

effect of a large reservoir of selenium on the quality of subsurface drainage............ 22
v

Figure 6. Projected high and low range of annual selenium discharges from five 

subareas of the western San Joaquin Valley using currently available data .............. 32

Figure 7. Projected high range of daily selenium discharges (in lbs) from five 

subareas shown as proportions of total discharge from the western 

San Joaquin Valley........................................................................................................................ 32

Figure 8. For a dry year (1994), the balance among flow of the San Joaquin River at Vernalis, 

total river inflow (San Joaquin at Vernalis and Sacramento River at Freeport 

combined), water diversions (pumping at Tracy and Clifton Court Forebay), and 

outflow to the Bay ......................................................................................................................... 37

Figure 9. For a wet year (1996), the balance among flow of the San Joaquin River at Vernalis, 

total river inflow (San Joaquin at Vernalis and Sacramento River at Freeport 

combined), water diversions (pumping at Tracy and Clifton Court Forebay), and 

outflow to the Bay ......................................................................................................................... 37

Figure 10. Hypothetical dilution profiles for selenium in the Bay-Delta: (1) the regional 

baseline profile shows selenium concentrations through the estuary as 

concentrations in the Sacramento River are diluted by concentrations in the 

Pacific Ocean as indicated by salinities; (2) the example mixing profile shows the 

selenium concentration in a hypothetical average freshwater endmember as it is 

diluted by concentrations in the Pacific Ocean...................................................................... 39

Figure 11. Dissolved selenium concentration profiles as function of salinity in the 

Bay-Delta during high and low flow seasons in 1986 and in 1995 – 96 .......................... 40

Figure 12. Particulate selenium profiles as a function of salinity in the Bay-Delta 

during high and low flow seasons in 1986 (9/86) and in 1996 (10/96) ............................. 46

Figure 13. Frequency distributions of selenium concentrations in (a) composite samples 

of C. fluminea from references sites and from Carquinez Strait collected between 

January 1985 and October 1986; and (b) composite samples of P. amurensis

from reference sites and from Carquinez Strait collected between May 1995 

and June 1997.......................................................................................................................... 48

Figure 14. Selenium concentrations in replicate composite samples of P. amurensis

and Delta outflows on a monthly basis from 1995 through 1997..................................... 48

Figure 15. Selenium concentrations in replicate composite samples of P. amurensis at 

21 locations in the Bay-Delta during October 1996 ........................................................... 49

Figure 16. Average selenium concentrations in fish collected from the North Bay 

during 1986. .............................................................................................................................. 53

Figure 17. Average selenium concentrations in bird liver tissue collected from 1986 to 1990 

in: (1) Suisun Bay and San Pablo Bay; and (2) Suisun Marsh, a large area of 

brackish wetland located north of Suisun Bay, not subject to the same direct 

selenium sources as Suisun Bay ......................................................................................... 53

Figure 18. Forecasts of composite freshwater endmember selenium concentrations 

for a series of concentration management scenarios for the San Joaquin River 

in low flow seasons of both wet and dry years ................................................................. 72

Figure 19. Forecasts of monthly composite freshwater endmember selenium concentrations 

under three discharge scenarios (San Joaquin River at 1 and 2 μg/L selenium; 

San Luis Drain extension at 62.5 μg/L selenium) contrasted to input concentrations 

and loads .................................................................................................................................. 73

Figure 20. Forecasts of selenium concentrations for a composite freshwater endmember 

at the head of the estuary and at Carquinez Strait (a point midway in the North Bay 

at a salinity of 17.5 practical salinity units) under three load scenarios (San 

Joaquin River at 1 and 2 μg/L selenium; San Luis Drain extension at 62.5 μg/L 

selenium) based on dilution of selenium through the estuary as function of 

salinity in October, 1997 ......................................................................................................... 73
vi

Figure 21. Forecasts of seasonal composite freshwater endmember concentrations under 

five discharge scenarios (San Luis Drain extension at 6,800, 18,700, 44,880, and 

89,760 lbs selenium per six months; San Joaquin River at 3,500 lbs selenium 

per six months ......................................................................................................................... 75

Figure 22. (a) Calculation of eight composite freshwater endmember selenium concentrations 

as derived from different combinations of total input load and total river inflow (as 

composited mass of water that reaches the estuary in a six-month period); and 

(b) examples of resulting wet and dry year selenium concentrations for three 

selenium load scenarios........................................................................................................ 75

Figure 23. Observed suspended particulate selenium concentrations as a function of 

observed total dissolved selenium concentrations during September 1986 and 

October 1996, with predicted particulate concentrations (using Kd's of 1,000 and 

10,000) superimposed on the plot......................................................................................... 78

Figure 24. Observed (October 1996) and predicted particulate selenium concentrations as 

occurring landward (zero practical salinity units) to seaward (35 practical salinity 

units) in the Bay-Delta projected from dissolved concentrations (see figure 23) 

and three different Kd's (1,000; 3,000; and 10,000).............................................................. 78

Figure 25. Observed selenium concentrations in (a) surf scoter liver, (b) white sturgeon 

flesh, and (c ) white sturgeon liver as a function of bivalve selenium 

concentrations ........................................................................................................................ 89

Figure 26. Schematic representation of forecasts of selenium concentrations in water, 

suspended material, a generic bivalve, and predators at the head of the estuary

under three projected selenium load scenarios (lbs per six months) for a San Luis 

Drain extension directly to the Bay-Delta for a critically dry year during the low

flow season.............................................................................................................................. 93

Tables

Table 1. Chronology of authorizing, planning, regulatory, and evidentiary events for 

construction of a valley-wide drain or a San Luis Drain...................................................... 10

Table 2. Chronology of investigative and regulatory events concerning selenium for the 

San Francisco Bay-Delta. ......................................................................................................... 12

Table 3. Selenium concentrations in shallow ground water and subsurface drainage in 

Westlands Water District, Grassland Drainage Problem Area, Tulare subarea, 

and Kern subarea ....................................................................................................................... 21

Table 4. Conversion factors for selenium and salt or total dissolved solids (TDS)......................... 25

Table 5. Annual discharge, average selenium concentration, and selenium loads from the 

Grassland Drainage Source area; Mud and Salt Sloughs; and the San Joaquin 

River at Crows Landing and Vernalis. ..................................................................................... 27

Table 6. Management alternatives and cumulative load scenarios for five subareas 

(Northern, Grassland, Westlands, Tulare, and Kern) using 50, 150, and 300 μg/L 

assigned selenium concentrations ......................................................................................... 30

Table 7. Calculated drainage scenarios for five subareas (Northern, Grassland, Westlands, 

Tulare, and Kern)......................................................................................................................... 31

Table 8. Projections of selenium loads from the western San Joaquin Valley under different 

drainage scenarios .................................................................................................................... 33

Table 9. Selenium loads conveyed to the Bay-Delta under different flow conditions if a 

constant concentration is maintained in the San Joaquin River or a San Luis 

Drain extension........................................................................................................................... 33
vii

Table 10. Ranges of annual and daily selenium loads from oil refineries located in the 

North Bay for the period 1986 to 1992 and 1999................................................................... 35

Table 11. Partitioning (Kd) between dissolved selenium and particulate or sediment 

selenium in ecosystems for which reliable analytical data is available......................... 44

Table 12. Selenium concentrations in fish from the Bay-Delta (North Bay including 

Suisun, San Pablo, Grizzly and Honker Bays) and Humboldt Bay .................................... 52

Table 13. Dietary selenium exposure guidelines for fish and selenium concentrations in 

the most abundant benthic prey organism in the North Bay (Suisun Bay and 

San Pablo Bay).......................................................................................................................... 56

Table 14. Tissue selenium guidelines for fish and selenium concentrations in tissues and 

eggs of white sturgeon from the North Bay (Suisun, San Pablo, Grizzly, and 

Honker Bays)............................................................................................................................. 58

Table 15. Tissue and dietary selenium guidelines for birds, selenium concentrations in 

ducks, grebes, and stilts from Kesterson National Wildlife Refuge, and selenium 

concentrations in surf scoter, greater scaup, and lesser scaup from the North 

Bay (Suisun and San Pablo Bays).......................................................................................... 60

Table 16. Selenium hazard ratings for various U.S. sites and for the Bay-Delta. ........................... 62

Table 17. Selenium loads employed in forecasts of selenium effects.............................................. 66

Table 18. Calculation of selenium concentrations for a composite freshwater endmember 

at the head of the estuary and at Carquinez Strait (a point midway in the North Bay 

at a salinity of 17.5 practical salinity units) under conditions simulating those prior 

to refinery cleanup.......................................................................................................................... 66

Table 19. Forecasts of selenium concentrations for a composite freshwater endmember 

at the head of the estuary and at Carquinez Strait (a point midway in the North 

Bay at a salinity of 17.5 practical salinity units) for a wet year in a high flow 

season under load scenarios for conveyance of agricultural drainage either 

through a San Luis Drain extension or the San Joaquin River.......................................... 67

Table 20. Forecasts of selenium concentrations for a composite freshwater endmember 

at the head of the estuary and at Carquinez Strait (a point midway in the North Bay 

at a salinity of 17.5 practical salinity units) for a wet year in a low flow season under 

load scenarios for conveyance of agricultural drainage either through a San Luis 

Drain extension or the San Joaquin River ................................................................................. 68

Table 21. Forecasts of selenium concentrations for a composite freshwater endmember 

at the head of the estuary and at Carquinez Strait (a point midway in the North 

Bay at a salinity of 17.5 practical salinity units) for a critically dry year in a low 

flow season under load scenarios for conveyance of agricultural drainage either 

through a San Luis Drain extension or the San Joaquin River.......................................... 69

Table 22. Forecasts of selenium concentrations for a composite freshwater endmember 

at the head of the estuary and at Carquinez Strait (a point midway in the North 

Bay at a salinity of 17.5 practical salinity units) under a restoration scenario that 

assumes greater San Joaquin River inflows enter the Bay-Delta to aid fish 

migration and the concentration in the river maintained at 5 μg/L. ................................. 70

Table 23. Summary of forecasts of selenium concentrations for a composite freshwater 

endmember at the head of the estuary and at Carquinez Strait (at 17.5 practical 

salinity units) under projected selenium load scenarios ................................................... 74

Table 24. Forecasts of selenium concentrations in particulate matter at the head of the estuary under projected selenium load scenarios, identified speciation/transformation 

regimes, and different climatic conditions........................................................................... 80

Table 25. Cumulative summary of forecasts of selenium concentrations in a composite

freshwater endmember and particulate matter at the head of the estuary under 

projected selenium load scenarios, identified speciation/transformation regimes, 

and different climatic conditions ........................................................................................... 81
viii

Table 26. Laboratory-derived physiological constants for selenium bioaccumulation by 

several species of bivalve and composite values for a generic bivalve......................... 83

Table 27. Modeled selenium concentrations in a generic bivalve when exposed to 

different concentrations of particulate organo-selenium or particulate 

elemental selenium .................................................................................................................. 84

Table 28. Summary of forecasts of selenium concentrations in a generic bivalve at the 

head of the estuary under projected selenium load scenarios, identified speciation/

transformation regimes, bivalve assimilation efficiencies (AE’s), and different 

climatic conditions ................................................................................................................... 86

Table 29. Cumulative summary of forecasts of selenium concentrations in a composite 

freshwater endmember, particulate material, and a generic bivalve at the head 

of the estuary under projected selenium load scenarios, identified speciation/

transformation regimes, bivalve assimilation efficiencies (AE’s), and different 

climatic conditions ................................................................................................................... 88

Table 30. Regression and curve-fit data (correlation coefficient, slope, and y-intercept) 

for two species of bivalve and three bivalve predators. ................................................... 90

Table 31. Data employed in regression of bivalve selenium concentrations and bivalve 

predator selenium concentrations ........................................................................................ 91

Table 32. Measured selenium concentrations in clams (C. fluminea, 1988 to 1990; 

P. amurensis, 1995 to 1996), scoter, scaup, and sturgeon (1988 to 1990); and 

a summary of forecasts of selenium concentrations in a generic bivalve, scoter, 

scaup, and sturgeon at the head of the estuary under two projected selenium 

load scenarios, identified speciation/transformation regimes, and bivalve 

assimilation efficiencies (AE’s) for the low flow season of a critically dry year............ 91

Table 33. Risk guidelines and cumulative summary of forecasts of selenium concentrations 

in water, particulate material, a generic bivalve, scaup, and sturgeon at the head 

of the estuary historically and under projected selenium load scenarios, identified 

speciation/transformation regimes, and bivalve assimilation efficiencies (AE’s) for 

the low flow season of a critically dry year............................................................................. 93
ix

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2

)

acre 0.4047 hectare (ha)

acre 0.4047 square hectometer (hm2

) 

acre 0.004047 square kilometer (km2

)

Volume

ounce, fluid (fl. oz) 0.02957 liter (L) 

 pint (pt) 0.4732 liter (L) 

quart (qt) 0.9464 liter (L) 

gallon (gal) 3.785 liter (L) 

gallon (gal) 0.003785 cubic meter (m3

) 

gallon (gal) 3.785 cubic decimeter (dm3

) 

million gallons (Mgal) 3,785 cubic meter (m3

)

cubic inch (in3

) 0.01639 liter (L)

cubic foot (ft3

) 28.32 cubic decimeter (dm3) 

cubic foot (ft3

) 7.4805 gallon (gal) 

cubic foot (ft3

) 0.7646 cubic meter (m3) 

cubic mile (mi3

) 4.168 cubic kilometer (km3) 

acre-foot (acre-ft) 1,233 cubic meter (m3

)

acre-foot (acre-ft) 0.001233 cubic hectometer (hm3

) 

Flow rate

acre-foot per day (acre-ft/d) 0.01427 cubic meter per second (m3

/s)

acre-foot per year (acre-ft/yr) 1,233 cubic meter per year (m3

/yr)

acre-foot per year (acre-ft/yr) 0.001233 cubic hectometer per year (hm3

/yr)

cubic foot per second (ft3

/s) 0.02832 cubic meter per second (m3/s)

cubic foot per second (ft3

/s) 1.98346 acre-foot per day (acre-ft/d)

Mass

pound, avoirdupois (lb) 0.4536 kilogram (kg) 

ton, short (2,000 lb) 0.9072 megagram (Mg) 

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 25 °C).

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) or 

micrograms per liter (μg/L).

Conversion table
x

 Abbreviations

AE

Central Valley Board

CALFED

Department of Fish and Game 

Drainage Implementation Program 

Drainage Program

Department of Water Resources

DYMBAM model

Interagency Drainage Program

State Board

Kd

San Francisco Bay Board

Se

TDS

USBR

USDOI

USEPA

USFWS

USGS

WY

Assimilation efficiency 

California Central Valley Regional Water Quality 

Control Board

A collaboration among 25 State and Federal agencies 

to improve water supplies in California and the health 

of the San Francisco Bay-Delta Estuary

California Department of Fish and Game

San Joaquin Valley Drainage Implementation Program

San Joaquin Valley Drainage Program

California Department of Water Resources

Dynamic Multi-Pathway Bioaccumulation Model

San Joaquin Valley Interagency Drainage Program

California State Water Resources Board

Partitioning coefficient

California San Francisco Bay Regional Water Quality 

Control Board

Selenium

Total Dissolved Solids

United States Bureau of Reclamation

United States Department of the Interior

United States Protection Agency

United States Fish and Wildlife Service

United States Geological Survey

Water year

Notes

The general term bioaccumulation can be applied to all of the biological levels of selenium 

transfer through the food web, but in this report the term is used explicitly in reference to 

particulate/invertebrate bioaccumulation.

A review by Coan (2002) concluded that the San Francisco Bay species Potamocorbula 

amurensis is now the genus Corbula, but the species name is still unclear. Because of this 

uncertainty, reference to the bivalve is now suggested as Corbula (Potamocorbula) amurensis (Thompson, 2005). However, we have retained the name Potamocorbula amurensis in 

this report to support reference to earlier seminal literature.
Forecasting Selenium Discharges

to the San Francisco Bay-Delta Estuary:

Ecological Effects of a Proposed San Luis Drain Extension

Theresa S. Presser and Samuel N. Luoma

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 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 landuse, 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 
2 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

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 BayDelta 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 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-ofvalley 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. 

Introduction

The sources and biogeochemistry of selenium combine 

to make contamination with this element an ecological issue 

of widespread concern [Trelease and Beath, 1949; National 

Research Council, 1976, 1989; U.S. Environmental Protection Agency (USEPA), 1980, 1987, 1992, 1998; Wilber, 1983; 

also see compilations in Frankenberger and Benson, 1994; 

Lemly, 1995; Frankenberger and Engberg, 1998; Skorupa, 

1998a; Seiler and others, 1999; Hamilton, 1999; Eisler, 2000; 

Hamilton, 2004] (fig. 1). Selenium is especially enriched in 

organic-rich shales that are source rocks for oil, coal, and 

phosphate ores (Cumbie and Van Horn, 1978; Presser, 1999; 

Piper and others, 2000; Presser and others, 2004). Release 

of selenium to aquatic systems is a result of weathering and 

anthropogenic activities such as refining, power production, 

and mining. Selenium also is enriched in the soils and runoff 

derived from these source sedimentary shales in many semiarid regions developed for irrigated agriculture, such as in the 

San Joaquin Valley, California (Presser, 1994a, b; Seiler and 

others, 1999). Salinization of some of these soils is accompanied by selenium contamination that increases the complexity 

of problems associated with farming of such lands [San 

Joaquin Valley Drainage Program (Drainage Program), 1990a; 

Dinar and Zilberman, 1991]. Irrigation, leaching, and generation of subsurface drainage can ultimately contaminate ground 

and surface waters as storage and export become necessary to 

sustain agriculture (Presser and Ohlendorf, 1987).

Treatment technologies for selenium have utilized both 

chemical and biological processes to remove selenium from 

the water column, but with little operational success or costeffectiveness [Drainage Program, 1990a; Hanna and others, 

1990; San Joaquin Valley Drainage Implementation Program 

(Drainage Implementation Program), 1998, 1999a]. Use of 

large-scale biological treatment technologies (such as wetlands 

or evaporation ponds) has generated serious ecological problems and hazardous selenium wastes for disposal (Presser and 

Piper, 1998; Skorupa, 1998a; Drainage Program, 1990b). Selenium removal is further hampered by the failure of traditional 

chemical methods to reduce selenium to levels acceptable for 

remediation and, in arid regions, by the problem of disposal of 

associated salts (Drainage Program, 1990a). Remediation has 

not been established other than that dependent on dilution in a 

larger body of water [Drainage Implementation Program, 1998; 

United States Department of the Interior (USDOI) National 

Irrigation Water Quality Program, 2000]. Management plans for 

the western San Joaquin Valley that include storage and reduc-
 3

tion of drainage through source control have been developed, 

but systematic and comprehensive implementation has not 

taken place (Drainage Program, 1990a; Drainage Implementation Program, 1991, 1998; Environmental Defense Fund, 1994). 

The biogeochemical cycling of selenium and its role 

as an essential nutrient lead, in general, to the dominance of 

biological reactions over thermodynamic reactions in aquatic 

systems and concern based on food webs (Shrift, 1964; 

Stadtman, 1974; National Research Council, 1976; Measures 

and Burton, 1978; Cutter and Bruland, 1984; Lemly, 1985; 

Presser and Ohlendorf, 1987; Oremland and others, 1989; 

Luoma and others, 1992; Maier and Knight, 1994; Presser, 

1994a; Lemly, 1997b; Wang and others, 1996; Luoma and 

Fisher, 1997; Dowdle and Oremland, 1999; Reinfelder and 

others, 1998). More specifically, the fate and ecological effects 

of selenium discharges are determined by a sequence of 

processes that link loads, concentrations, speciation, bioavailability, trophic transfer, and effects on predators (Luoma 

and others, 1992; Luoma, 1996; Wang and others, 1996; 

Reinfelder and others, 1997, 1998; Luoma and Fisher, 1997; 

Luoma and Rainbow, 2005) (as exemplified for the Bay-Delta, 

fig. 2). Pathway-specific models allow consideration of (1) 

speciation and transformation between dissolved and particulate forms (2) biotransfer from different types of suspended/

particulate matter (for example, phytoplankton, detritus, and 

sediment); (3) bioaccumulation via the lower trophic food 

web; and (4) uptake of food by predator species. Because 

selenium concentrations can biomagnify during food web 

transfer (see, for example, USEPA, 1980; Saiki, 1986; Maier 

and Knight, 1994; Reinfelder and others, 1998; Stewart and 

others, 2004; Luoma and Rainbow, 2005), upper trophic level 

species are the species most vulnerable to adverse effects from 

selenium contamination. Aquatic species found at risk from 

selenium contamination include ducks, shorebirds, grebes, 

suckers, salmon, trout, sunfish, sturgeon, and crab (White 

and others, 1987, 1988, 1989; Urquhart and Regalado, 1991; 

Luoma and others, 1992; Lemly, 1993a, 1998a, b; Skorupa, 

1998a; Hamilton, 1998; Presser and Piper, 1998; Stewart and 

others, 2004) (figs. 1 and 2). Some species of amphibians and 

reptiles also may be at risk from selenium [Skorupa, 1998b; 

U.S. Fish and Wildlife Service (USFWS) and National Marine 

Fisheries Service (NMFS), 1998 and amended, 2000].

Analysis of any one of the above sets of processes, in 

isolation, is inadequate to characterize selenium problems 

(Luoma and Fisher, 1997). If correlations made among factors 

or processes skip links, then serious uncertainties will result. 

Failure to consider the full sequence of interacting processes 

is a major cause of controversy surrounding many interpretaGeologic sources

Anthropogenic activity

Source waters

Receiving waters

Biota at risk

Coal

Power generation

Fly ash leachate

Belews Lake, North Carolina

Bluegill, sunfish,

bass, bullhead

Soils and alluvium

Irrigation

Subsurface drainage

Kesterson National Wildlife 

Refuge, San Joaquin River,

Tulare Basin, California

Coot, duck, grebe, avocet,

stilt, sculpin, splittail, salmon

Oil

Refining

Wastewater

San Francisco Bay-Delta

Estuary, California

Scoter, scaup, sturgeon, 

splittail, flounder,

salmon, crab

Phosphorite

Mining

Waste-rock drainage

Blackfoot River watershed,

Idaho

Trout, coot, horse, sheep,

elk, cow

Freshwater Seawater

Organic carbon-enriched sediment

Figure 1. Conceptual model of selenium pollution with examples of source deposits, anthropogenic activities, 

source waters, receiving waters, and biota at risk.
4 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

tions of selenium effects on the environment (see, for example, 

O’Toole and Raisbeck, 1998; Hamilton and Lemly, 1999; 

Chapman, 1999; Lemly, 1999a; Skorupa, 1998a, 1999). In 

view of advances in the understanding of the environmental 

chemistry of selenium, the USEPA has recently proposed 

revising selenium criteria for the protection of aquatic life 

(USEPA, 1998; Renner, 1998; USEPA, 2005). 

Selenium contamination of aquatic ecosystems is of 

special concern in large areas of California and other semi-arid 

regions of western North America (Presser, 1994a, b; Seiler 

and others, 1999). Selenium issues are of particular concern 

in the San Joaquin River basin and the Bay-Delta (fig. 3). 

Here, selenium issues are intricately interwoven with issues 

of water management, urbanization, irrigated agriculture, and 

protection of fish and wildlife resources [Conomos, 1979; 

Conomos and others, 1985; Cloern and Nichols, 1985; Nichols 

and others, 1986; California State Water Resources Control 

Board (State Board), 1994, 1999a; USFWS, 1995; Hollibaugh, 

1996; Presser and Piper, 1998; CALFED, 1998a, b, 1999a, 

b, c, d; Thompson and others, 2000; United States Bureau of 

Reclamation (USBR), 2005b]. The San Joaquin Valley also 

has suffered major losses of crucial habitat for migratory birds 

(Gilmer and others, 1982; Vencil, 1986). 

The purpose of this report is to present a systematic 

and comprehensive approach for forecasting the ecological 

effects of selenium in the estuarine food web under an array of 

scenarios that could result from different resolutions of water 

and waste management issues for the San Joaquin Valley and 

Bay-Delta. The analysis focuses on selenium loads that would 

result from engineering solutions that convey selenium-laden 

drainage from the western San Joaquin Valley to the Bay-Delta 

through a proposed extension of the San Luis Drain (Barcellos, 

1986; Wanger, 1994; State Board, 1996b, c, 1999a, d; Stevens 

and Bensing, 1994; Contra Costa County, 1997; San Joaquin 

River Exchange Contractors Water Authority, 1999; Trinity 

County, 1999; U.S. House of Representatives, 1999; Hug and 

others, 2000; USBR, 2005a). Also considered is using the San 

Joaquin River as a conveyance facility (the river, in effect, as a 

drain) because it is the only natural outlet from the San Joaquin 

Valley. A history is presented of the discussions surrounding 

construction of the drain and use of the San Joaquin River to 

convey selenium outside the San Joaquin Valley. 

The scope of the analysis involves using empirical 

observations from the Bay-Delta hydrologic system and 

mechanistic models to (1) convert proposed selenium loads to 

concentrations in receiving waters under several scenarios; and 

(2) forecast bioaccumulation in lower trophic level prey organisms (bivalves) from a likely range of particulate speciation/

transformation regimes and bivalve assimilation efficiencies. 

Selenium concentrations in Bay-Delta clams are compared to 

–: =

Dissolved selenium species

(selenate, selenite, organo-selenium)

Transformation

partitioning (Kd)

Phytoplankton, algae, bacteria,

 suspended particulate material and bed sediment

(elemental selenium, particulate organo-selenium, adsorbed selenite/selenate)

Composite source load

(oil refinery discharges, agricultural drainage

through San Joaquin R. or proposed 

San Luis Drain extension, Sacramento R.)

Composite volume

(Sacramento and San Joaquin Rivers)

Composite freshwater

endmember concentration

(head of estuary)

Prey Clams

Predators

Zooplankton

Bioaccumulation

Amphipods

Sturgeon, diving

ducks, splittail Striped bass

Trophic transfer

Splittail, flounder

Impaired reproduction, teratogenesis, selenosis

Effects

Figure 2. Conceptual model (the Bay-Delta Selenium Model) describing linked factors that determine the effects 

of selenium on ecosystems. (Note: The general term bioaccumulation can be applied to all of the biological 

levels of selenium transfer through the food web, but in this report the term is used explicitly in reference to 

particulate/invertebrate bioaccumulation.)
 5

0 30 km

N

0 30 mi

CALIFORNIA

Map area

Tulare

Lake Bed

S i e r r a N e v a d a

S a n J o a q u i n V a l l e y

C o a s t R a n g e s

Fresno

San Luis Drain

(closed)

Delta Mendota Canal

Kesterson National

Wildlife Refuge

California Aqueduct

Kings River

Panoche Cr

San Luis Drain

(reopened)

San Luis Drain

(proposed)

San

Joaquin River

Merced R.

Tuolumne R.

Stanislaus R.

Delta

Sacramento

San Francisco

Sacramento River

San Francisco Bay

P

A

C

I

F

I

C

O

C

E

A

N

Cantua Cr

Kern

subarea

Tulare subarea

Westlands

subarea

Grassland subarea

Northern

subarea

Vernalis

Crows

Landing

Kesterson

National

Wildlife

Refuge

Delta-Mendota

Canal

California

Aqueduct

Proposed San Luis Drain

San Luis Drain

Grassland Wetlands

Crows Landing

Patterson

San

Joaquin R.

Merced R.

Salt Sloug

Mud Slough h

Oil Refineries

Chipps Island

Grizzly

Bay

San Pablo

Bay

a

b

Carquinez

Strait

San Luis Drain extension

(proposed)

DELTA

Honker

Bay

Suisun

Marsh

Suisun Bay

Figure 3. Map showing the San Francisco Bay-Delta Estuary and the San Joaquin Valley of California, with subareas for 

management of agricultural drainage highlighted (adapted from Presser and Piper, 1998). Insets show details of (a) the 

North Bay including locations of oil refineries; (b) San Joaquin River riparian wetlands area including locations of the San 

Luis Drain, Kesterson National Wildlife Refuge, and Grassland wetland area. 
6 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

protective dietary selenium guidelines for fish and birds. Selenium concentrations in the tissues of a few key predators are 

predicted from correlations with concentrations of selenium in 

bivalves (food) using data from the existing literature. Because 

the relation between tissue concentrations and adverse effects 

are relatively constrained for selenium in wildlife, predictions 

of tissue residues in waterfowl and fish provide a first order 

estimate of potential adverse effects of selenium discharges.

Presentation and understanding of the processes by which 

the ecological effects of selenium are evaluated are as important as the specifics of the data and discussion as applied to the 

Bay-Delta. The general process of a linked bioaccumulation 

model, which uses a bioindicator organism to assess potential 

adverse effects on predators, can be applied to other ecosystems subjected to selenium loading. Thus, this approach can 

help in the development of national or site-specific selenium 

criteria for aquatic-life and wildlife protection. 

Generic Selenium Issues

Existing knowledge concerning the biogeochemistry of 

selenium allows the following generalizations: 

Geologic sources of selenium are widespread (fig. 1).

Development of energy sources (oil and coal), mining of 

phosphate ore, irrigation of areas underlain by organicrich marine shales, and irrigation of lands where alluvium 

is derived from such shales, mobilize geologic selenium 

and ultimately result in the contamination problems found 

today (see examples in fig. 1).

Linked biological and geochemical reactions determine 

the form of selenium. Geochemical form (speciation) 

determines how readily selenium enters aquatic food webs, 

initiates food web transfer, and cycles through particulate 

matter, consumer organisms, and predators. 

The biochemistry of selenium is also complicated by 

selenium being an essential dietary nutrient and a toxicant. Effects can occur in animals at a concentration of 

selenium in diet only slightly above that which is nutritionally required because the difference is small between 

the amount of selenium that is adequate and the amount 

that is toxic (Luckey and Venugopal, 1977; Wilber, 1983; 

National Research Council, 1976; USEPA, 1980, 1998; 

Haygarth, 1994; Skorupa, 1998a, b). 

Hydrologic connections also determine the reactions of 

selenium. Compartmentalized ecological systems can 

interact at critical hydrologic junctures such as in estuaries. 

Seemingly harmless concentrations of selenium in a riverine 

system may become problematic in downstream impoundments, marshes, or wetlands, where cycling and bioaccumulation are accentuated (Luoma and others, 1992; Skorupa, 

1998a; Lemly, 1999b). The geographic scale of selenium 

issues can extend beyond local conditions and therefore, an 

analysis of downstream effects needs to follow.

1.

2.

3.

4.

5.

Traditional toxicity tests are problematic because they 

determine toxicity only from direct water-borne exposures. 

Direct transfer of selenium from solution to animals such 

as fish and bivalves is a small proportion of exposures. 

Bioaccumulation and uptake in food is the most important 

route of selenium transfer to upper trophic level species (Ohlendorf and others, 1986; Saiki and Lowe, 1987; 

Presser and Ohlendorf, 1987; Lemly, 1985; Luoma and 

others, 1992; Presser and others, 1994). Selenium efficiently bioaccumulates through aquatic food webs and 

biomagnifies in many components of the food web (Saiki, 

1986; Presser and Ohlendorf, 1987; Luoma and others, 

1992; Maier and Knight, 1994; Reinfelder and others, 

1998; Stewart and others, 2004; Schlekat and others, 

2004). Biomagnification is important when considering 

effects to upper trophic levels and relating effects to environmental concentrations. If an element is biomagnified at 

each trophic step, then biota several steps from the base of 

the food web could be affected to a greater degree than the 

rest of the food web (that is, predators are more at risk than 

their prey) (Reinfelder and others, 1998).

Invertebrates may be the best indicator for monitoring 

predator exposure. Consumer species, such as bivalves, 

integrate the influences of environmental concentrations, 

speciation, and transformations of selenium and are practical to sample.

Bioaccumulation models link food sources to predator 

animals to predict biotic effects (as exemplified for the 

Bay-Delta, fig. 2). Bioaccumulation models use speciesspecific data for assimilation efficiency, ingestion rate of 

food, rate of loss, and growth rate for prey species. 

A predator’s choice of food, which varies widely among 

species, results in some trophic pathways being more efficient accumulators of selenium than others (Lemly, 1982, 

1985; Luoma and others, 1992; Luoma and Fisher, 1997; 

Skorupa, 1998a; CH2M HILL, 1996, 1999a; Stewart and 

others, 2004; Schlekat and others, 2002a, b, 2004). Hence, 

determination of food webs helps identify which predators 

are vulnerable to seemingly modest environmental levels 

or whether more massive contamination is necessary to 

trigger toxic exposure. 

Birds and fish (predators) are the two taxa of animals most 

sensitive (that is, they are the first to express the effects 

of selenium within the ecosystem) to aquatic selenium 

contamination, with embryonic and larval life-stages 

being of particular concern (Ohlendorf, 1989; Ohlendorf 

and others, 1989a; Hamilton and others, 1990; Lemly, 

1996b, c; Skorupa, 1998a, b, c; Hamilton, 2003, 2004). In 

contrast to many other contaminants, significant environmental damage due to selenium contamination has been 

well documented. Skorupa (1998a) described case studies 

showing different degrees of selenium effects in a variety 

of wetlands and reservoirs affected by agricultural drain6.

7.

8.

9.

10.

11.
 7

age, burning of fossil fuels, or refining of oil. An especially well-documented case study exists for Belews Lake 

in North Carolina where selenium contamination caused 

reproductive impairment and teratogenesis in fish leading to local extinctions of most fish populations (Cumbie 

and Van Horn, 1978; Lemly, 1985, 1997a). The most well 

known case of selenium poisoning in a field environment is at Kesterson National Wildlife Refuge in the San 

Joaquin Valley of California (Ohlendorf and others, 1986; 

Presser and Ohlendorf, 1987; Skorupa and Ohlendorf, 

1991; Drainage Program, 1990b, c). There, deformity and 

death in embryos and hatchlings of aquatic bird populations were widespread; toxicity and immune deficiency 

contributed to the death of adult aquatic birds; multi-species warm-water fish assemblages disappeared; and a high 

incidence of stillborne fry occurred in pollution-tolerant 

mosquitofish (Ohlendorf, 1989; Skorupa, 1998a). 

Although extreme selenium contamination causes death 

in adult organisms, the responses of greatest concern are 

impairment of reproductive success (for example, failure 

of eggs to hatch) and teratogenesis (deformities in embryos 

and juveniles) in birds and fish (Skorupa and Ohlendorf, 

1991). Selenium is a strong reproductive toxin in birds and 

fish when it is present in sufficient concentrations in their 

food (see reviews in Skorupa, 1998b and Hamilton, 2004). 

These organisms efficiently transfer selenium to their 

eggs. Data exist that relate teratogenesis, hatchability, and 

reproductive success to selenium concentrations in food, 

avian eggs, and fish larvae (reviews in Heinz, 1996; Lemly, 

1998b; Maier and Knight, 1994; Skorupa, 1998a, b). Doseresponse curves for aquatic birds, although varying in 

sensitivity, are remarkably steep (Skorupa, 1998). Inhibition of growth, mass wasting, depression of the immune 

system, and oxidative stress also are toxicity endpoints of 

concern, with winter stress syndrome known to increase 

the toxicity of dietary selenium to birds and fish during 

low winter temperatures (Ohlendorf, 1989; Lemly, 1993b, 

1998a; CH2M HILL, 1997, 1999b; USFWS and NMFS, 

1998 and amended, 2000; Santolo and others, 1999; Holm 

and others, 2003; Palace and others, 2004). Ecological risk 

guidelines and a risk index based on selenium concentrations in water, sediment, diet, and tissue (both whole-body 

and egg) are currently available, with some risk levels still 

under debate (Peterson and Nebeker, 1992; Engberg and 

others, 1998; Lemly, 1995; Skorupa, 1998a, b, c; Presser 

and others, 2004a.)

Uncertainty exists in the USEPA selenium criteria for 

the protection of aquatic life, especially for acute criteria 

derived from water-only, short-term exposure of surrogate 

species. The toxicity-testing database does not consider 

bioaccumulation, although bioaccumulation from food 

determines the ecological effects of selenium. Uncertainty 

also exists for chronic criteria based on limited field data for 

food chain exposure, if few studies are available at the time 

of criteria promulgation (USEPA, 1992, 1998). A selenium 

12.

13.

criterion derived primarily from food web exposure would 

be more relevant to field conditions in aquatic systems. 

Effects of selenium on human health are of concern 

[USEPA, 1998 and 2000; California Department of Fish 

and Game (Department of Fish and Game), 1985, 1986, 

1988, all ongoing, 1987; Fan and others, 1988; Drainage 

Program, 1989, 1990b]. National and state human health 

advisories restrict consumption of fish when selenium 

concentrations exceed a certain criterion specific to meal 

amounts, rate of consumption, and reference dose. Pregnant women, children, and subsistence populations are 

special categories where contaminated ecosystems and 

landscapes are a concern. Consumption of wildlife (hunted 

birds) also can be under advisories.

No satisfactory chemical, physical or biological treatment 

technology yet exists to remove selenium contamination from irrigation drainage waters (Hanna and others, 

1990; Hansen and others, 1998; Drainage Implementation Program, 1999a, b, c, d). Treatment technologies that 

work on small effluent streams are expensive to employ on 

large volumes of contaminated water (Drainage Program, 

1990a; Drainage Implementation Program, 1998; USDOI 

National Irrigation Drainage Program, 2000). Variations 

of flow-through wetlands and biological precipitation 

technologies remain in pilot studies (Hansen and others, 

1998; Drainage Implementation Program, 1999a; USBR, 

2005), even though large-scale biological treatments have 

generated serious ecological problems (Presser and Piper, 

1998; Skorupa, 1998a). A management plan specific to the 

arid western San Joaquin Valley has demonstrated through 

in-depth studies that comprehensive and systematic implementation of components, such as source control and land 

fallowing, can reduce the amount of drainage generated 

and substantially contribute to the eventual resolution of 

the drainage problem (Drainage Program, 1990a).

Selenium Issues in the Bay-Delta

The surface and ground waters of the San Joaquin 

Valley are part of a complex, hydrologic system that extends 

from the riparian wetlands of the Sacramento River and 

San Joaquin River through the Bay-Delta to the Pacific 

Ocean (Presser and Piper, 1998) (fig. 3). This natural system 

provides the framework for the Central Valley Project which 

is a massive engineered complex of dams; off-stream storage 

reservoirs; pumping facilities; irrigation and drinking-water 

supply canals; and agricultural drainage systems (USBR, 

1984a). Figure 4 presents a detailed schematic of the hydrologic connections of the San Joaquin Valley to the Bay-Delta 

including the Sacramento River and San Joaquin River. The 

sustainability of the balance and quality of water in this 

system are crucial to the welfare of California, especially to 

the arid San Joaquin Valley and biologically productive 

Bay-Delta. 

14.

15.
8 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Selenium issues within the Bay-Delta ecosystem are of 

special concern because: 

Selenium contamination exists under present conditions in 

the Bay-Delta from known sources of selenium within the 

estuary and in watersheds draining to the estuary. Watershed sources are linked to San Joaquin Valley farmland 

activities. Here, irrigation of salinized soils has led to 

management proposals to sustain agriculture by exporting salts and selenium, collected as subsurface drainage, 

to the Bay-Delta through the San Joaquin River or San 

Luis Drain [see, for example, State Board, 1985; Drainage Program, 1990a; Presser and Ohlendorf, 1987; Presser 

and Piper, 1998; Skorupa, 1998a; California Central 

1.

Valley Regional Water Quality Control Board (Central 

Valley Board), 1998a, b; USFWS and NMFS, 1998 and 

amended 2000)(fig.4). Detailed proposals for construction 

of a collector drain, and more recently for construction 

of an extension of the existing San Luis Drain, to remove 

salts and selenium from the San Joaquin Valley have been 

under consideration for approximately 50 years (table 1; 

also see detailed discussion in appendix A). Water quality 

in the San Joaquin River has degraded significantly since 

the 1940s because of disposal of agricultural wastewater 

from the San Joaquin Valley (Central Valley Board, 1995). 

Even though the San Joaquin River flows into the BayDelta, selenium sources and contamination linked mainly 

Central Bay

Suisun Bay Sacramento-San Joaquin Delta

Sacramento River

Grizzly Bay

Chipps

Island

Clifton Court Forebay

Delta

Pumps

Tracy

Pumps

Honker Bay

NORTH BAY

Pacific

Ocean

Sierra

Nevada

San Pablo Bay

South Bay

to San Joaquin R.

Stanislaus R.

Tuolomne R.

Merced R.

San Joaquin R.

Drains

Drains

Mud Sl.

Salt Sl.

Kesterson

NWR

Grassland Wetlands

Drains/

evaporation ponds

Discharge

1981–86

Drains/

evaporation ponds

Proposed

San Luis Drain

extension

Existing

San Luis

Drain

Grassland

Bypass

Proposed

San Luis

Drain

extension

Contra Costa Canal

California

Aqueduct Delta Mendota CanalSan Joaquin R. recycle

to

Los Angeles

Northern

Subarea

Oil refineries

Grassland

Subarea

Westlands

Subarea

Tulare

Subarea

Kern

Subarea

Coast

Ranges

Vernalis

Freeport

Crows Landing

Patterson

New Exchequer Dam

Friant Dam

New Don Pedro Dam

New Melones Dam

Kings R. Pine Flat Dam

Friant Kern Canal

Kern R. Isabella Dam

San Francisco Bay-Delta Estuary System 

Delta

Mendota

Pool

Figure 4. Schematic showing detailed hydrologic connections of the San Francisco Bay-Delta Estuary with the San 

Joaquin Valley, California (not to scale; enlarged arrows are for emphasis only and are not representational of flow). 

(Note that the only natural outlet from the valley is the San Joaquin River and that an extension of the San Luis Drain 

would provide a constructed outlet to the Bay-Delta for agricultural drainage from the western San Joaquin Valley.)
 9

to oil refineries within the Bay-Delta are better documented (Johns and others, 1988; Cutter, 1989; Cutter and 

San Diego-McGlone, 1990). Oil refiners discharge waste 

from processing selenium-enriched crude oil from the San 

Joaquin Valley and adjacent Coast Ranges into the North 

Bay (fig. 3). 

Selenium contamination documented from 1982 to the 

mid-1990s was sufficient to threaten reproduction in key 

species within the Bay-Delta estuary ecosystems [White 

and others, 1987, 1988, 1989; Urquhart and Regalado, 

1991; San Francisco Estuary Project, 1991, 1992; Harvey 

and others, 1992; California San Francisco Bay Regional 

Water Quality Control Board (San Francisco Bay Board), 

1992a, b, 1993; Luoma and others, 1992; Brown and 

Luoma, 1995a; Luoma and Linville, 1997; USFWS and 

NMFS, 1998 and amended, 2000); Linville and others, 

2002] (table 2). The most severely threatened species 

appear to include, but are not restricted to, white sturgeon 

(Acipenser transmontaus), starry flounder (Platichthys 

stellatus), Dungeness crab (Cancer magister), surf scoter 

(Melanitta perspicillata), greater scaup (Aythya marilla), 

and lesser scaup (Aythya affinis) (Ohlendorf and others, 

1986; White and others, 1987; 1988; 1989; Ohlendorf and 

others, 1989b, c; Urquhart and Regalado, 1991; Luoma 

and others, 1992; USFWS, 1995; Hothem and others, 

1998). From 1989 to 1990 in the North Bay, average selenium concentrations in surf scoter liver tissue and sturgeon 

flesh exceeded reproductive toxicity guidelines (Heinz, 

1996; Lemly, 1998b and 2002) by at least eightfold and 

twofold, respectively. Currently, populations and catches 

per unit effort (where applicable) of all predator species 

mentioned above are in decline. A number of causative 

factors may be involved (CALFED, 1998a, b, 1999a, b, 

c, d; USFWS and NMFS, 1998 and amended, 2000), but 

because selenium concentrations in tissues of prey and 

predators exceed adverse effect guidelines, selenium cannot be excluded as one. 

Some food webs in the Bay-Delta may be particularly 

vulnerable to moderate selenium contamination. Analyses 

from 1982 through 1996 showed that the animals with the 

highest selenium tissue concentrations from the North Bay 

ingested bivalves (Corbicula fluminea prior to 1986 and 

Potamocorbula amurensis in subsequent samplings) as a 

major component of their diet. Selenium concentrations 

in the predominant bivalve in the Bay-Delta were higher 

in the mid-1990s (Linville and others, 2002) than in 1977 

through 1990 (White and others, 1987, 1988, 1989; Cutter, 

1989; Johns and others, 1988; Urquhart and Regalado, 

1991), partly because a new species (P. amurensis) had 

become predominant in the Bay-Delta. The specific 

bioaccumulation pathway from sediment and benthic/suspended biomass to bivalves to predators may be the most 

important route of selenium transfer to upper trophic levels 

(bottom feeding fish, diving ducks, and crab) in the estuary. Selenium concentrations in P. amurensis reached 20 

2.

3.

micrograms per gram (μg/g) dry weight in the North Bay 

in October 1996, exceeding by twofold a dietary guideline 

(>10 μg/g dry weight) that has been shown with a high 

degree of certainty to result in adverse reproductive effects 

to predators. 

Portions of the Bay-Delta and the San Joaquin River are 

currently listed by the State as being subjected to contamination from a suite of chemicals (such as mercury, 

diazinon, PCBs, dioxin, PAHs, and selenium) (Central 

Valley Board, 1994a, 1998b; State Board, 1999b, c). State 

or Federal criteria have been exceeded in these listed water 

bodies, causing adverse aquatic life and human health 

effects (see, for example, Fairey and others, 1997; Davis 

and others, 1997; Dubrovsky and others, 1998). Waterquality limited segments of the Bay-Delta listed because 

of selenium under the Clean Water act as of 2002 are: 

Sacramento-San Joaquin Delta, Suisun Bay, Carquinez 

Strait, San Pablo Bay, Central Bay, South Bay, Oakland 

Inner Harbor, and San Leandro Bay (State Board, 2002). 

Portions of the San Joaquin River and its tributaries designated as water-quality limited due to selenium are the San 

Joaquin River from Mud Slough to the Merced River, Mud 

Slough, the Mendota Pool, and Panoche Creek.

Selenium contamination affects the quality of the already 

limited acreage of wetlands and other crucial habitat in 

the Bay-Delta (CALFED, 1998a, b, 1999a, b, c, d). The 

decreasing extent and degraded quality of these wetlands 

leaves in doubt the future status of many wildlife populations (Harvey and others, 1992; CALFED, 1998a, b; San 

Francisco Estuary Project, 1999). A recovery plan was 

deemed necessary for Sacramento/San Joaquin Delta 

native fishes (USFWS, 1995). The plan includes designation of critical habitat (which means that slight changes 

in habitat condition may cause large changes in population status) for Delta smelt (Hypomesus transpacificus), 

a threatened species (58 Federal Register 12854). Critical 

habitat for the Sacramento splittail (Pogonichthys macrolepidotas) (64 Federal Register 5963) is not currently 

designated because of recent de-listing from threatened 

status (68 Federal Register 183, 2003). 

Environmental safeguards enacted after the ecological crisis 

at Kesterson National Wildlife Refuge may be inadequate 

for the specific problems of the Bay-Delta. For example:

The equality of the criterion for the protection of 

aquatic life and the ecological threshold at which 

substantive risk occurs (i.e., 5 μg/L selenium) demonstrates a need to establish a set of criteria that fully 

encompasses both aquatic and semi-aquatic food 

web components and protects wildlife in addition 

to aquatic life (Skorupa 1998b; Engberg and others, 1998; USEPA, 1989, 1998, 2005; USFWS and 

MNFS, 1998 and amended 2000; Reiley and others, 

2003). Review and revision of estuary and ocean 

selenium criteria has not taken place as scheduled, 

4.

5.

6.

a.
10 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Table 1. Chronology of authorizing, planning, regulatory, and evidentiary events for construction of a valley-wide drain or a San Luis Drain.

Date Agency or industry Event

1950 USBR Begins Central Valley Project Delta-Mendota Service Area water deliveries

1955 USBR Feasibility report for drainage canal (300 cubic feet per second capacity; 197 miles length) 

from the San Joaquin Valley

1960 Federal Law (Public Law 86-488)a Authorizes San Luis Unit of Central Valley Project and makes provision for constructing 

interceptor drain to the Bay-Delta 

1962 USBR Definite Plan Report for San Luis Unit (includes capacity for other areas)

1965 State of Californiaa Proposes expansion of drainage plans to install valley-wide master drain

1965 

to

present 

U.S. Congressb Includes a rider to Central Valley Project appropriations act specifying development of a 

plan which conforms with state water quality standards as approved by USEPA to minimize any detrimental effects of the San Luis Unit drainage waters

1967 State of California Declines to participate in valleywide master drain

1968 USBR Begin (1) Central Valley Project water deliveries to the San Luis Service Area and (2) construction of San Luis Drain for use by Westlands Water District 

1969 Drainage Advisory Group Issues final report recommending drain to the Delta

1970 USBR and USFWS Designate Kesterson Reservoir, a regulating reservoir for the San Luis Drain, as a new 

USFWS National Wildlife Refuge

1972 USBR Environmental Impact Statement on San Luis Unit filed with Council on Environmental 

Quality

1975 USBR Completes 85-mile San Luis Drain to Kesterson Reservoir, 120 miles of collector drains, 

and 1,200-acre reservoir; agrees to supplemental Environmental Impact Statement on 

impacts of San Luis Drain 

1975 USBRa Halts construction of remainder of San Luis Drain due to Federal budget restrictions and 

increasing environmental concerns regarding discharge to the Delta

1975 USBR and state water agenciesa Recommend completion of the San Luis Drain to the Bay-Delta

1977 Federal Law (Public Law 95-46)b Authorizes study of problems related to completion of San Luis Drain

1977 USBRb Asks USEPA about requirements for a waste discharge permit for San Luis Drain

1979 USBR and California water 

agenciesa,b

Issues study of alternatives and final report recommending construction of drain; issues 

First Stage Environmental Impact Report for discharge at Suisun Bay (Chipps Island)

1981 USBRa,b Begins drainwater flow into Kesterson Reservoir; begins San Luis Special Study to fulfill 

state requirements for obtaining a permit for discharge of drainage to the Bay-Delta at 

Chipps Island

1983 USFWS Advises USBR of bird deformities/deaths at Kesterson National Wildlife Refuge

1984 USFWS and USGSb Studies show environmental damage from selenium at Kesterson National Wildlife Refuge

1985 Secretary of the USDOI and California Governora

Establish Federal-State San Joaquin Valley Drainage Program to conduct comprehensive 

studies to identify magnitude and sources of problem, the toxic effects of selenium on 

wildlife, and actions needed to resolve these issues

1985 Secretary of the USDOI Orders cessation of discharge to Kesterson Reservoir and closure of San Luis Drain; initiates National Irrigation Water Quality Program to study effects of agricultural drainage 

on refuges across the western U.S.

1985 State Board Issues order No. WQ85-1 for regulation of agricultural drainage to the San Joaquin River

1986 USBR Closes San Luis Drain; issues Environmental Impact Statement for cleanup alternatives for 

Kesterson Reservoir

1986 Barcellos Judgment, U.S. District 

Courta

Calls for a Drainage Plan, Service Facilities, and a Drainage Trust Fund
 11

a

Recommendation for completion of drainage facility (i.e., San Luis Drain).

b

Call for environmental review or notice of environmental concerns; CVP includes the San Luis and Delta-Mendota Service Areas. 

Table 1. Chronology of authorizing, planning, regulatory, and evidentiary events for construction of a valley-wide drain or a San Luis 

Drain – Continued.

Date Agency or Industry Event

1987 Federal and State Interagency Committeeb

Issues report of potential out-of-valley areas for disposal; due to environmental groups 

and coastal communities opposition, future studies limited to in-valley options

1988 USBR as ordered by State of CaliforniaFills and grades Kesterson Reservoir as part of Kesterson Cleanup Program 

1990 Federal and State Interagency CommitteeCompletes Drainage Management Plan for in-valley solutions to drainage problem

1991 Federal and State Interagency CommitteeForms Drainage Implementation Program and signs Memorandum of Understanding to 

help implement in-valley recommendations; Department of Water Resources is lead 

agency

1992 USBRa As part of Barcellos Judgment, submits Draft Environmental Impact Statement for San 

Luis Unit Drainage Program; Environmental Impact Statement suggests in-valley approaches and stated the social and environmental unacceptability of completing a drain 

precludes further consideration; court rejects Environmental Impact Statement as not 

complying with judgment 

1992 Federal Law 102-575 (CVPIA) Calls for water allocations for the protection of fish and wildlife; and land retirement in 

the San Joaquin Valley

1993 U.S. House of Representatives (Subcommittee on Natural Resources)Oversight Hearing on agricultural drainage issues in the Central Valley including reuse of 

a portion of the San Luis Drain by Grassland Area Farmers 

1993 Porgans, Carter, USFWS, and environmental groupsPetition state over adequacy of Environmental Impact Statements for operation of privately owned drainage evaporation ponds where unavoidable bird loss was occurring

1994 Wanger Decision, U.S. District 

Courta,b

Decides to send the salty water north; calls for initiation of process to obtain a discharge 

permit for the San Luis Drain to the Bay-Delta

1995 USBR; Contra Costa County and 

others

Appeals Wanger decision; environmental groups intervene; decision pending

1995 – 96 USBR and San Luis Delta-Mendota 

Water Authority

Issues Environmental Assessment for reuse of the San Luis Drain by Grassland subarea; 

28-miles of the San Luis Drain reopens to convey drainage to the San Joaquin River

1996 State Boarda State re-emphasizes that valley-wide drain is best technical and feasible solution for water 

quality and salt balance in the San Joaquin Valley, but calls for National Pollutant 

Discharge Elimination System permit

1997 Department of Water Resources Starts preparing update of Drainage Management Plan due to non-implementation

1999 Department of Water Resources Declares Drainage Management Plan to have been unsuccessful

1999 USBR, Department of Water Resources, and State Water Rights 

Decision 1641a,b

Recommend completion of the San Luis Drain to Bay-Delta or other out-of-valley alternative; call for Memorandum of Understanding to initiate environmental review for 

consideration of discharge application for the San Luis Drain

1999 U.S. House of Representatives Field hearing to examine agricultural drainage issues including completing San Luis 

Drain 

2000 Hug, and others, 2000, U.S. Court of 

Appeals

Reverses previous decision to compel USBR to build a drain to Bay-Delta, but rules 

USBR has duty to provide drainage service; drainage plan pending

2000 USBR Initiates a process for providing drainage service to the San Luis Drain

2000 CALFED Issues Programmatic Record of Decision for 30-year plan of Bay-Delta restoration and 

management

2005 USBR Issues Draft Environmental Impact Statement on the San Luis Drainage Feature ReEvaluation

2005 USBR Issues Draft Environmental Impact Statement for renewal of long term San Luis Unit contracts independent of drainage considerations
12 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Table 2. Chronology of investigative and regulatory events concerning selenium for the San Francisco Bay-Delta.

[Compiled with assistance of Khalil Abu-Saba, San Francisco Bay Regional Water Quality Control Board, and Kim Taylor, formerly with San Francisco Bay 

Regional Water Quality Control Board and now with the U.S. Geological Survey, Sacramento CA.]

Date Agency, industry, or reference Event

1975 Report to Association of Bay Area Governments 

(regional monitoring program, Risebrough and 

others, 1977)

Samples of transplanted Mytilus edulis show some of highest concentrations in Carquinez Strait

1982, 1985 USFWS Elevated selenium concentrations found in scoter and scaup from South and 

North Bay

1985 State Board Initiates 5-year Selenium Verification Study for intensive sampling of biota 

in areas of concern including Bay-Delta and San Joaquin River 

1985– 86 USGS and USBR Samples of Corbicula fluminea and Macoma balthica show enrichment in 

North Bay 

1986 Department of Water Resources and Cutter (1989) Sampling shows internal sources of selenium from oil refineries in the midestuary

1986 Department of Water Resources and USGS Invasion of the Asian clam in Suisun Bay changes benthic macroinvertebrate community 

1986– 1991 Department of Fish and Game and USFWS As part of Selenium Verification Study, sampling shows elevated levels 

of selenium in scoter, scaup, white sturgeon, starry flounder, crab and 

shrimp

1986 Department of Health Services/Office of Environmental Health Hazard Assessment Issues human health advisory for consumption of waterfowl (scaup and 

scoter) for Bay

1987– 1988 Department of Water Resources; Cutter and San 

Diego-McGlone (1990)

Sampling shows anthropogenic selenium source is 52 to 92 percent of total 

selenium

1988 San Francisco Bay Board Directs oil refineries to investigate selenium; crude oils from the San Joaquin 

Valley are targeted as source; calls for selenium control technologies rather 

than best management practices for waste streams 

1988 Department of Health Services/Office of Environmental Health Hazard Assessment Reaffirms human health advisory for consumption of waterfowl (scaup and 

scoter) and extends it to entire estuary

1988 USEPA Establishes San Francisco Estuary Project as part of National Estuary 

Program

1988– 1989 San Francisco Bay Board Because water-quality standards not met in the North Bay, requests comprehensive conservation and management plan by 1992

1989 USEPA Because of bioaccumlation in predators, overrules regional board and 

places North Bay on 304(l) list as substantially impaired by point sources 

of selenium; mandates control strategies to be implemented to reduce 

loads resulting in standards being met within 3 yrs 

1991 San Francisco Bay Board Issues selenium mass limits in National Pollutant Discharge Elimination System 

permits maximum limit for daily concentration is 50 μg/L

1991– 1992 USEPA’s National Estuary Program and San 

Francisco Estuary Project

Issues series of reports on status of pollutants, wildlife, wetlands, and 

aquatic resources of Bay-Delta

1992 USEPA Promulgates 5 μg/L selenium standard for Bay-Delta because salt water 

objective of 71 μg/L selenium is underprotective 

1992 USGS Modeling studies show importance of phytoplankton-particulate-bivalve 

foodweb to predator tissues selenium concentrations

1992 Oil refiners Appeal permits and sue regional board

1992 USEPA Promulgates 5 μg/L selenium guideline in National Toxics Rule

1992 San Francisco Bay Board Proposes Basin Plan Amendment that takes iterative mass reduction approach

1993 San Francisco Bay Board Settlement agreement and issuance of cease and desist order for non-compliance of mass reductions

1993 USEPA’s National Estuary Program and San 

Francisco Estuary Project

Workbook on Comprehensive Conservation and Management Plan for the 

Bay-Delta
 13

leaving productive saltwater waterbodies unprotected 

based on the current knowledge of selenium effects 

(USEPA, 2005). Criteria to specifically protect 

wildlife, although called for in 1989, have not been 

promulgated (USEPA, 1989 and 2005).

The USEPA criterion for the protection of aquatic 

life (5 μg/L selenium) is not in effect for upstream 

inflows to the Bay-Delta (the San Joaquin River and 

its tributary sloughs) due to State postponements 

of compliance until 2010 (USEPA, 1992; Central 

Valley Board, 1996d). Selenium concentrations in 

the San Joaquin River have exceeded USEPA criteria 

50 percent of the time for the period 1987 to 1997 

at Crows Landing (figs. 3 and 4) (Central Valley 

Board, 1996a, b, 1998f). Load limits enacted by 

the State in 1996 were exceeded in 1996 through 

1998. Although called for in 1985, a comprehensive 

study of the effects of selenium on the San Joaquin 

River system has not been completed (State Board, 

1985; Presser and others, 1996; Presser and Piper, 

1998). An aquatic hazard assessment of a tributary 

slough receiving the greatest effect from agricultural 

drainage found the selenium hazard as high (Lemly, 

1995, 1996a; USBR and others, 1998 and ongoing). 

Replacement of native species in the San Joaquin 

River has led to a rating of poor on the index of biological integrity (Moyle and others, 1986) for river 

sites above and below drainage discharges. Populations of fish in the San Joaquin River and adjacent 

sloughs are now dominated by introduced species 

having broad environmental tolerances (USBR and 

b.

others, 1998 and ongoing). The role of selenium in 

these changes is not proven, but effects on native 

fish populations are documented elsewhere (see, for 

example, Lemly, 1997b; Hamilton, 1998, 1999).

Refinery discharges of selenium to the Bay-Delta 

have declined since 1998. State waste discharge permits now limit oil refinery effluents based on selenium loads (table 2). Effluents, however, are permitted to reach a daily maximum of 50 μg/L selenium, 

which is tenfold above the USEPA criterion (San 

Francisco Bay Board, 1992b; USEPA, 1987, 1992). 

It is expected that food web contamination attributable to the refineries will decline; however, dilution 

of the effluent discharges by low selenium inflows 

is critical. In 1995, deformed embryos were found 

in 30 percent of mallard (Anas platyrhynchos) nests 

and in 10 percent of American coot (Fulica americana) nests at a marsh used for selenium remediation 

in the North Bay receiving refinery effluent (20 μg/L 

selenium inflow into the constructed wetland and 5 

μg/L selenium outflow) (Skorupa, 1998a).

Selenium concentrations were below recommended 

water quality protection guidelines (2 to 5 μg/L) in 

both the Delta and the Bay in all surveys of the BayDelta from 1982 to the mid-1990s (Cutter, 1989; 

Cutter and San Diego-McGlone, 1990; Cutter and 

Cutter, 2004). Nevertheless, selenium in the food 

web was sufficient to be a threat to some species 

and a concern to human health if those species were 

consumed (Department of Fish and Game, 1988 and 

c.

d.

Table 2. Chronology of investigative and regulatory events concerning selenium for the San Francisco Bay-Delta– Continued.

Date Agency or Industry Event

1993 to 

present

Oil refiners Research and implement selenium reduction technologies on mandated time 

schedule

1993 and 

1994

San Francisco Estuary Institute Issues annual report on regional monitoring program for trace substances

1994 San Francisco Bay Board and oil refiners Mandated avian risk study showed elevated concentrations in avian eggs and 

embryo deformities in Chevron marsh, a constructed wetland receiving oil 

refinery effluent

1995– 1996 USGS and Interagency Ecological Program 

for the Sacramento-San Joaquin Estuary

Sampling in North Bay shows elevated selenium concentrations in Potamocorbula amurensis 

1996 USFWS Issues recovery plan for Sacramento/San Joaquin Delta native fishes

1998– 2000 CALFED Ecosystem Restoration Plan for Bay-Delta

1998, 

amended in 

2000

USEPA in consultation with USFWS Issues California Toxics Rule withholding rule on selenium

1998 San Francisco Bay Board and Oil Refiners Scheduled to meet load reductions

1999 USEPA’s National Estuary Program and San 

Francisco Estuary Project

Report on Comprehensive Conservation and Management Plan for the BayDelta

2000 State Board Lists Bay-Delta as toxic hot spot
14 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

ongoing; Fan and others, 1988; Drainage Program, 

1990b; San Francisco Bay Board, 1992a, b). 

A biological opinion and formal consultation by the 

USFWS and NMFS (1998 and amended, 2000) for 

USEPA’s proposed California Toxics Rule (Proposed 

Rule for the Promulgation of Water Quality Standards: Establishment of Numeric Criteria for Priority Toxic Pollutants for the State of California, 1997 

and amended, 2000) found that the USEPA criterion 

for selenium jeopardizes several Bay-Delta or San 

Joaquin River fish [Delta smelt (Hypomesus transpacificus), Sacramento splittail (P. macrolepidotus), 

steelhead trout (Oncorhynchus mykiss) and chinook 

salmon (Oncorhynchus tshawytscha]; birds [California light-footed rail (Rallus longirostris levipe), 

California clapper rail (Rallus longirostris obseletus), California least tern (Sterna antillarum browni), 

and marbled murrelet (Brachyramphus marmoratus)]; and amphibians and reptiles [giant garter snake 

(Thamnophis gigas), and California red-legged frog 

(Rana aurora draytonii)] that are presently endangered or proposed threatened species (Endangered 

Species Act, 1973). The agencies recommend a 2 μg/

L chronic selenium criterion for protection of aquatic 

life for all waters within range of the listed species to 

aid in their survival and recovery in critical habitats.

State permits for selenium discharges to private 

evaporation ponds used for agricultural drainage disposal in the southern San Joaquin Valley are limited 

to a selenium hazardous waste criterion of 1,000 

μg/L (California Code of Regulations, 1979 and as 

amended). The southern San Joaquin Valley, including the Tulare Basin, is located in part of the Pacific 

Flyway heavily used by migratory birds. A State 

health hazard warning for consumption of American 

coot was posted for a 16-pond area in 1987 (Department of Fish and Game, 1987; Drainage Program, 

1989, 1990b). A 10 to 50 percent rate of embryo 

teratogenesis was documented during the period 1987 

to 1990, causing the closure of most ponds (Skorupa, 

1998a, b). An attempt to regulate evaporation ponds 

on the basis of field observations of effects to birds 

was not adopted in lieu of altering remaining drainage evaporation ponds to limit bird-use (bird-free

ponds) and of providing compensatory and alternative wetland habitats (State Board, 1996a). Deformed 

birds also were found in 1996 at a constructed solar 

evaporation pond used as part of a drainage reduction 

plan. The incidence of teratogenesis in black-necked 

stilt (Himantopus mexicanus) (56.7 percent) was the 

highest ever reported (Skorupa, 1998a). 

Discharges to more recently constructed solar or 

accelerated evaporation ponds (integrated on-farm 

drainage management systems) are under even less 

e.

f.

g.

restriction than traditional evaporation ponds, not 

needing to meet a hazardous waste code for selenium 

(California Code of Regulations, 2003). 

Federal (40 CFR 131.12) and State (Central Valley 

Board, 1994a, 1996a) anti-degradation regulations 

may apply to impaired water quality segments of the 

San Joaquin River or the ground water aquifers of 

the San Joaquin Valley, but these rules have not been 

enforced. In addition to the degradation of the San 

Joaquin River noted above, mobilization of selenium 

by irrigation and contamination of ground water have 

resulted in concentrations of selenium > 1,000 μg/L 

selenium (a hazardous waste; California Code of 

Regulations, 1979 and as amended) in some aquifer 

locations in the San Joaquin Valley (Deverel and others, 1984; Gilliom and others, 1989). 

Human health advisories against consuming selenium-contaminated edible tissue of fish [bluegill (Lepomis macrochirus) and largemouth bass (Micropterus salmodes)] and 

birds (ducks and coots) are presently posted for the San 

Joaquin Valley (Department of Fish and Game, 1985 and 

ongoing; 1986 and ongoing; Fan and others, 1988; Drainage Program, 1990b). Advisories also exist for consuming 

birds (scoter and scaup) from the Bay-Delta (Department 

of Fish and Game, 1988 and ongoing). The advisories are 

issued when selenium concentrations in flesh reach or 

exceed 2 μg/g wet weight (8 μg/g dry weight, assuming 75 

percent moisture) (Drainage Program, 1990b; Saiki and 

others, 1991) and restrict consumption to not exceed 112 

grams of flesh per two-week period or 20 grams of fish or 

bird muscle per day in addition to the regular daily intake 

(Fan and others, 1988). Children and pregnant women are 

advised not to consume any fish or game from the posted 

areas of contaminated ecosystems and landscapes.

Important gaps occur in existing knowledge (Luoma and 

Fisher, 1997; Clements, 2000; Presser and Piper, 1998). 

Most selenium studies have taken place in freshwater 

wetlands and reservoirs, but many of the processes and 

mechanisms that determine selenium effects can be 

applied generically. There is a deficit of knowledge about 

the fate and effects of selenium in estuarine and ocean 

environments similar to the Bay-Delta and Pacific Ocean, 

and important data gaps exist for specific regions of the 

Bay-Delta. On the other hand, knowledge of some of the 

most complex processes-influences of speciation, mechanisms of bioaccumulation, food web transfer, and effects 

on predators– is probably better known for selenium than 

for many other contaminants. 

Comprehensive implementation of the Drainage Program’s 

management components to help control drainage in 

contributing watersheds did not take place (Drainage 

Implementation Program, 1998). Drainage Program goals 

for San Joaquin Valley fish and wildlife protection were 

left unmet, although some wetland channel and evaporah.

7.

8.

9.
 15

tion pond protection (a 2 μg/L objective) has been enacted 

(Central Valley Board, 1998b). The Drainage Program’s 

broadly shared effort to sustain agriculture through (1) 

reduction of the amount of drainage water; (2) placement 

of remaining water under control; and (3) containment and 

isolation of selenium were thought able to largely correct 

waterlogging of farmland and reduce adverse impacts on 

fish and wildlife. These recommended in-valley actions, 

which provide a regional drainage infrastructure, also 

would be necessary for any eventual export of salt from the 

valley (Drainage Program, 1990a).

This report primarily: 

presents selenium issues and their history in the San Joaquin Valley, the San Joaquin River, and the Bay-Delta; 

projects potential loads of selenium from the western 

San Joaquin Valley based on engineering solutions and 

management alternatives proposed historically;

details the state of knowledge of processes that determine the fate and effects of selenium released to the 

Bay-Delta; 

summarizes existing knowledge concerning selenium 

contamination in the Bay-Delta ecosystem; 

characterizes existing knowledge for each set of processes that link loads and effects; 

forecasts concentrations, form, bioaccumulation, 

trophic transfer, and effects of selenium on predators 

under various load scenarios; and

defines research needs and actions that might help 

narrow the uncertainties about proposed discharges of 

selenium to aquatic ecosystems. 

Selenium discharges to the Bay-Delta are changing, or 

could be changed, by activities expected to occur within the 

Bay-Delta and in the San Joaquin River/San Joaquin Valley 

watershed (see specific listing in next section). Forecasts of the 

effects of such changes are essential to a holistic, successful 

restoration or rehabilitation of the Bay-Delta. Scientific data 

and models are necessary to develop such forecasts. 

Changing Selenium Issues 

The probability is high in the future that discharges of 

selenium will increase to the Bay-Delta. A proposed 100-mile 

extension of the existing San Luis Drain would convey subsurface agricultural drainage from the western San Joaquin Valley 

to a discharge point near Chipps Island in Suisun Bay (figs. 3 

and 4). The drain extension would help alleviate the build-up 

of salt and selenium in agricultural soils and the aquifers of 

the valley by exporting them from the valley and disposing of 

them in the Bay-Delta. 

•

•

•

•

•

•

•

Existing policies for the western San Joaquin Valley 

are probably not sustainable (Wanger, 1994; Stevens and 

Bensing, 1994; State Board, 1997a, 1999a, d; Westlands Water 

District, 1996, 1998; U.S. House of Representatives, 1999; 

Hug and others, 2000). In general, soil and ground water 

quality are deteriorating in undrained lands and storage of salt 

and selenium is occurring in surface management areas and 

aquifers of the western San Joaquin Valley (Drainage Implementation Program, 1998). Disposal sites of sufficient scale 

for collected drainage (such as at Kesterson National Wildlife 

Refuge and Tulare Basin evaporation ponds) have resulted in 

adverse ecological effects. Disposal options for drainage have 

long been discussed, environmental impact reports prepared, 

and engineering studies of the problem made (table 1), but no 

systematic regional solution to the drainage problem, although 

proposed in 1990, has been implemented. Drainage problems 

continue to grow and to affect both agriculture and ecosystems 

[see, for example, USBR, 1962; California Department of 

Water Resources (Department of Water Resources), 1965a, b, 

1969, and 1974; USBR, 1978; San Joaquin Valley Interagency 

Drainage Program (Interagency Drainage Program), 1979a, 

b; Brown and Caldwell, 1986; Drainage Program, 1990a; 

Drainage Implementation Program, 1998). As discussed 

later in more detail (also see appendix A), drainage disposal 

studies have provided insufficiently holistic evaluations of the 

problem. These studies have not comprehensively assessed 

(1) the ongoing affect of management actions aimed at more 

storage and less leaching; (2) ecological effects of agricultural 

drainwater disposal on receiving-water food webs and higher 

trophic level predators; and (3) the stressed and degraded 

nature of existing ecosystems. 

Salinization and selenium contamination issues in the 

western San Joaquin Valley ultimately stem from the geologic 

setting, an imbalance in the hydrologic cycle, and clay layers 

impeding drainage (Interagency Drainage Program, 1979a; 

CH2M HILL, 1988; Drainage Program, 1989, 1990a). High 

evaporation rates in the semi-arid climate cause salinization of 

valley soils. Accumulated salts are rich in selenium because 

of the geologic origin of the soils. Salt build-up will inevitably 

reduce agricultural potential. Irrigating soils and draining the 

irrigation waters into buried, perforated pipe help alleviate salinization. This drain water is then collected, and transported to a 

disposal site. The waters draining from the saline soils are not 

only elevated in salts, but are especially elevated in selenium. 

Because of the nature of valley conditions, selenium is mainly 

oxidized to mobile selenate. (Presser and Ohlendorf, 1987). 

Where drainage has been halted, selenium is accumulating in 

the internal reservoir of ground water in the San Joaquin Valley 

(Drainage Program, 1990a; Drainage Implementation Program, 

1998; Westlands Water District, 1996, 1998). The accumulation of salts and contaminants in ground water will eventually 

impede beneficial use of this resource (State Board, 1985, 

1987, 1994, 1999a, d; Central Valley Board, 1988, 1996a, 

1998b). Where drainage water is being collected, its disposal 

results in increases in selenium contamination of surface water 

resources, with possible effects on ecological integrity (see 
16 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

mandated environmental reviews for proposed San Luis Drain 

in 1965, 1975, 1977, 1979, 1981, 1984, 1985, 1987, 1991, 

1994, and 1999 listed in table 1). No feasible engineering solutions yet exist for treating irrigation drainage to remove selenium from the water-column, at least not at the scale necessary 

to alleviate the problem of waste disposal in the San Joaquin 

Valley (Hanna and others, 1990; Drainage Program, 1990a; 

Drainage Implementation Program, 1999a). 

The State continues in their belief that the best solution to 

salt buildup in the San Joaquin Valley is out-of-basin disposal 

(table 1). This action is an effort to seek relief for California 

farmers. As in earlier proposals, the final point of discharge of 

this drain is the Bay-Delta. The State asserts that ultimately if 

salt is not removed from the basin, it will continue to impact 

water quality (State Board, 1999a; Central Valley Board, 

1998b). The State, with final approval from USEPA, would be 

responsible for permit applications and environmental documentation for a master drain (an extension of the San Luis 

Drain) to remove salts from the western San Joaquin Valley.

On the Federal level, the U.S. 9th Circuit Court of 

Appeals decision concluded that the USDOI must provide 

drainage service, but the agency had discretion to meet the 

court order with a plan other than an extension of the San Luis 

Drain (Hug and others, 2000). In response to this court order, 

a plan of action was adopted which culminated in issuance of 

a draft environmental statement that evaluated several alternatives for drainage relief, one of which is Bay-Delta discharge 

from an extension of the San Luis Drain (USBR, 2001a, 

2001b, 2002a, 2005a). Significant adverse environmental 

effects to aquatic resources because of selenium bioaccumulation are predicted for all action alternatives of the proposed 

project. The USBR is continuing to balance resource values in 

order to designate a preferred alternative and to develop feasibility plans for action alternatives. The no-action alternative 

analysis (e.g., not providing drainage service) also predicts 

adverse effects to aquatic receptors related to changes in selenium bioaccumulation, mainly because of the magnitude of 

continuing irrigation supplies affecting seepage and migration 

of selenium into ecosystems.

Environmental groups and proposed recipients of drainage 

remain opposed to a drain alternative as a solution to drainage 

problems; rather, in-valley source control, water conservation, 

drainage reuse, and land retirement (cessation of irrigation in 

areas of elevated selenium concentrations in shallow ground 

water) is preferred (The Bay Institute and others, 2003). Environmental actions being pursued to help better manage water 

supplies and control drainage impacts in the San Joaquin Valley 

and Bay-Delta include efforts to (1) initiate tradable loads 

programs for non-point sources of selenium; (2) limit exports 

of Bay-Delta water; (3) restore San Joaquin River flows; (4) 

plan recovery of threatened and endangered species; and (5) 

monitor the ecological health of important ecosystems (Environmental Defense Fund, 1994; Save the Bay and others, 1998; 

Karlton, 2004; The Bay Institute, 2005).

The San Joaquin River is the only current means (that is, 

the only natural channel) by which selenium and salts can 

be removed from the San Joaquin Valley. Some agricultural 

drainage is currently discharged into the San Joaquin River 

(USBR, 1995 and 2001c; USBR and San Luis and DeltaMendota Water Authority, 1995 and 2001), but inflows of 

selenium from the San Joaquin River to the Bay-Delta have 

traditionally been small compared to other sources (Cutter, 

1989; Cutter and San Diego-McGlone, 1990; Johns and 

others, 1988). This is because although the San Joaquin River 

is hydrologically connected to the Bay-Delta, prior to the 

1990s, the river was almost completely diverted and recycled 

back south to supply canals for agricultural and urban use 

before it reached the Bay-Delta (figs. 3 and 4). Hence, little 

selenium discharged to the river reached the Bay-Delta. 

Proposed management changes call for (1) less recycling 

of the river combined with alteration of flow patterns of the 

lower river to improve throughput to the Bay-Delta; and (2) 

increased flow to the river itself for restoration purposes. 

Changes in selenium discharges to the San Joaquin River will 

be manifested in downstream receiving waters (south Delta, 

Suisun Bay, Carquinez Strait, San Pablo Bay) to the extent 

that those waters are managed so that they reach the downstream estuary ecosystems. 

Recent changes that could affect the quantity and quality 

of selenium discharges to the Bay-Delta and relevant regulations and policies that affect the interface of the San Joaquin 

River and Bay-Delta are summarized below (also see tables 1 

and 2). 

The 1994 Bay-Delta Water Accord (State Board, 1994) 

mandates greater inflows to the Bay-Delta from the San 

Joaquin River. In 1995, the CALFED Bay-Delta Program 

began to comprehensively address management and restoration in the estuary and watersheds. In 2000, a programmatic Record of Decision with a 30-year plan was issued 

(CALFED, 1998a, b; 1999a, b, c, d; 2000; 2005). Specific 

objectives include providing an environmental water 

account to benefit fish and habitats; installing fish screens 

and operable flow gates; increasing State Water Project 

diversions to 8,500 cubic feet per second (and eventually 

to 10,300 cubic feet per second); and increasing storage, 

conjunctive use, and conveyance.

A reduction in recycling of the San Joaquin River and an 

increase in drainage discharge from the San Joaquin Valley 

during seasons of elevated flows are strategies for slowing the salinization of agricultural soils (EA Engineering, 

Science, and Technology, 1999). Hence, a net increase or 

an increase during some months (during high flows) in 

selenium discharges to the San Joaquin River is possible 

in the future depending on river inflow and management 

scenarios.

A Federal agreement and a State permit adopted in 1995 

and renewed in 2001 (Grassland Bypass Channel Project), 

specify conditions from WY 1997 through WY 2009 [a 

water year (WY) begins in October] for use of an existing 28-mile section of the San Luis Drain. Renamed the 

Grassland Bypass Channel, this drain conveys subsur1.

2.

3.
 17

face agricultural drainage to the San Joaquin River from 

approximately 100,000 acres in the northernmost area that 

requires drainage (USBR, 1995, 2001c; USBR and San Luis 

Delta-Mendota Water Authority, 1995 and 2002; USBR 

and others, 1998 and ongoing). This project is in response 

to listing of segments of the San Joaquin River by the State 

as impaired in water quality because of selenium. Even 

though agricultural drainage is considered non-point source 

pollution, tools to control sources and trade loads among 

drainage districts traditional to regulation of point-source 

pollution were applied to this agricultural area (EDF, 1994). 

Compliance with USEPA’s 5-μg/L selenium criterion for 

the upper San Joaquin River is scheduled for October 2010, 

based on decreasing selenium and salt load targets for 

agricultural discharges. Other project allowances include (1) 

management alternatives store some salts and selenium in 

surface management areas and in aquifers; (2) uncontrolled 

discharge of stored drainage is permitted under periods of 

wet weather; and (3) degradation of a tributary of the San 

Joaquin River (Mud Slough) that connects the San Luis 

Drain to the river is allowed until 2009. Drainage alternatives, such as to construct a pipe to directly drain to the 

river, are necessary by 2009 to address degradation of Mud 

Slough. Further assessment at that time will be conducted 

to determine overall drainage conditions in the western San 

Joaquin Valley and future management actions.

Real-time dilution of salt, boron, or dissolved oxygen 

could occur in portions of the San Joaquin River in response 

to State regulated objectives and USEPA regulation of nonpoint source pollution through TMDLs (Total Maximum 

Daily Loads) or TMMLs (Total Maximum Monthly Loads). 

This approach would change the amount and timing of 

selenium loading to the Bay-Delta (Central Valley Board, 

1994b, 1996a, 1998a, 2000a; State Board, 1997a, 1999a; 

USEPA, 2000) as loads are integrated with flows.

Proposed restoration of the San Joaquin River includes 

increasing flows in the river to aid fish passage (Natural 

Resources Defense Council and others, 1988, 1989, 1992, 

1999; CALFED, 1999a; URS Greiner Woodward Clyde, 

2000).

A State water rights decision reinforces the need for the 

USBR to meet salinity objectives at Vernalis on the San Joaquin River and at three locations in the interior of the southern Delta (State Board, 1999a; EA Engineering, Science, 

and Technology, 1999). Salinity objectives adopted in 1991 

were violated most months of the year (67 to 78 percent 

from 1986 to 1998). This state requirement would result in 

changes in flow management to help dilute salt discharges.

Construction of an isolated conveyance facility (similar to 

the peripheral-canal conveyance proposed in California in 

the 1980s, but rejected by voters) or modifications of current diversion and export channel dimensions could result 

in an exchange of Sacramento River inflow for San Joaquin River inflow to the Bay-Delta (CALFED, 1998a, b).

4.

5.

6.

7.

Reduction of selenium loads and changes in treatment 

technologies to meet goals set by the San Francisco Bay 

Board (1992a, b, 1993, 1996, 1997) (table 2) means that 

concentrations of at least some forms of selenium (specifically, selenite) in the Bay-Delta are decreasing (Cutter and 

Cutter, 2004).

Biogeochemical transformation pathways and bioavailability of selenium could change as predominant sources 

to the Bay-Delta change. Refinery selenium was dominated by selenite; selenium from the San Joaquin Valley is 

dominated by selenate, with some apparent conversions to 

organo-selenium in receiving waters (Cutter, 1989; Cutter 

and San Diego-McGlone, 1990; San Francisco Bay Board, 

1992a, b, 1996, 1997).

Changes in residence times of water in the south Delta and 

the North Bay could result from changes in water management. For example, greater diversion of water would result 

in increased residence times in the Bay-Delta during some 

times of year. Mean hydraulic freshwater residence times 

in Suisun Bay were estimated at 0.5 days during periods of 

high flow and at 35 days for period of low flow (Walters 

and others, 1985). Longer hydraulic residence times seem 

to be associated with greater selenium contamination in 

the food web (Lemly, 1997a; Zhang and Moore, 1997a; 

Skorupa, 1998a). 

Biological changes also are occurring in the Bay-Delta 

ecosystem, and some of these appear to affect selenium 

cycling: 

The dominant consumer organism in the Bay-Delta 

changed with the invasion of the Asian clam P. amurensis

in 1986 (Nichols and others, 1986; Carlton and others, 

1990; Brown and Luoma, 1995b). It is possible that this 

species is especially efficient at bioaccumulating selenium, 

although studies directly addressing the mechanisms of 

selenium bioaccumulation by P. amurensis are not yet 

complete (Brown and Luoma, 1995a; Luoma and Linville, 

1997; Linville and others, 2002). Invasion of this species was helped by a depauperate benthic community in 

mid-1986 and the complexities of salinity gradients and 

hydraulic residence times present in the North Bay (Cloern 

and Nichols, 1985; Peterson and others, 1989; Nichols and 

others, 1986). 

One implicit goal of a successful estuary restoration is to 

develop a more complex, native species-dominated food 

web (CALFED, 1998a, b and 1999a, b, c, d). Selenium 

might bioaccumulate more efficiently through more complicated food webs (a question under study), which casts 

doubt on the compatibility of existing or greater levels of 

selenium contamination with restoration goals. 

The cause of the declines of some key species in the BayDelta (such as white sturgeon, Sacramento splittail, starry 

flounder, surf scoter) may include selenium effects on 

reproduction and ultimately, on survival of the population. 

8.

9.

10.

1.

2.

3.
18 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Increased selenium in the Bay-Delta could increase that 

threat. 

Marsh restoration in the Bay-Delta, if accompanied by 

increased selenium discharges, could result in the trapping 

and recycling of increased quantities of selenium in the 

system, with the possibility of greater selenium contamination in some species. Under the worst scenarios, it is 

conceivable that management of the concomitant issues of 

water and salt rather than selenium contamination could 

create an ecological crisis in the Bay-Delta similar to 

that created at Kesterson National Wildlife Refuge in the 

1980s.

Refinements of selenium water quality criteria, especially 

for the Bay-Delta, also are likely. The current USEPA criterion 

for the protection of aquatic life (5 μg/L) is based on bioaccumulation-related toxicity observed in Belews Lake and Hyco 

Reservoir (USEPA, 1987 and 1992). The USFWS recommended criterion (2 μg/L) is based on a series of case studies 

of selenium contamination and effects on birds in western 

wetlands (Skorupa, 1998a; USFWS and NMFS, 1998 and 

amended 2000). The Canadian criterion for wildlife protection 

(1 μg/L) is lower than both the current USEPA criterion and 

the recommended USFWS criterion (Environment Canada/

Health Canada, 1995; Outridge and others, 1999). The technical limitations for the basis of existing and recommended 

water quality criteria raise questions about their suitability 

as the sole standard to assure protection of the Bay-Delta

(Skorupa 1998b; Engberg and others, 1998; USEPA, 1989, 

1998, 2005; USFWS and MNFS, 1998 and amended 2000; 

Reiley and others, 2003) (see previous discussion). As noted, 

selenium concentrations were below recommended guidelines 

in both the Delta and the Bay in the latest surveys in 1996. 

Nevertheless, selenium in the food web was sufficient to be a 

threat to some species and a concern to human health if those 

species were consumed (Linville and others, 2002; Department 

of Fish and Game, 1988 and ongoing; Fan and others, 1988; 

San Francisco Bay Board, 1992a, b) (table 2). The Bay-Delta 

is probably best suited for site-specific selenium guidelines, 

but the details of such guidelines have yet to be identified. 

Given the dynamic nature of this debate, Federal and 

State agencies may be required to further evaluate proposals 

and discharge permits that could significantly change selenium 

inputs to the Bay-Delta. Particularly affected would be the San 

Joaquin River watershed, the south Delta, and the North Bay, 

which includes Suisun Bay, Carquinez Strait, and San Pablo 

Bay (fig. 3).

Approach to Understanding Changing 

Issues

Linked factors that determine effects of selenium on 

aquatic food webs and higher trophic levels are systematically 

described in this evaluation of selenium issues (Bay-Delta 

4.

selenium model, fig. 2). The approach presented here differs 

from earlier attempts that skip links in tying waterborne 

selenium to its ecological effects (Stephan and others, 1985; 

USEPA, 1980, 1987, 1992, 1997 and amended 2000, 1998, 

2005; USFWS and NMFS, 1998 and amended 2000; Reiley 

and others, 2003). This comprehensive approach offers opportunities to more accurately forecast ecological effects from 

loads and to identify resolutions of difficult questions involved 

in water, salt, and selenium management. Steps in the BayDelta selenium model are (fig. 2):

Developing loads scenarios from potential sources 

of selenium. Selenium loads calculated from available 

concentration and drainage volume data provide the 

basis for upper and lower limits of selenium discharge 

that can be expected to enter the Bay-Delta. Analyzing the annual, monthly, daily, and hourly variability 

of selenium loading is necessary to address trends 

and patterns in discharges. The accuracy of selenium 

load calculations on any timescale is dependent on the 

number and frequency of the measurements used to 

determine flow and selenium concentration (Presser 

and others, 1996; Presser and Piper, 1998). Large 

uncertainties are associated with data compiled for 

annual average loads of selenium from agricultural, 

refining, and natural sources. Annualized, generalized averages of concentration, flow, and load hide 

infrequent samplings, sampling that does not reflect 

flow-dependent concentration changes, or spatially 

dispersed samplings. Annual average data presented 

here, although documented as to source and type (see, 

for example, appendices A through D), should be used 

with caution and are applied here to obtain ranges of 

projected selenium loads.

Identifying implications of modes of conveyance 

that determine transport of selenium loads to the 

Bay-Delta. A proposed San Luis Drain extension or 

the San Joaquin River are the most likely modes of 

conveyance from the San Joaquin Valley (fig. 3). If 

a San Luis Drain extension is constructed to Chipps 

Island in the Delta, selenium and salts from the soils 

of the San Joaquin Valley would be released directly 

into the Bay-Delta. During the period when studies 

of selenium were conducted in 1986 to 1990, the San 

Joaquin River was mostly recycled, so little selenium 

reached the Bay-Delta from this source. The passage of the San Joaquin River into and through the 

Delta is not well known at present, but hydrologic 

models exist that can be used as frameworks for 

future modeling (see, for example, Cheng and others, 

1993; Monsen, 2000). Throughput of San Joaquin 

River flows into the Bay-Delta could be influenced 

by changes in water management to aid fish passage 

including construction of elaborate Delta barriers and 

scheduling of flushing flows. 

•

•
 19

Identifying effects of projected loads on concentrations in receiving waters. Loads and seasonal variability in Sacramento River and San Joaquin River inflows 

are critical factors. Consideration of seasonal (six 

month low or high flow) and climatic (wet or dry year) 

effects enhance predictability. Evaluation on a monthly 

basis provides additional improvement in determining 

concentrations in the Bay-Delta. 

Identifying changes in and implications of biogeochemical speciation of selenium and biogeochemical 

transformations of selenium between dissolved and 

particulate forms. Speciation of selenium is critical in 

that it drives routes and efficiency of transformation of 

selenium from dissolved to particulate forms. Understanding particulate selenium and its speciation cycle is 

critical in determining biological effects. 

Incorporating factors controlling bioavailability and 

biotransfer of selenium to macroinvertebrate primary consumers under different concentration and 

speciation conditions. Pathway-specific bioaccumulation models consider (1) the form and concentration of 

particulate selenium; and (2) the physiology (ingestion 

and efflux rates) of prey organisms. Benthic food webs 

of the Bay-Delta result in more bioaccumulation than 

other food webs (Luoma and others, 1992; Stewart and 

others, 2004; Schlekat and others, 2004). 

Determining exposure of sensitive predators from 

modeled selenium concentrations in invertebrate 

and vertebrate prey in the Bay-Delta ecosystem.

Existing data from 1988 to 1999 for selenium concentrations in bioindicator clams in the Bay-Delta show 

elevated concentrations compared to uncontaminated 

reference areas (Johns and others, 1988; Brown and 

Luoma, 1995a; Luoma and Linville, 1997; Linville 

and others, 2002). Exposure of predators is determined 

by the level of bioaccumulated selenium in these prey 

organisms (San Francisco Bay Board, 1992a, b, 1993, 

1996, 1997). 

Estimating effects of selenium on predators from 

tissue residues. Adverse effects have not been demonstrated in predators in the Bay-Delta primarily because 

of the complexity of reproduction in the most affected 

species (Conomos, 1979; Conomos and others, 1985; 

Nichols and others, 1986; Davis and others, 1991; 

Harvey and others, 1992; Monroe and others, 1992; 

and USFWS, 1995). Many threatened species are not 

resident in the system all year, but some important species are vulnerable residents. Through 1996, both selenium concentrations in tissue of predators and in their 

food pointed to threats to the reproductive health of the 

predators (White and others, 1987, 1988, 1989; Cutter, 

1989; Johns and others, 1988; Cutter and San DiegoMcGlone, 1990; Urquhart and Regalado, 1991; San 

•

•

•

•

•

Francisco Estuary Project, 1991; 1992; San Francisco 

Bay Board, 1992a; b; Luoma and others, 1992; Brown 

and Luoma, 1995a; Luoma and Linville, 1997; Linville 

and others, 2002). However, such estimates of risk are 

derived from laboratory and field studies conducted 

elsewhere (USEPA, 1998; Lemly, 1993a, 1995, 1996a, 

1998a; Skorupa, 1998a; Engberg and others, 1998).

For each of the above factors, we define the principles 

that govern its influence and describe the existing knowledge 

for the Bay-Delta.

Sources of Selenium in the Bay-Delta

Major sources of selenium in the Bay-Delta are 

(figs. 3 and 4):

discharges of irrigation drainage conveyed from agricultural lands of the western San Joaquin Valley into 

the San Joaquin River or potentially from an extension 

of the San Luis Drain; 

effluents from North Bay refineries which refine crude 

oil from the western San Joaquin Valley along with 

crude oil from other sources; and

Sacramento River inflow which is the dominant freshwater contribution (high water volume) to the Bay-Delta. 

Effluents from Bay-Delta wastewater treatment plants 

and industries other than refineries are minor sources of selenium (Cutter and San Diego-McGlone, 1990) and will not be 

considered further. 

Selenium from the Western San Joaquin Valley

The problem

The Coast Ranges, which border the San Joaquin Valley 

on the west, are composed of marine sedimentary rocks that 

are enriched in selenium (fig. 3; also see appendices A and B) 

(Presser and Ohlendorf, 1987; Presser and others, 1990). An 

internal reservoir of salt (and by inference selenium) has accumulated for 1.0 to 1.2 million years within the San Joaquin 

Valley soils and aquifers as a result of runoff and erosion from 

the Coast Ranges (Bull, 1964; Milam, 1985; McGuire, 1988; 

Deverel and Gallanthine, 1989; Gilliom and others, 1989; 

Presser and others, 1990; Presser and others, 1994; Presser, 

1994b) (see appendices for detailed analysis). The most 

selenium-rich region of the San Joaquin Valley is the Panoche 

Creek alluvial fan, which supports intensively irrigated land 

(Tidball and others, 1986, 1989). Salts and selenium buildup 

on soils as a result of both the arid climate (<10 inches of 

precipitation and >90 inches of evaporation) and poor drainage 

(clay layers impede downward movement of water causing 

water-logging of the root zone). 

•

•

•
20 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

The San Joaquin Valley has a net negative annual water 

budget (evaporation exceeds precipitation). Prior to development of the water management system, a permanent shallow 

ground-water table only occurred in ground-water discharge 

zones near the trough of the San Joaquin Valley. The present 

shallow ground water and attendant subsurface drainage flows 

are mainly the result of water management including massive 

irrigation. Micro-management seemingly has enabled agricultural production to continue at a high rate without excessive 

abandonment of lands (see detailed discussion, appendix A). 

Massive irrigation leaches salt and selenium and 

moves them into aquifers and surface waters. Installation of 

subsurface drains increases the speed, volume, and control 

of drainage of shallow ground water that impedes agricultural production. Collection of drainage from irrigated soils 

in drainage canals enables efficient discharge into surface 

waters. In 1960, both the Federal government and the State 

of California committed to provide irrigation and subsequent 

drainage of irrigation wastewater for the Central Valley Project 

of the San Luis Unit of the western San Joaquin Valley (Public 

Law 86-488, 1960; California Burns-Porter Act, 1960). A 

history of legislation and planning since the inception of a 

master-drain is given in table 1 and detailed in appendix A. 

The San Luis Unit includes agricultural lands that total over 

700,000 acres in the Westlands, Panoche, Broadview, Pacheco, 

and San Luis Water Districts of the Westlands and Grassland 

regions or subareas (USBR, 1981) (figs. 3 and 4). It was hoped 

that the increased water supply (to satisfy moisture demand 

by climate and crops) would be balanced by salt leaching and 

drainage, even though amounts of water required are on a 

massive scale (USBR, 1955, 1962, 1978; Department of Water 

Resources, 1979 and 1982). Simple water and mass balance 

observations explain the attractiveness of an engineering solution that would increase salt and water discharge from the San 

Joaquin Valley. 

Prediction of long-term reservoir: how 

sustainable is discharge 

In planning for envisioned hydrologic balance, a distinction was made between managing the accumulated hydrologic imbalance (area of affected land) and managing the 

annual imbalance (rate of water table rise) (CH2M HILL, 

1988; Drainage Program, 1989). Short-term objectives would 

work toward hydrologic balance by stemming the rate of 

deterioration, while reclaiming existing problem lands would 

require releasing from storage a large accumulation of water 

and salt. Achieving hydrologic balance would not achieve 

salt balance. Salts would continue to accumulate in the soils 

and aquifers of the San Joaquin Valley. Managed volume of 

drainage discharge would increase over a hypothesized 100-

year planning period (USBR, 1978, 1983) (appendix A, table 

A1). Salt loads were calculated for a period of 50 years into 

the future, with a maximum release occurring after 40 years 

of discharge. Later estimates (USBR, 1983), also planned 

for 100 years of discharge to the San Luis Drain, showed a 

slowing in the rate of increase after 40 years (appendix A, 

fig. A3). 

The geohydrologic balance of selenium (or salt) ultimately determines the degree of contamination build-up in 

the San Joaquin Valley (appendix A, tables A2 and A3). The 

primary geologic inventory of selenium in the Coast Ranges is 

the ultimate source of influx. Drainage from the San Joaquin 

Valley is the source of efflux, whether natural or artificially 

accelerated by engineering means. The internal labile reservoir of selenium in San Joaquin Valley is growing because 

the rate of removal of selenium-enriched salts from the valley 

is naturally slow. In general, calculations of the amounts of 

selenium in the reservoir within the Panoche Creek alluvial fan 

also confirm the massive nature of selenium accumulation in 

the San Joaquin Valley. Calculations based on two scenarios 

(appendix A, tables A2 and A3) show that no long-term reduction in selenium discharge would be expected for 63 to 304 

years at the lower range of reservoir projections and assumed 

removal rate (42,785 pounds of selenium/year). Drainage of 

wastewaters outside of the San Joaquin Valley may slow the 

degradation of San Joaquin Valley resources, but drainage 

alone cannot alleviate the salt and selenium build-up in the 

San Joaquin Valley, at least within a century, even if influx of 

selenium from the Coast Ranges could be curtailed.

Several observations lead to further understanding of 

selenium source loads. On a current, yearly scale for selenium loads and concentrations from the western San Joaquin 

Valley: (1) the selenium load from the Panoche Creek upper 

watershed (137 pounds in January and February 1997; 8,045 

pounds in February 1998, an exceptionally wet month ) is a 

small percentage of a projected total annual load from the San 

Joaquin Valley (42,785 pounds assumed from all subareas); (2) 

16 percent of the Panoche Creek selenium load (962 pounds) 

was in the dissolved fraction and 84 percent (5,033 pounds) 

was in the suspended fraction in February, 1998 (appendix A, 

table A3) (U.S. Geological Survey, 1999; Kratzer and others, 

2003); (3) selenium concentrations in sediment samples from 

Panoche Creek were relatively low historically and remained 

so in 1998 (1 to 2 μg/g), thus depending on the large mass of 

sediment eroded during storms to accounts for the large fraction of suspended matter loading of selenium during runoff 

from large magnitude storms (appendix A, table A4) (Presser 

and others, 1990; (4) dissolved selenium concentrations in 

runoff samples ranged from 31 to 85 μg/L in monitored storms 

in WY 1998 (appendix A, table A3) (U.S. Geological Survey, 

1999; Kratzer and others, 2003). 

Selenium concentrations in source waters 

The effect of the large reservoir of selenium calculated above can be seen in the quality of ground water in the 

western San Joaquin Valley (table 3). Extensive measurement and study of ground-water aquifers in the San Joaquin 

Valley have been made since 1917 (Mendenhall and others, 

1916; Davis and Poland, 1957), but selenium concentration 

analyses were not a part of water quality studies until the 
 21

1980s (Presser and Barnes, 1984, 1985; Deverel and others, 

1984; Drainage Program, 1989, 1990a). Selenium concentrations in shallow ground water surveyed in 1984 varied based 

on physiographic zone (alluvial fan, basin rim or basin trough) 

(Deverel and others, 1984). Average selenium concentrations 

in drainage sumps in the area of the Panoche Creek alluvial 

fan ranged from 140 to 4,200 μg/L (Presser and Barnes, 1985). 

These concentrations are reflective of shallow ground-water 

conditions as opposed to managed drainage, which may be 

blended. Studies in 1989 in the area of the Panoche Creek 

alluvial fan showed selenium concentrations ranged from 

96 to 7,300 μg/L selenium in individual sump discharges or 

well samples at depths up to 50 ft below land surface in areas 

served by subsurface drains (Gilliom and others, 1989) (table 

3). Selenium concentrations depend, in part, on the number 

of years the fields were drained. Concentrations of selenium 

in subsurface drain water in the area of sampled wells ranged 

from 400 to 1,000 μg/L. A more recent compilation used in 

the evidentiary process (Wanger, 1994; Stevens and Bensing, 

1994; Westlands Water District, 1996) and in regulatory planning showed concentrations in shallow ground water ranged 

from 75 to 277 μg/L selenium (range of means) (Drainage 

Program, 1990a; Central Valley Board, 1996c, d) (table 3). 

Data presented in testimony and by the State projected an 

Source and Sampling Selenium 

(μg/L)

San Luis Drain and agricultural sumps 

(State Board, 1985; Presser and Barnes, 1985)

 San Luis Drain, discharge (1983– 84) 330– 430

 San Luis Drain discharge, 1984 340

 Westlands subarea drainage sumps 140 –1,400

 Grassland subarea drainage sumps 8– 4,200

Westlands subarea 

(Stevens and Bensing, 1994; Wanger, 1994; Westlands Water 

District, 1996)

 San Luis Drain discharge (1981– 84) 230 – 350

 Westlands Water District drainage (from 

USGS data dependent on grid size)

208–277

(range of means)

 Westlands Water District drainage estimate 300

 Westlands Water District drainage (63 sites 

within 42,000 drained acres, 1993)

163

(mean)

 Westlands Water District estimate of drainage 

with treatment

50

 USBR (conservative estimate) at least 150 ppb

Grassland Drainage Problem Area 

(Central Valley Board, 1996a,b; Drainage Program, 1990)

 Subsurface tile drainage estimate 150

 Subsurface tile drainage modeling estimate 120

 Subsurface drainage sumps (annual survey) 211 (mean); 

134 (median)

 Model of estimated of drainage problem area 

(effluent surface plus subsurface)

80 (average)

 Estimated subsurface discharge to San Joaquin 

River for 1990

150

 Estimated subsurface discharge to San Joaquin 

River for 2040

75

Source and Sampling Selenium 

(μg/L)

Panoche Creek alluvial fan (Grassland and Westlands subareas) (Gilliom and others, 1989) 

 Murietta field well (10–15 feet) 320 – 7,300

 Murietta field subsurface drains 800 – 1,000

 Wells associated with agricultural field 

drained for 15 years (10–15 feet)

96 – 1,000

 Subsurface drains associated with agricultural field drained for 15 years400 

Tulare and Kern Basins evaporation ponds (1988 and 1989) 

(Central Valley Board, 1990 a, b)

 Inflows to evaporation ponds <1– 760

 Evaporation ponds <1– 6,300

Tulare and Kern subareas observation wells (12–25 feet) (Fujii 

and Swain, 1995)

Alluvial fan zone (median) (maximum)

 West-side alluvium 8 520

 East-side alluvium < 1 25

 Basin zone

 West-side basin 3 240

 East-side basin < 1 320

 Tulare Lake Zone

 Northeastern margin < 1 4

 Southern/western margin 34 1,000

 Lake bed < 1 2

Table 3. Selenium concentrations in shallow ground water and subsurface drainage in Westlands Water District, Grassland 

Drainage Problem Area, Tulare subarea, and Kern subarea.
22 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

average concentration of selenium in shallow ground water 

and hence, subsurface drainage, of at least 150 μg/L selenium 

in the farming areas affected by the Panoche Creek alluvial fan 

(table 3).

Distribution of selenium and selenium concentrations in 

shallow ground waters of southern San Joaquin Valley (Tulare 

and Kern subareas, figs. 3 and 4) vary based on (1) sources of 

sediment (Coast Range or Sierra Nevada); (2) location within 

depositional zones (alluvial fan, basin trough, or lake bed); and 

(3) depositional environment (oxidation or reducing) (Fujii 

and Swain, 1995) (table 3). The median selenium concentration in the most affected areas in the southwestern margin of 

the lake zone was 34 μg/L, with a maximum concentration 

of 1,000 μg/L selenium in that area. Selenium concentrations measured in drainage discharges to evaporation ponds 

from 1988 to 1997 also reflect shallow groundwater conditions (table 3 and detailed in appendix B, tables B19 through 

B21). Most selenium concentrations in currently regulated 

discharges to evaporation ponds in the southern San Joaquin 

Valley are above those associated with avian risk, and consequently dischargers are required to provide mitigation and 

alternative habitat (State Board, 1996c).

Most selenium concentrations in shallow ground water 

listed in table 3 are above the concentration presently regulated as the maximum for oil refinery effluent (50 μg/L) and 

above the concentration estimated that is possible with treatment (50 μg/L) (Westlands Water District, 1996).

The effect of a large reservoir of selenium on recent 

subsurface drainage flow and quality (fig. 5) is generalized 

from data collected during frequent sampling of drainage 

source water (current agricultural discharges to the San 

Joaquin River in WYs 1997 and 1998 from the Grassland 

subarea, see appendix A, figs A7 to A10; appendix B, tables 

B9 and B10; and appendix D) (USBR and others, 1998 and 

ongoing). Selenium concentration in source agricultural 

drainage is not diluted when outflow or volume of drainage 

increases, except in extreme precipitation events. Rather, 

when considering selenium source waters as opposed to 

receiving waters, increasing input of applied water results in 

increased selenium concentrations and output loads, indicating massive selenium storage that is now subject to transport. Additionally, testimony in State water rights hearings 

reaffirm that the action of massive irrigation supply (mainly 

from the Federal Central Valley Project) is a principal cause 

of the discharge of salinity, and hence, the cause of violations of water quality objectives for salinity for the Bay-Delta 

(State Board, 1999a). 

Removal of salt (and selenium) also is slowed by the 

recycling of the San Joaquin River. The San Joaquin River 

can be almost completely diverted back into the San Joaquin 

Valley, with little river flow entering the Bay-Delta. In the 

past, recycling has occurred during most months of the year 

and during all months of many years (USBR Central Valley 

Operations Office, Daily Delta Outflow Computation; EA 

Engineering, Science, and Technology, 1999) (fig. 4). Recycled San Joaquin River water is applied again in the Northern 

and Grassland subareas as irrigation (fig. 3). The degree of 

recycling is determined by water management. Water management began changing toward less recycling in 1994 and direct 

throughput of the San Joaquin River may increase in the years 

ahead to help restore San Joaquin River fish and fish habitat. 

A reduction in recycling and an increase in drainage discharge 

during seasons of elevated flows are proposed strategies 

for slowing the salinization of agricultural soils. However, 

management to meet all goals including salinity standards for 

the San Joaquin River at Vernalis is complex. Strategies may 

include constructing storage or holding ponds to optimize 

timed release of drainage. Agricultural drainage discharges 

currently are not, in general, coordinated with periods of high 

river flows (appendix A, fig. A11). 

Drainage management: history 

Management plans have considered in-valley and outof-valley drainage alternatives. Out-of-valley solutions mean 

export of the salt-laden drainage (and its selenium load) to 

somewhere else. The most frequently mentioned of these 

solutions is an extension of the San Luis Drain with discharge 

to the Bay-Delta. In-valley solutions imply local storage and 

treatment of selenium-rich drainage. However, satisfactory 

treatment technologies have not yet been demonstrated and 

storage does not seem sustainable (see previous discussion and 

Drainage Program, 1990a).

Planning for a drain to carry salt-laden irrigation return 

water (and the accompanying selenium) from the San Joaquin 

Valley began in 1955 (table 1). An 85-mile section of the 

San Luis Drain was completed in 1975, to collect irrigation 

drainage water from one section of the valley, the Westlands 

Water District (figs. 3 and 4, Westlands subarea). The San Selenium concentration

Water flux

Load

Concentration

Fall Summer El Niño

Selenium load

Figure 5. Schematic of selenium concentration in drainage (source 

waters) as a function of flow (water flux) and resultant selenium 

load illustrating the effect of a large reservoir of selenium on the 

quality of subsurface drainage.
 23

Luis Drain began discharging concentrated drainage water 

in 1981 to Kesterson National Wildlife Refuge (figs. 3 and 

4), a heavily populated bird sanctuary on the Pacific Flyway 

(USBR, 1986; Presser and Ohlendorf, 1987). The Kesterson 

National Wildlife Refuge ponds were used as terminal evaporation ponds until the remaining miles of the canal could be 

built. In 1983, deformed birds were discovered at Kesterson 

Reservoir, a reservoir consisting of 12 ponds. Subsequent 

monitoring revealed a contaminated ecosystem with elevated 

concentrations of selenium throughout sampled water, sediment, plants, and invertebrates (Saiki and Lowe, 1987). Avian 

deformities were ultimately linked to selenium exposure from 

food web contamination (Ohlendorf and others, 1986; Presser 

and Ohlendorf, 1987). The San Luis Drain was ordered closed 

by the U.S. Department of Interior in 1985 and the low-lying 

parts of Kesterson National Wildlife Refuge were buried under 

18 inches (46 centimeters) of imported topsoil in 1988 (USBR, 

1986). Elevated selenium concentrations persist in the remediated terrestrial ecosystem at Kesterson Reservoir (CH2M 

HILL, 1996, 1997, 1999a, b; Presser and Piper, 1998). 

Management of selenium currently differs among regions 

(subareas) in the San Joaquin Valley. Five subareas (Westlands, Tulare, Kern, Grassland, and Northern) of the western 

San Joaquin Valley were designated based on hydrologic and 

geologic features and on options for management of irrigation and agricultural wastewater discharge (Drainage Program, 

1990a) (fig. 3). Selenium-laden wastewater is recycled or stored 

in groundwater aquifers in the Westlands subarea. In the Tulare 

and Kern subareas, drainage is collected in privately owned 

evaporation ponds located on farms. Reproductive effects in 

aquatic birds were observed in some of these ponds and associated wetlands (Skorupa, 1998a). Drainage from the Grassland 

subarea prior to 1995 was discharged into canals, sloughs, and 

wetlands that eventually flowed into the San Joaquin River 

(fig. 3). Implemented in 1995, the Grassland Bypass Channel 

Project collects drainage under permit from the Grassland 

subarea and transports it through an existing 28-mile section 

of the San Luis Drain to Mud Slough, a tributary of the San 

Joaquin River (USBR, 1995; 2001c; USBR and San Luis DeltaMendota Water Authority, 1995 and 2002; USBR and others, 

1998 and ongoing) (fig. 3; appendix B). Most estimates suggest 

that drainage needs for the Northern subarea are relatively small 

compared to other areas, although conditions and estimates of 

acres requiring drainage have not been updated since 1990. 

Selenium loads: general considerations

The problem of progressive soil salinization and the 

build-up of groundwater contamination could require collection of drainage from larger and larger areas of the San 

Joaquin Valley if agricultural activities continue and a drainage 

outlet is available to help alleviate annual imbalances. A 

realistic, long-term evaluation of the potential for selenium 

discharge must fully consider both the present and the future 

extent of the problem (appendix B).

Identification and classification of problem lands in the 

San Joaquin Valley took place as early as 1930 (Ogden, 1988). 

Since the 1950s, technical studies have estimated the extent 

of the acreage requiring drainage under varying conditions of 

water import, water export, salinity, and ground-water levels. 

In general, all of these early studies predicted a worsening 

fate if an out-of-valley drainage conveyance is not provided. 

For example, in 1955, developers of the Central Valley Project 

San Luis Unit projected the acreage affected by salinity would 

increase from 12,000 acres in 1967 to 35,000 acres in 1976 

(USBR, 1978; Gaines, 1988; Ogden, 1988; Prokopovich, 1989). 

The water purveyors thought land requiring drainage would 

increase from 96,000 acres in 1954 to 270,000 acres in 1967. 

In more recent studies, the Drainage Program conducted 

comprehensive studies to identify the magnitude and sources 

of the drainage problem, the toxic effects of selenium on wildlife, and what actions need to be taken to resolve these issues

(Drainage Program, 1989). Between 1985 and 1990, the joint 

Federal/State program (Drainage Program, 1990a) predicted 

areas of problem acreage (land characterized by waterlogging and related water quality problems) and volumes of 

problem water (the annual drainage water volume that must be 

managed because of adverse effects on agriculture or aquatic 

resources) (appendix B). The program developed an in-valley

manage­ment plan for the next 50 years for agricultural subsurface drainage with specific management alternatives (Drainage 

Program, 1989; 1990a). The goal was to make progress both in 

managing and treating drainage-water toxicants and developing long-term solutions to address the elevated groundwater conditions and the annual salt build-up that eventually 

limit the uses of valley lands and ground water. The Drainage 

Program’s regional studies and data provide much of the 

information used in the assessment of loads presented here for 

subareas of the San Joaquin Valley (appendix B). The benefits 

expected, during the 50-year management period, included 

continued agricultural production at present levels without 

predicted abandonment of lands due to salinization; and 

restoration/protection of fish and wildlife resources from the 

adverse effects of selenium in receiving waters. Recommended 

monitoring based on the developed regional framework, 

if implemented, would add site-specific data and analysis 

necessary for long-term success of the Drainage Program. 

Recommendations for treatment techniques were not included 

because success of technology on a large-scale was not proven 

as of 1990 (Drainage Program, 1990a). Implementation of the 

management plan was only partial and systematic monitoring 

and data analysis has not yet occurred (Drainage Implementation Program, 1998). 

The Drainage Program (1990a) management plan estimated a problem area of 444,000 acres would create 314,000 

acre-ft of problem water annually by the year 2000. The 

problem area would increase to 951,000 acres with an increase 

in problem water to 666,000 acre-ft by year 2040. For these 

estimates of acreage, the Drainage Program used a criterion

of sufficiently elevated salinity and boron concentrations in 

ground water to limit use of the water and affect crop selec-
24 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

tion (lands with an actual drainage problem). The Drainage 

Program also estimated acreage with a potential drainage 

problem using a criterion of an area with a shallow ground 

water within 0 to 5 ft of land surface. Using this criterion, estimates ranged from 765,000 acres in 1990, to 918,000 acres in 

year 2000, to 1,057,000 acres in year 2040. Using a criterion

of lands contributing the largest percentage of selenium to 

drainage discharge (that is, lands overlying areas of shallow 

ground water with selenium concentrations of > 50 μg/L), 

264,000 acres were projected as affected in 1990. It was estimated that 84,000 acres of land would have to be abandoned 

by 2000 and 460,000 acres by 2040 if the Drainage Program 

management plan was not implemented. Land retirement 

recommended by the Drainage Program by 2000 was 21,000 

acres and by 2040, was 75,000 acres.

Further documentation provided in 1992 for the San Luis 

Unit Drainage Program simply stated that all the major USBR 

and interagency studies (in table 1, those for 1955, 1962, 1964, 

1972, 1979, 1984, and 1990) found similar magnitudes of the 

drainage problem (USBR, 1992). As noted in recent testimony given in State water rights hearings, the total acreage of 

lands affected by rising water tables and increasing salinity is 

about 1,000,000 acres in the San Joaquin Valley (State Board, 

1999a). A recently instituted land retirement program has 

identified willing sellers of up to 15,000 acres in the Westlands 

and Tulare subareas and has acquired several hundred acres as 

of 1998 (USDOI Interagency Land Retirement Team, 1999; 

Drainage Implementation Program, 1999b).

Factors in calculating selenium loads

One approach to calculating selenium loads is to 

examine historical records and planning efforts for agricultural discharges with the goal of developing relations among 

acreage, drainage generated or discharged, selenium concentration, and load of selenium. Selenium load scenarios in 

this report are developed from historical annualized drainage 

volumes and assigned concentrations reflective of compiled 

measured concentrations in ground water and drainage 

because these are the data and tools available (appendix B). 

Recent monitoring programs have failed to collect the data 

necessary to develop cause and effect relations; for example, 

between selenium distribution or concentration in ground and 

surface water and implementation of management actions. The 

limitations of the available record are significant (appendices 

C and D and see discussion of each subarea); nevertheless, 

broad estimates are feasible. 

Management of selenium loads involves three factors 

(Drainage Program, 1990a): 

Acreage requiring drainage. Acreage is expressed 

as either the extent of problem acres or tile-drained 

acres. Problem acres generate a generic problem water

as an expression of the extent of affected acres. In 

the context of this report, tile-drained or subsurface 

drained acres would be expected to generate concentrated drainage as opposed to problem water. Neither 

•

categorization adequately addresses the regional pooling of drainage to include upslope components. In the 

analysis presented here, the distinction made between 

problem water and subsurface drainage helps in projecting future loads by enabling an assignment of water 

quality based on this distinction. 

The volume of drainage generated per acre. A factor 

is applied (acre-feet per acre) to the amount of affected 

acreage (acres) to estimate the amount of drainage 

generated (acre-feet). The average annual volume of 

problem water generated from problem lands under 

conditions in 1990 was estimated as 0.7 acre-ft per acre 

per year (Drainage Program, 1990a). The Drainage 

Program predicted that changes in on-farm drainage 

management practices could reduce the volume generated to approximately 0.4 acre-ft per acre per year. 

Recent updates of conditions in the Grassland subarea 

show an average annual volume per acre of 0.38 to 

0.47 acre-ft per year (appendix B, table B8). An average annual pollution abatement objective of 0.2 acre-ft 

per acre per year has been considered as necessary to 

meet selenium load limits in the Grassland subarea 

(Environmental Defense Fund, 1994). 

The concentration of selenium in irrigation drainage. Reconnaissance-level data on selenium concentrations in shallow ground waters are available from all 

areas except the Northern subarea (also see appendices 

A through D for details) (Drainage Program, 1989, 

1990a) (table 3). The concentration of selenium in 

effluent drainage reflects a managed balance of input, 

output, and storage. Treatment technologies (mostly 

unspecified) or dilution with selenium-poor water 

(blending) can be used to reduce concentrations below 

those found in shallow ground water. Most technical 

evaluations have not applied concentrations to estimates of drainage volumes to calculate potential loads 

of selenium (for example, Drainage Program, 1990a).

All three factors can vary greatly depending upon 

assumptions about management strategies. Two possible 

alternative management futures were defined by Drainage 

Program: (1) no implementation of the Drainage Program 

management plan, 0.60 to 0.75 acre-ft per acre per year 

generated drainage, namely, without future; and (2) with 

implementation of the Drainage Program management plan, 

0.40 acre-ft per acre per year generated drainage, namely, 

with future (Drainage Program 1989, 1990a). A third condition defined for use in load scenarios presented here is called 

with targeted future. The targeted future condition applies a 

factor of 0.20 acre-ft per acre per year of generated drainage, 

exemplifying the lowest, although probably not realistic, 

irrigation water return. The without future alternative, in which 

the management plan is not implemented, result in less volume 

of drainage because of the predicted abandonment of approximately 84,000 acres of land due to salinization by the year 

2000 (appendix B, tables B11 through B17). If the Drainage 

•

•
 25

Program plan was implemented, the amount of drainage would 

be reduced to 0.4 acre-ft per acre per year, but the total land in 

production would be preserved. 

A mixture of metric and English units is used in selenium 

load calculations provided here and in the following discussion. This is unconventional for a scientific report, but is done 

here to aid communication with the widest audience in the 

most recognizable terms. Loads of selenium are expressed in 

pounds (lbs); area is described in acres; volume of discharge 

is expressed in acre-feet (acre-ft) or million acre-ft; selenium 

concentrations are expressed as μg/L (equivalent to the regulatory term parts per billion) or μg/g (equivalent to the regulatory term parts per million). Conversion between these units 

and other scientific units, which are used in the analysis of 

selenium ecological effects, can be found in table 4. Selenium 

(Se) load in lbs is calculated using the equation:

[Se concentration (μg/L) × volume of drainage (acre-ft)] 

× 0.00272 = Se load (lbs), 

 or 

[Se concentration (μg/L) × [(acres) × (acre-ft per acre)] 

× 0.00272 = Se load (lbs), 

where 0.00272 lbs Se per acre-foot is equal to a concentration 

of 1 μg/L Se in an acre-foot of water. 

Characteristics of agricultural subareas 

Evaluation of demand for drainage and estimates of 

potential selenium loads requires consideration of specific 

agricultural subareas in the San Joaquin Valley (Northern, 

Grassland, Westlands, Tulare, and Kern subareas, figs. 3, 4, 

and appendix B). Subarea analysis presented here depends on 

understanding the history, agricultural activity, and geohydrologic characteristics of each designated area. A brief summary 

is given below for each subarea designated by the Drainage 

Program (1989 and 1990a). Data given in parentheses are 

from the Drainage Program (1989). Detailed data are given in 

appendix B.

Westlands Water District and Subarea 

(770,000 total acres; 576,000 irrigated acres; 5,000 acres with 

subsurface drains, alleviating salinization in 42,000 acres)

The Westlands subarea (figs. 3 and 5) was the first to 

discharge irrigation drainage to the San Luis Drain (appendix 

B, table B1). Drainage was released into Kesterson National 

Wildlife Refuge from 1981 to 1986. As a result of the ecological crisis associated with Kesterson National Wildlife Refuge, 

the Westlands subarea now has a policy of no discharge. 

Drainage is recycled onto farmlands and/or stored in underlying ground-water aquifers, where irrigation and aquifer 

supplies are used for dilution. As a result of a recent U.S. 

Court of Appeals decision (Hug and others, 2000), the USBR 

is initiating a process to provide drainage service to the San 

Luis Unit (USBR, 2002a, 2005).

The data record from the Westlands subarea is particularly limited with no specific monitoring for selenium since 

closure of the San Luis Drain in 1986. Only data on groundwater elevations (Westlands Water District, 1998) are available 

in the area most affected by geologic sources of selenium. 

This area is potentially the greatest generator of selenium in 

San Joaquin Valley because it, more than any other subarea, 

encompasses the Panoche Creek alluvial fan (Presser and 

others, 1990). This fan and interfan area receive the most seleniferous runoff and erosion from the Coast Ranges (Tidball 

and others, 1986, 1989; Presser, 1994b). 

Used here are the estimates of areas of shallow ground 

water that affect farming presented in management plans, 

testimony, and a recent status report (Westlands Water District, 

1996, 1998). The Westlands Water District specifically 

contended (State Board, 1985) that the 5,000 drained acres 

actually represented drainage from 42,000 acres because of the 

downslope location of the drainage collection system. 

Historic management plans predicted 170,000 acres of 

the Westlands Water District would be affected by salinization by the year 2000 and 227,000 acres would be affected 

by 2040. It is estimated that immediate drainage needs exist 

for 200,000 acres, resulting in 60,000 acre-ft of drainage 

per year (for example, 200,000 acres × 0.3 acre-ft per acre = 

60,000 acre-ft) (USBR, 1992; Westlands Water District, 1996) 

(appendix B, table B2). 

Table 4. Conversion factors for selenium and salt or total 

dissolved solids (TDS).

Selenium (Se) Salt or Total Dissolved Solids 

(TDS)

1 part per billion (ppb) = 

1 microgram/liter (μg/L)

1 part per million (ppm) = 

1 milligram/liter (mg/L)

1 gallon = 3.785 liters 1 gallon = 3.785 liters

1 acre-foot = 325,900 gallons = 

1,233,532 liters

1 acre-foot = 325,900 gallons = 

1,233,532 liters

1,233,532 micrograms/acre-foot at 

1 μg/L

1,233,532 milligrams/acre-foot at 

1 mg/L

1.23 grams/acre-foot at 1 μg/L 1,234 grams/acre-foot at 1 mg/L

454 grams = 1 pound (lb) 454 grams = 1 pound (lb)

0.00272 lbs/acre-foot at 1 μg/L 2.72 lbs/acre-foot at 1 mg/L

[1 μg/L = 0.00272 lbs/acre-foot] [1 mg/L = 2.72 lbs/acre-foot]

2000 lbs = 1 ton

1 mg/L = 0.00136 tons/acre-foot

Volume

1 cubic foot per second (ft3/s) = 1.98 acre-feet/day
26 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Because discharges from the Westlands subarea were 

discontinued in 1986, no current direct measurements of 

effluent quality are available. Historic discharges provide some 

guidance. In 1983 and 1984, average selenium concentrations 

in discharges from the San Luis Drain to Kesterson National 

Wildlife Refuge ranged from 330 to 430 μg/L selenium (State 

Board, 1985; Presser and Barnes, 1984, 1985) and as quoted 

from regulatory documents, from 230 to 350 μg/L (Westlands 

Water District, 1996) (table 3). This resulted in an annual 

discharge of 4,776 lbs selenium and a discharge of 17,400 

lbs to Kesterson Reservoir over the history of drain usage by 

Westlands Water District (January 1981 to September 1985) 

(USBR, 1986) (appendix B, table B1). The cumulative 17,400 

lbs selenium is termed here as one kesterson (kst). The use 

of this unit provides perspective on the mass of selenium that 

was a hazard to wildlife when released directly to a wetland 

(Presser and Piper, 1998).

Testimony in legal proceedings summarized data for selenium concentrations in broader areas of shallow ground water 

in the Westlands Water District (table 3). Mean concentrations 

ranged from 163 μg/L to 300 μg/L in different studies. The 

USBR suggested the most likely estimate of average selenium 

concentration in shallow ground water is 150 μg/L. With treatment or blending, management plans asserted that concentrations could be reduced to as low as 50 μg/L. 

Grassland Subarea 

(707,000 total acres; 311,000 to 329,000 irrigated acres; 51,000 

drained acres) 

The Grassland subarea is the second subarea requiring 

drainage included in the original agreement to provide 

drainage service (see San Luis Unit, Delta-Mendota Service 

Area, table 1). This area of the western San Joaquin Valley is 

to the north and downslope of the Westlands Water District 

(Drainage Program, 1990a) (fig. 3). The Grassland subarea 

contains 70,000 to 100,000 acres of land that have historically 

contributed the majority of subsurface drainage to the San 

Joaquin River (appendix B, table B3). Adjacent Federal, State, 

and private riparian wetlands contain the largest tract of habitat 

remaining in the San Joaquin Valley. Varying lengths of the 

complex channel system within the wetlands convey agricultural drainage to the San Joaquin River. Mud and Salt Sloughs 

(figs. 3 and 4) are examples of tributaries flowing through 

the wetlands of the Grassland Resource Conservation District 

and the San Luis National Wildlife Refuge Complex that have 

conveyed drainage at certain times. In 1995, the discharge 

from about 100,000 acres of farmland was consolidated into a 

28-mile segment of the original San Luis Drain (renamed the 

Grassland Bypass Channel) in order to reduce contaminated 

wetland water supplies, but discharge to the San Joaquin River 

via Mud Slough remains (USBR, 1995, 2001c; USBR and San 

Luis Delta-Mendota Water Authority, 1995 and 2001; USBR 

and others, 1998 and ongoing).

The available historical record from the Grassland 

subarea includes data from discharges to the San Joaquin 

River. This type of monitoring was used mainly to compare 

selenium concentrations in the river to water quality objectives 

(table 5; appendix B, tables B4 to B7; and appendix C, fig. 

C1). Historic data documenting selenium and salt loading to 

the San Joaquin River show limitations in flow and concentration measurements; and in the methodology used to calculate 

loads and regulatory targets (Central Valley Board, 1998f). 

Only recently are measurements of flow being conducted more 

consistently (USBR and others, 1998 and ongoing). 

The effects of selenium discharges on water quality are 

monitored at upstream drainage source areas, at tributaries 

to the San Joaquin River (Mud and Salt Sloughs), and at 

sites on the San Joaquin River (figs. 3 and 4, Crows Landing 

downstream of the Merced River; and Vernalis, where the 

San Joaquin River enters the Delta). In general, monitoring 

data from 1986 to 1998 (table 5; appendix B, tables B4 to B7) 

showed:

Average selenium loads at four San Joaquin River locations were: upstream source (Grassland Area Farmers 

Drainage Problem Area), 8,698 lbs; Mud and Salt Sloughs 

combined, 7,335 lbs; Crows Landing, 8,807 lbs; and Vernalis, 9,788 lbs.

Annual selenium loads at the upstream source ranged 

from 5,083 to 11,875 lbs; at Crows Landing from 3,064 to 

15,501 lbs; and at Vernalis from 3,611 to 17,238 lbs (table 

5). 

Variability in load was at least partly driven by precipitation, with larger loads discharged in wetter years than in 

drier years (appendix A, figs. A9 and A10). 

Estimated selenium loads for source waters (agricultural 

drains or canals) differed from load estimates for the San 

Joaquin River monitoring sites. Some downstream estimates were higher and some were lower than the drainage 

source estimates. The difference among sites was usually 

small compared to the year-to-year variability in initial 

load except for unusually wet years (such as 1995 and 

1998). 

Determinations of selenium in suspended sediment, bed 

sediment, or biota were not performed in conjunction 

with water-column selenium concentrations. Reductions 

in downstream loads may occur because of uptake by 

sediment and biota (Presser and Piper, 1998). Monitoring 

for these types of components to determine a selenium 

mass balance would help to characterize the biochemical 

reactions that may account for the variability seen between 

upstream and downstream sites (Presser and Piper, 1998). 

Additionally, monitoring was not sufficiently frequent to 

accurately characterize loads during variable flows. 

Analysis of available data for WYs 1997 and 1998 

showed that monthly average total selenium concentrations in 

blended drainage ranged from 40.6 to 105.5 μg/L in (USBR 

and others, 1998 and ongoing) (appendix B, tables B9 and 

B10). The daily range was 15 to 128 μg/L over this period 

(appendix D, figs. D15 and D16). The annual average sele1.

2.

3.

4.

5.
 27

nium concentration observed in collected drainage from the 

Grassland area was 62.5 μg/L in WY 1997 and 66.9 μg/L 

in WY 1998 (USBR and others, 1998 and ongoing) (table 

5 and appendix B, tables B9 and B10). These averages are 

comparable to the historical average of 67 μg/L from 1986 to 

1994 and the planning estimate of 150 μg/L used by the State 

(Central Valley Board, 1998d, e, f, g, h) (table 3). Modeled 

discharges from the Grassland subarea were estimated at 80 to 

120 μg/L selenium (Drainage Program, 1990a; Central Valley 

Board, 1996a, b) (table 3). 

Tulare Subarea

(883,000 total acres; 506,000 to 551,000 irrigated acres; 42,000 

drained acres) 

Kern Subarea 

(1,210,000 total acres; 686,000 irrigated acres; 11,000 drained 

acres) 

The Tulare and Kern subareas are located in the southern 

San Joaquin Valley and discharge to privately owned evaporation ponds. Discharges to evaporation ponds are considered here in selenium load scenarios, although it is not clear 

whether an extension will be built to the south to include the 

Tulare and Kern subareas in the overall drainage solution. The 

inclusion of the Tulare and Kern subareas when considering 

the extent of the San Joaquin Valley contamination is also 

consistent with other comprehensive assessments. 

Table 5. Annual discharge, average selenium concentration, and selenium loads from the Grassland Drainage Source area; Mud and Salt 

Sloughs; and the San Joaquin River at Crows Landing and Vernalis.

[Grassland Drainage Source: problem acres 65,200 to 103,390; drained acres 47,500 to 51,000; historic drainage quality average from 1986 to 1994 was 64 μg/L. 

The San Joaquin River at Crows Landing is the compliance point for State regulation. The USEPA 5 μg/L water-quality criteria was exceeded at the compliance 

point >50 percent of the year during WYs 1987 through 1991 and during 1994. A drainage prohibition of 8,000 lbs selenium per year was enacted in 1996. NA = 

data not available]

WateryearGrassland Drainage 

Source Areas

Mud and Salt Sloughs San Joaquin River 

at Crows Landing

San Joaquin River 

at Vernalis

Volume 

(acre-ft)

Selenium 

(μg/L)

Selenium 

load

(lbs)

Volume 

(acre-ft)

Selenium 

(μg/L)

Selenium 

load

(lbs)

Volume 

(million 

acre-ft)

Selenium 

(μg/L)

Selenium 

load

(lbs)

Volume 

(million 

acre-ft)

Selenium 

(μg/L)

Selenium 

load

(lbs)

1986 67,006 52 9,524 284,316 8.6 6,643 2.67 1.6 11,305 5.22 1.0 14,601

1987 74,902 54 10,959 233,843 12.0 7,641 0.66 4.9 8,857 1.81 1.8 8,502

1988 65,327 57 10,097 230,454 13.0 8,132 0.55 6.2 9,330 1.17 2.7 8,427

1989 54,186 59 8,718 211,393 14.1 8,099 0.44 6.3 7,473 1.06 3.0 8,741

1990 41,662 65 7,393 194,656 14.6 7,719 0.40 5.6 6,125 0.92 3.0 7,472

1991 29,290 74 5,858 102,162 14.0 3,899 0.29 4.5 3,548 0.66 2.0 3,611

1992 24,533 76 5,083 85,428 12.6 2,919 0.30 3.7 3,064 0.70 1.9 3,558

1993 41,197 79 8,856 167,955 15.0 6,871 0.89 3.5 8,379 1.70 1.9 8,905

1994 38,670 80 8,468 183,546 16.0 7,980 0.56 4.8 7,270 1.22 2.3 7,760

1995 57,574 76 11,875 263,769 14.9 10,694 3.50 1.6 14,291 6.30 1.0 17,238

1996 52,978 70 10,034 267,344 13.0 9,697 1.44 3.0 10,686 3.95 1.1 11,431

1997 37,483 62.5 7,097 NA 30.0a NA 4.18 2.9 8,667–

9,054

6.77 0.6 11,190

1998 45,858 66.9 9,118 NA 27a NA 5.13 1.6 13,445–

15,501

8.5 NA 15,810

1986 –

1995

0.4 – 286b 0.5 – 59b 0.4 – 17b 0.4 – 9.6b

1997– 

1998)

15 – 134b 3 – 104b 0.1– 8.2b 0.1– 8.2b

Data sources: Drainage Problem Area, Central Valley Board, 1996b, c; 1998d through h; 2000b, c (note: In 1996, the board recompiled data from 1985 through 

1995; therefore, some calculations and referenced values may be based on earlier versions of compiled data). Grassland Bypass Channel Project monthly, quarterly, and annual reports (http://www.sfei.org/grassland/reports/gbppdfs.htm; USBR and others, 1998 and ongoing).

a

 Mud Slough only.

b

 Daily range.
28 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

From 1975 to 1990, 16 ponds covering 5,900 acres were 

developed in the Tulare subarea; ponds covered 1,300 acres 

in the Kern subarea (Drainage Program, 1989). Since that 

time, no new ponds have been built and many ponds have 

closed (Central Valley Board, 1997, 1998c) (appendix B, 

tables B19 to B21). The subareas are internally drained basins 

with relict lakebeds (Tulare, Goose, Buena Vista, and Kern) 

as dominant geologic features. The lakebeds are little influenced by the Panoche Creek alluvial fan, but are surrounded 

by geologic sources of trace elements from the Coast Ranges 

and the Sierra Nevada. The geochemistry of soils and shallow 

ground waters is controlled by depositional zones (alluvial 

fan, basin trough, or lake bed) and depositional environments 

(oxidizing or reducing). Concentrations of selenium, uranium, 

arsenic, molybdenum, and boron are elevated in specific zones 

(Fujii and Swain, 1995). Geomorphological features affect 

the placement and number of subsurface drains installed in 

the subareas. Subsurface drains are mainly limited to lower 

elevations of the lakebeds (42,000 acres in Tulare subarea and 

11,000 acres in Kern subarea) (Drainage Program, 1989). 

Initial estimates made by the Drainage Program (1989) 

showed the Tulare subarea with 320,000 acres of land with 

ground-water levels within 5 ft of land surface. Estimates for 

the Kern subarea showed 64,000 acres are affected. For 2000, 

the estimate of affected acres increased to 366,000 in Tulare 

subarea and 100,000 acres in Kern subarea. Data collected 

by the State of acreage adversely affected by shallow ground 

water were considered gross estimates because of sparse data 

and extrapolation over a 696,000-acre study-area (the Tulare 

Lake region) (Department of Water Resources, 1997). The 

State study area boundaries differed from those given above as 

part of the Drainage Program designation.

Evaluation of selenium concentrations in Tulare and 

Kern subareas was limited to annual reporting by dischargers 

as required by the State as part of permit requirements for 

discharges to privately owned evaporation ponds (Central 

Valley Board, 1993, 1997, 1998c; State Board, 1996a; Anthony 

Toto, Central Valley Board, personal commun., January, 1998) 

(appendix B, tables B19 to B21). Selenium concentrations 

in discharges from the Tulare subarea to private evaporation 

ponds are remarkable for being low when compared to selenium concentrations in discharge from Westlands or Grassland 

subareas. The record is limited, but values measured in 1988, 

1989, and 1993 through 1997 showed most selenium concentrations were below 10 μg/L, with the exception being the South 

Tulare Lake Drainage District discharge of up to 30 μg/L. Some 

higher selenium concentrations, ranging up to 760 μg/L, have 

been reported in some discharges to smaller ponds (table 3 and 

appendix B, tables B19 to B21). For the Kern subarea, limited 

data on discharges to evaporation ponds in 1988, 1989 and 1993 

to 1997 showed selenium concentrations ranged from 83 to 671 

μg/L, with the exception being the Lost Hills Ranch discharge 

of about 2 μg/L (Central Valley Board, 1990a, b). In general, 

selenium concentrations in discharges from the Tulare subarea 

are < 50 μg/L and for the Kern subarea are > 180 μg/L.

Northern subarea 

(236,000 total acres; 157,000 irrigated acres; 26,000 drained 

acres)

The Northern subarea is considered here and in load 

scenarios for consistency with other regional evaluations. The 

Northern subarea presently drains to the San Joaquin River 

through both discharge and ground-water seepage. Estimates 

of acres requiring drainage have not been updated since 1990 

and current records evaluating selenium are not available for 

compilation from this subarea. Most estimates suggest that 

drainage needs are relatively small compared to other areas 

(CH2M HILL, 1988; Drainage Program, 1990a) and will 

remain so if access to the San Joaquin River for drainage is 

available to the same degree (that is, the subarea remains in 

hydrologic balance). 

Development of load scenarios

While most technical evaluations stop with estimates of 

problem acreage and problem water volumes, understanding 

the range of possible selenium concentrations in drainage is 

critical to evaluating potential loads. To bracket possible selenium concentrations in different scenarios of selenium loads 

from the western San Joaquin Valley, three concentrations are 

used in conjunction with different estimates of drainage and 

acreage to generate load projections (see detailed analysis in 

appendix B). In general, a concentration of 50 μg/L selenium 

in drainage is considered potentially available with treatment. 

Testimony in court hearings have centered around the fact that 

a non-specified treatment could lower the selenium concentration to an overall 50 μg/L; then this product water would be 

disposed of in an extension of the San Luis Drain. Therefore, 

one scenario used here is that such treatment options will be 

available, and/or mixtures of drainage water will resemble 

those presently being released from the Grassland subarea (62 

to 66 μg/L selenium). For this case, a selenium concentration 

of 50 μg/L is used to represent treated or blended (diluted) 

drainage.

Other load scenarios used here will assume a maximum 

case of 300 μg/L selenium and an intermediate possibility of 

150 μg/L selenium [an average for present day subsurface 

drainage waters in the Grassland subarea (Central Valley 

Board, 1996c); near the mean (163 μg/L) presented for 

the 42,000 acres in Westlands Water District (Stevens and 

Bensing, 1994); and a conservative estimate (at least 150 μg/L) 

in Westlands Water District by USBR (Wanger, 1994)]. Even 

though the recent public record is limited, these estimates may 

be conservative given the quality of the ground water and the 

magnitude of selenium accumulation in the internal reservoirs of the western San Joaquin Valley (table 3; appendix 

A). Adequate monitoring to trace ground-water movement 

and selenium concentrations as a function of time is needed 

to assess the ongoing affect of management actions aimed at 

more storage and less leaching (also see appendix D).
 29

One further approach used here to project potential total 

selenium loads from the San Joaquin Valley is to generate 

scenarios using a compilation of data on selenium concentration and volume that has become available for each subarea 

since the Drainage Program (1985 to 1990) (appendix B, 

tables B9, B10 and B19 to B21). It is recognized that this 

involves use of data that all have significant limitations. 

However, the existing area-specific data incorporate the 

geographical heterogeneity of drainage in establishing the 

boundaries of potential selenium discharges. Hence, this type 

of approach to develop scenarios may be particularly reflective 

of specific geologic and hydrologic conditions in each of the 

five subareas.

Load scenarios based on management 

alternatives for all subareas

The total out-of-valley drainage selenium load is the sum 

of annual selenium loads potentially discharged from all five 

subareas (figs. 3 and 4) (table 6). Each scenario is specific 

to a Drainage Program management option (implementation, with future; no implementation, without future; and with 

targeted future) and a projected year (years 1990, 2000, and 

2040) (table 6). These scenarios based on the broad Drainage 

Program approach, do consider, to some extent, addressing the 

longer-term problem of an accumulated imbalance of water, 

salt, and selenium and the sustainability of agriculture in the 

San Joaquin Valley, rather than only managing an annual 

imbalance.

A wide range of selenium loads from the western San 

Joaquin Valley is possible in the future given the ranges of 

acre-feet of drainage and drainage quality compiled from 

management options of the Drainage Program. If the volume 

of drainage water is assumed not to increase beyond the 

volume of subsurface drainage that existed in 1990 (100,000 

acre-ft) and the assigned concentration of selenium is 50 μg/L, 

then 13,600 lbs selenium per year are projected. Assigned 

selenium concentrations of 150 μg/L or 300 μg/L would yield 

loads of 40,800 or 81,600 lbs selenium per year, respectively. 

Total drainage can be projected using problem acreage

across all subareas of the San Joaquin Valley (table 6). Specifically, a scenario using an assigned concentration of 50 μg/L 

selenium to represent blended generic drainage in conjunction 

with the most quoted estimate from the Drainage Program of 

314,000 acre-ft of problem water (year 2000 without implementation of the specified management plan) yields a load of 

42,704 lbs selenium per year. For year 2040, the amount of 

problem water would increase to 666,000 acre-ft, generating a 

load of 90,576 lbs selenium per year at an assigned concentration of 50 μg/L selenium. 

 A scenario using an assigned concentration of 150 

μg/L selenium to represent generic subsurface drainage and a 

Drainage Program estimate of subsurface drainage of 144,000 

acre-ft (with future) in year 2000 yields a load of 58,752 lbs 

selenium per year. For year 2040 under the condition of implementation of the Drainage Program (303,600 acre-ft per year), 

the discharged load would be 41,290 lbs selenium per year. 

Using an assigned concentration of 300 μg/L selenium in 

year 2000 and the least amount of estimated drainage (72,000 

acre-ft per year with targeted future), the load discharged 

would be 58,573 lbs selenium per year. In year 2000, 163,000 

acre-ft (without future) at 150 μg/L selenium would produce 

a load of 66,504 lbs selenium per year. In year 2040, 223,000 

acre-ft (without future) at 150 μg/L selenium would produce a 

load of 90,984 lbs selenium per year.

Load scenarios based on management 

alternatives for individual subareas

Using the same approach as above, specific loads can be 

projected for each of the five subareas based on detailed data 

given by the Drainage Program for year 2000 (see appendix B 

for further analysis). Assigning concentrations of 50, 150, and 

300 μg/L selenium to compiled estimates of problem water 

and subsurface drainage for each subarea generates all possibilities that result from application of different management 

alternatives (appendix B, table B18). A range of total loads 

for all subareas is also given to compare to loads projected in 

table 6. Appendix B (fig. B2) also illustrates use of a graphical 

tool to enable projection of an annual selenium load for any 

of the three assigned concentrations given a specific drainage 

volume. This type of application gives versatility and flexibility for future planning estimates.

Load scenarios based on individual subarea 

discharges

Loads also can be derived based on a compilation 

presented here of currently available data on problem acreage, 

drainage volume, and selenium concentration (appendix B, 

tables B9, B10 and B19 to B21). The values based on current 

data show only that amount discharged on the surface (such 

as to the San Joaquin River or to the evaporation ponds of 

Tulare and Kern subareas), and hence only address the present 

discharge being used to manage an annual imbalance of water, 

salt, or selenium (table 7). Depending on the type of data 

available from each subarea, projections are made concerning 

concentration or load. Because of the limited data and broad 

range of management alternatives across the subareas, 

maximum and minimum selenium concentrations are given 

to bracket possible load scenarios at each specific volume of 

drainage.

For the Northern subarea no current data is available, 

so a nominally assigned selenium concentration of 5 μg/L is 

applied as a minimum to adhere to USEPA’s selenium criteria 

for the protection of aquatic life; a selenium concentration 

of 10 μg/L is applied as a maximum. The projected selenium concentration range is 68 to 152 μg/L for the Grassland 

subarea; 49 to 150 μg/L for the Westlands subarea (note, no 
30 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Table 6. Management alternatives and cumulative load scenarios for five subareas (Northern, Grassland, Westlands, Tulare, and Kern) 

using 50, 150, and 300 μg/L assigned selenium concentrations. 

[Data for management alternatives, acreage, acre-feet, and acre-feet/acre/year are from Drainage Program (1990a). Problem acres are assumed to generate 

a generic problem water as an expression of affected acres. Tile-drained or subsurface drained acres would be expected to generate concentrated drainage as 

opposed to problem water. In the analysis here, the distinction between problem water and subsurface drainage helps in assigning water quality. The Drainage 

Program defined without future (no implementation of recommended plan) and with future (implementation of recommended plan) management alternatives. 

A third condition defined here as with targeted future applies a factor of 0.20 acre-feet/acre/year of generated drainage to estimate the lowest, although probably not realistic, irrigation water return. Also defined here is a year 2000 projection for problem water, which applies a factor of 0.4 acre-feet/acre/year.]

Management

alternative

Problem or tile 

drained acreage 

(acres)

Generated drainage 

(acre-feet/acre/year)

Problem 

water or 

drainage 

(acre-feet)

Selenium load (lbs) at assigned

selenium concentrations

50 μg/L 150 μg/L 300 μg/L

1990

 Without future 

 Subsurface drainage basis

133,000 0.60– 0.75 100,000 13,600 40,800 81,600

 With future 

 Subsurface drainage basis 133,000 0.40 53,200 7,235 21,706 43,411

2000

 Without future 

 Subsurface drainage basis 269,000

Northern 0.75 

Tulare 0.65– 0.70

others 0.50– 0.55

163,000 22,168 66,504 133,008

 With future

 Subsurface drainage basis 360,000 0.40 144,000 19,584 58,752 117,504

 With targeted future 

 Subsurface drainage basis 360,000 (assumed 

from above case)

0.20 (assumed for 

minimum drainage)

72,000 9,793 29,376 58,753

 Without future 

 Problem water basis 444,000 0.70 (range 0.60– 0.75) 314,000 42,704 128,112 256,224

 0.4 acre-feet/acre/year future 

 Problem water basis 444,000 0.40 177,600 24,154 72,460 144,922

2040

 Without future 

 Subsurface drainage basis 386,000 Northern 0.75 

all others 0.55

(minimum progress)

223,000

(243,000)a

30,328 90,984 181,968

 With future 

 Subsurface drainage basis 759,000 0.40 (assumed) 303,600 41,290 123,869 247,738

 Without future 

 Problem water basis 951,000 0.75 (steady increase) 666,000 90,576 271,728 543,456

a

 The Drainage Program (1990a) estimate difffers from that calculated here.
 31

current data, only testimony on acreage is available); 1.7 to 9.8 

μg/L for the Tulare subarea; and 175 to 254 μg/L for the Kern 

subarea. Current conditions for each subarea (table 7) give 

ranges for annual selenium load scenarios of:

 • Northern subarea 350 to 700 lbs selenium per year

 • Grassland subarea 6,960 to 15,500 lbs selenium per year

 • Westlands subarea 8,000 to 24,480 lbs selenium per year

 • Tulare subarea 91 to 519 lbs selenium per year

 • Kern subarea 1,089 to 1,586 lbs selenium per year

 • Sum total 16,490 to 42,785 lbs per year

A graphical depiction of these projections for each subarea 

is given in appendix B (fig. B3). The high and low ranges of 

possible annual discharges are illustrated in figures 6 and 7. 

As noted above, the largest selenium loads come from the 

Westlands subarea and the Grassland subarea because of their 

combination of high problem acreage, and thus problem water

volume, and high selenium concentration.

Choice of load scenarios (supply and demand)

Total selenium load scenarios from various combinations of subareas that might be included in a drainage collection system are summarized in table 8. These projected loads 

of selenium provide the basis for determining the upper and 

lower limits of selenium discharge from the western San 

Joaquin Valley that can be expected to enter the Bay-Delta 

either through a proposed direct conveyance to the Bay-Delta 

or the San Joaquin River. Secondarily, the projections provide 

the basis for determining the magnitude of selenium load 

reduction that may become necessary to achieve a specific 

load of selenium. Projections like those summarized (table 8) 

implicitly assume that selenium loads will be primarily driven 

by the demand for drainage, with different degrees of management superimposed. Of course, different demand scenarios 

than those shown also are possible. 

The first four scenarios (table 8) show that the load of 

selenium increases from a minimum of 6,960 lbs per year to 

42,785 lbs per year as additional area is added to drainage 

collection systems and/or as drainage volume and quality is 

less managed. The specific conditions for each scenario are: 

• Only the existing discharges from the Grassland subarea 

would be carried to the Bay-Delta through an extension 

of the San Luis Drain. It seems unlikely that demand 

would remain at this level once an out-of-valley conveyance was available. Increasing acreages of saline soils, 

rising ground water tables, and the availability of a conveyance facility are likely to generate strong pressures 

from other areas to use the facility. 

• Discharge from the Grassland subarea through a San Luis 

Drain extension or San Joaquin River would be discontinued and only the Westlands subarea would use an 

extension of the San Luis Drain. 

• Grassland subarea discharges and Westlands subarea 

discharges both would be carried to the Bay-Delta; this 

seems a likely outcome if a conveyance is constructed. 

• Drainage is collected valleywide from all five subareas. 

This would require extensions of the San Luis Drain into 

Table 7. Calculated drainage scenarios for five subareas (Northern, Grassland, Westlands, Tulare, and Kern).

[Calculations are based on evidence presented by Westlands Water District or currently available ranges of drainage volume, selenium concentration, or selenium load, except for the Northern subarea where there is no management plan recommended by the Drainage Program (tables 

3, 5; appendix B, tables B9, B19– 21) (Drainage Program, 1990a). Data details for subareas (also see appendices A and B): Northern: nominal 

5 and 10 μg/L selenium concentrations are assigned; drainage volume is from the Drainage Program (1990, Table 3 for year 2000). Grassland: 

minimum is volume and load measured for WY 1997 as part of the Grassland Bypass Channel Project; maximum is an assigned selenium 

concentration of 150 μg/L applied to the same volume. Westlands: minimum is for condition presented as evidence for Westlands Water District; maximum condition is for the same volume of drainage, but with an assigned concentration of 150 μg/L. Tulare and Kern: volume and 

selenium concentration for 1993– 97 (Anthony Toto, Central Valley Board, personal commun., January, 1998) from which an average volume 

(1993– 1997) is calculated; the minimum and maximum loads are selected as the range]. 

Subarea or 

area

Drainage 

volume 

(acre-feet/

year)

Selenium

Minimum Problem areas

(lbs/year)

Minimum 

(μg/L)

Maximum 

(lbs/year)

Maximum 

(μg/L)

Maximum and 

minimum (lbs/

acre-feet)

Northern 26,000 350 5 700 10 0.014 – 0.027 −

Grassland 37,483 6,960 68 15,500 152 0.186 – 0.414 97,000

Westlands 60,000 8,000 49 24,480 150 0.133 – 0.408 200,000

Tulare 19,493 91 1.7 519 9.8 0.005 – 0.027 −

Kern 2,292 1,089 175 1,586 254 0.475 – 0.692 −

Total 145,268 16,490 − 42,785 − − −
32 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Kern and Tulare subareas, in addition to an extension to 

the Bay-Delta. 

A future that considers only agricultural needs might call 

for draining all 444,000 acres of problem lands. The fifth and 

sixth scenarios (table 8) provide projections of selenium loads 

for a valley-wide drain that includes all potential problem 

lands estimated for the year 2000 (table 8). The first of these 

calculations shows the range of selenium loads expected 

if drainage management follows the plan submitted by the 

Drainage Program. If both quality (treating drainage to 50 

μg/L) and quantity (such as reducing acre-feet per acre per 

year of drainage from 0.7 to 0.4) are managed, loads would be 

19,584 lbs per year. If only quality is managed, total selenium 

loads for the problem lands then would be 42,704 lbs per year. 

It is also possible that no management would be employed or 

management becomes less and less feasible. Drainage volumes 

in this scenario are not controlled and the quality of drainage 

deteriorates to 150 μg/L. In this case, selenium loads would 

rise from a minimum in the range of 42,704 lbs per year to as 

much as 128,112 lbs per year (all problem lands, 0.7 acre-ft 

per acre per year, and 150 μg/L selenium drainage). 

As a comparison, the final forecast (table 8) lists load 

targets given in recent TMDL or TMML management plans 

for discharge to the San Joaquin River from the Grassland 

subarea, a supply-driven strategy (USBR, 1995; Central Valley 

Board, 1998a) (see specifics in discussion of the San Joaquin 

River as a conveyance facility and appendix C). The targeted

selenium loads range from 1,394 lbs per year to 6,547 lbs per 

year depending on flow (wet or dry year) (see appendix C for 

details; tables C1 and C2). Selenium loads measured from WY 

1997 to WY 2002 under regulated Grassland Bypass Channel 

Project management conditions, which include storage in aquifers and surface management areas, ranged from a maximum 

of 9,118 lbs selenium to a minimum of 3,939 lbs selenium 

(USBR and others, 1995; USBR and San Luis Delta-Mendota 

Water Authority, 1995). Load targets for this project continue 

to ramp downward to 3,088 lbs in a wet year and 2,421 lbs in 

a dry year in WY 2009 (USBR, 1995, 2001c; USBR and San 

Luis Delta-Mendota Water Authority, 1995 and 2001). 

Load scenarios based on the capacity of an 

extension of the San Luis Drain 

Exports of selenium from the San Joaquin Valley also 

could be determined by assigning a water quality goal to the 

drainage in a San Luis Drain extension and operating the drain 

at some pre-defined capacity (table 9). The drain is presently 

designed to flow at 300 ft3/s or carry about 220,000 acre-ft 

per year. That capacity could be a factor limiting loads, if a 

water quality standard is employed. Scenarios are given for 

(1) 50 μg/L representing an overall average given in testimony 

that treatment technologies or blending could achieve and 

near present day discharge from Grassland Bypass Channel 

Project to the San Joaquin River (62 to 67 μg/L); (2) 150 

μg/L selenium representing an average for current subsurface 

drainage without blending in the Grassland subarea (Central 

Valley Board, 1996c) and near the mean (163 μg/L) presented 

for shallow ground water from 42,000 acres in the Westlands 

subarea (Wanger, 1994); and (3) 300 μg/L representing a 

concentration approaching that discharged from Westlands 

Water District to Kesterson Reservoir from 1981 to 1985. It is 

notable (and probably a function of the original drain design, 

USBR, 1978; Brown and Caldwell, 1986) that the range of 

loads derived from current or potential discharges for the sum 

of the Grassland and Westlands subareas (table 7; 14,960 to 

39,980 lbs) and that from a drain managed at full capacity at 

50 μg/L (table 9; 29,920 lbs), is within the probable scenario 

derived from demand for drainage to manage the current 

annual imbalance from specific subareas (valleywide drain, 

all potential problem lands with management of drainage 

quantity and quality (19,584 to 42,704 lbs selenium, table 8). 

If a drainage conveyance discharges 150 μg/L selenium, at full 

capacity, the loading forecast (89,760 lbs selenium, table 9) 

0 0.4

0.04

0.02

0.09

1.4

0.89

0.46

0.4

0.062

0.03

0.005

0.8 1.2 1.6

Kestersons (ksts) per year

(1 kesterson = 17,400 lbs selenium)

Kern

Tulare

Westlands

Grassland

Northern

SUBAREAS

High

Low

RANGE

Grassland

42

Kern

4.3

Tulare

1.4

Northern

1.9

Westlands

67

Figure 6. Projected high and low range of annual selenium 

discharges (in kestersons, 1 kst equals 17,400 lbs selenium as 

a measure of potential ecological damage based on load) from 

five subareas of the western San Joaquin Valley using currently 

available data.

Figure 7. Projected high range of daily selenium discharges (in lbs) 

from five subareas shown as proportions of total discharge from the 

western San Joaquin Valley.
 33

converges on that estimated from all problem lands with little 

management (42,704 to 128,112 lbs selenium, table 8). 

Despite the range of assumptions and range of possible 

outcomes considered in tables 7, 8 and 9, there is some convergence of the forecasts, irrespective of how they are derived. 

Load targets result in the smallest and most easily managed 

selenium discharges to the Bay-Delta (1,394 to 6,547 lbs 

selenium). Selenium loads based on the demand for drainage 

converge on a mass discharge of 15,000 to 43,000 lbs of 

selenium per year, if volumes and concentrations are carefully 

managed. Loads quickly increase beyond this level if more 

land is drained and/or volumes or drainage quality are poorly 

managed or controlled (up to 128,112 lbs selenium).

Load scenarios based on the San Joaquin River as 

a conveyance facility (the river, in effect, as a drain)

The above projections assume drainage is conveyed in 

a proposed extension of the San Luis Drain and that loads 

are primarily defined by demand from agriculture. An alternative is to assume that water quality in the San Joaquin 

River would determine selenium discharges, and no drain 

would be constructed. Two approaches for use of the river to 

convey agricultural drainage have been discussed historically. 

Appendix C details the historical record used for derivation 

of loads for the San Joaquin River at Crows Landing and the 

load allocations for dischargers using these approaches. Both 

approaches consider only the amount of dilution water availTable 8. Projections of selenium loads from the western San Joaquin Valley under different drainage 

scenarios. 

[A kesterson (kst) is defined here as 17,400 lbs selenium, the cumulative load that caused ecological damage when 

released to Kesterson National Wildlife Refuge, California) (Presser and Piper, 1998)]. 

Scenario 

(subarea(s) discharging to a proposed 

San Luis Drain extension)

Selenium load

(lbs/year)

Selenium load 

(kestersons/

year)

Cumulative 5-year 

selenium load 

(kestersons)

Grassland (based on current data) 6,960 – 15,500 0.4 – 0.89 2.0 – 4.45

Westlands (based on 50 – 150 μg selenium in drainage and 60,000 acre-feet)8,000 – 24,500 0.46 – 1.41 2.3 – 7.05

Grassland and Westlands (from above) 14,960 – 40,000 0.86 – 2.30 4.3 – 11.5 

Valleywide Drain (current conditions and 

Westlands from above)

16,490 – 42,785 0.95 – 2.46 4.75 – 12.3

Valleywide Drain (all potential problem 

lands with management of drainage 

quantity and quality)

19,584 – 42,704 1.12 – 2.45 5.6 – 12.2

Valleywide Drain (all potential problem 

lands with minimum management of 

quality and quantity)

42,704 – 128,112 2.45 – 7.36 12.2 – 36.8

Total Maximum Daily or Monthly Load 

Model management (load targeted for 

environment safeguards, Grassland 

subarea or drainage basin)

1,394 – 6,547 0.08 – 0.38 0.4 – 1.9

Table 9. Selenium loads conveyed to the Bay-Delta under 

different flow conditions if a constant concentration is 

maintained in the San Joaquin River or a San Luis Drain 

extension. 

[Flow conditions: high flow (3.0 million acre-feet/year); low flow (1.1 

million acre-feet/year); and annual flow assumed for a proposed San Luis 

Drain extension at maximum capacity or a small San Joaquin River input in 

a dry year (approximately 220,000 acre-feet/year)].

Selenium concentration

 in river or 

drain extension (μg/L)

Selenium load (lbs/year)

3.0 million 

acre-feet/

year

1.1 million 

acre-feet/

year

216,810 acrefeet/year

(300 ft3

/s)

0.1 816 299 60

1.0 8,160 2,990 598

2.0 16,320 5,980 1,197

5.0 40,800 14,960 2,992

50 − – 29,920

150 − – 89,760

300 − – 179,520
34 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

able; no consideration is given to defining the assimilative 

capacity of the receiving water (the San Joaquin River) based 

on the bioaccumulative nature of selenium. These approaches 

encompass both quasi-static and dynamic modeling of flows.

Total Maximum Daily Load (TMDL) or Total Maximum Monthly Load (TMML) models. This approach 

models load allocations based on historical flows in the 

San Joaquin River. A water quality standard is applied to 

design flows to calculate a selenium load limit for dischargers (Environmental Defense Fund, 1994). This is the 

technique mandated by USEPA for discharges to impaired 

water bodies such as the San Joaquin River (Clean Water 

Act, as amended, 1987; USEPA, 2000; State Board, 2002). 

The San Joaquin River compliance site for the 130 miles 

of impairment is the San Joaquin River at Crows Landing. 

This site is below the confluence with the Merced River, 

but above the San Joaquin River at Vernalis. The San 

Joaquin River at Vernalis, the monitoring station before 

the Bay-Delta, is traditionally considered the entrance to 

the Bay-Delta (figs. 3 and 4). Between the Merced River 

confluence and Vernalis, the Tuolumne and Stanislaus Rivers flow into the San Joaquin River. Inherent in the TMDL 

model approach are an identification of sources and a program of load reduction to achieve compliance with water 

quality objectives.

Real-time model. This approach goes one step further 

than TMDL modeling in that discharges are allocated 

based on real-time updates of flow (instantaneous measurements). This means maintaining a constant selenium 

concentration at or below a water quality criterion (5 

μg/L, the USEPA criterion is one suggestion) by varying load with flow (Karkoski, 1996). (Note: If real-time 

discharge were instituted, salinity measurements would 

need to act as a surrogate for selenium measurements, 

since technology is not available to assess selenium on 

a real-time basis). Loads based on real-time dilution 

maximize disposal of selenium by adjusting the timing of 

discharges to coincide with dilution capacity of the river. 

Large loads may be released in months of high flow during 

the winter and spring. Holding ponds may be necessary 

for storage of drainage during low flow seasons in the San 

Joaquin River to avoid violations of water quality objectives. This approach provides no certainty for the amount 

discharged per month or per year, nor does it provide a 

means to assess long-term progress toward load reduction 

for impaired water-bodies. As such, it is of less value that 

the TMDL approach in regulating the San Joaquin River as 

a selenium-source water for the Bay-Delta.

The derived loads from the quasi-static TMDL and 

TMDL models would range from 1,394 to 6,547 lbs selenium 

per year. Initial estimates for the dynamic real time model 

suggested loads would vary from 2,605 to 17,605 lbs per year 

(Karkoski, 1996) depending on flow regimes. 

The approach presented here to develop selenium load 

scenarios conveyed by the San Joaquin River to the Bay-Delta

1.

2.

considers the river as a selenium source water for the estuary 

using an annual static inflow for the San Joaquin River at 

Vernalis. The calculations also consider wet or dry year conditions and recycling. In developing this type of scenario, the 

starting point is the targeted load and the San Joaquin River 

is considered a drain from the San Joaquin Valley. This is a 

supply-driven strategy, with consideration of environmental 

protection a priority, rather than a strategy driven by agricultural demand. The effects on the San Joaquin River itself, of 

managing a constant concentrations in view of bioaccumulation, are not known and are not considered here. 

In development of load scenarios, several assumptions 

about flow conditions were made (table 9): 

little recycling of the San Joaquin River occurs in a wet 

year, therefore 3.0 million acre-ft enters the Bay-Delta 

annually. 

1.1 million acre-ft of San Joaquin River inflow is 

allowed to enter the Bay-Delta annually indicative of 

partial San Joaquin River inflows in a wet year or total 

San Joaquin River inflow in a dry year.

nearly complete San Joaquin River recycling is 220,000 

acre-ft, which is a volume comparable to the capacity of 

the existing San Luis Drain.

A range of 60 to 2,992 lbs selenium would actually reach 

the Bay-Delta under the latter flow condition (probably as in 

the drought years between 1987 through 1994) and selenium 

criteria conditions spanning 0.1 to 5 μg/L selenium (table 9). 

Maintaining a criterion of 5 μg/L in the San Joaquin River 

allows loads of 14,960 lbs and 40,800 lbs selenium per year 

to enter the Bay-Delta at the two higher hydraulic discharges. 

Maintaining a concentration at the USFWS recommended criterion of 2 μg/L at these two hydraulic conditions would result in 

loads of 5,980 and 16,320 lbs selenium per year. 

Summary 

Even though the full range of possible selenium loads to the 

Bay-Delta from the western San Joaquin Valley is large, current 

proposals, management plans, and history narrow the possibilities into three groups, depending on management strategy: 

Supply-driven management (3,000 to 8,000 lbs 

selenium per year) By this is meant management that 

puts a priority on environmental protection and targets a 

load that cannot be exceeded. For example, the TMDL/

TMML approach derives annual loads for the San Joaquin River from the Grassland subarea alone of 1,400 to 

6,500 lbs to remain below a 5 μg/L selenium criterion, 

depending on flow regime for the San Joaquin River. 

The present prohibition for discharge from the Grassland subarea or drainage basin is a load of 8,000 lbs.

Demand-driven load with management of land and/

or drainage quality (15,000 to 45,000 lbs selenium 

per year) By this is meant selenium loads are driven 

•

•

•

•

•
 35

by agricultural demands for draining saline or waterlogged soils. The quality and quantity of the drainage 

are assumed controlled by managing volume per acre 

and/or quality of the drainage. For example, a range 

of loads projected from the amount of problem water

defined by the Drainage Program for year 2000 with 

and without implementation of the management plan 

(demand driven volume) in conjunction with a concentration of 50 μg/L selenium (controlled concentration), 

yields a selenium load range of 19,584 to 42,704 lbs 

selenium per year. The various approaches converge on 

loads (rounded off) that range from 15,000 to 45,000 

lbs per year.

Demand-driven load with minimum management 

(45,000 to 128,000 lbs selenium per year) This will 

occur if the demand for restoring saline soils drives 

drainage and neither quantity nor quality objectives 

can be (or are chosen to be) met. For example, a range 

of loads projected from the amount of problem water

defined by the Drainage Program for year 2000 without implementation of the management plan (demand 

driven volume) in conjunction with a concentration 

of 150 μg/L selenium (non-controlled concentration), 

yields a selenium load range of 42,704 to 128,112 lbs 

selenium per year. This approach is likely to result in 

loads that exceed the managed maximum of 45,000 lbs 

per year and could approach as much as 128,000 lbs 

selenium per year or even more. 

Selenium from Oil Refineries

Heavy crude oils produced in the San Joaquin Valley and 

refined in the Bay-Delta are especially enriched in selenium 

(400 to 600 μg/L) (Cutter and San Diego-McGlone, 1990). So, 

refinery effluents have historically provided a quantitatively 

important load of selenium to the Bay-Delta. Furthermore, 

selenium in these effluents is highly concentrated in a relatively small volume of wastewater, so discharges increase 

the ambient concentration of selenium, especially around 

Carquinez Strait (Cutter, 1989). In eight determinations of 

refinery effluents in 1987 and 1988, Cutter and San DiegoMcGlone (1990) estimated that annual selenium loads could 

vary from 2,035 to 4,641 lbs per year from all refineries 

combined. Annual loads from 1986 to 1992 ranged from 3,103 

to 7,457 lbs selenium as reported by the State (San Francisco Bay Board, 1993) (table 10). In March 1988, refineries 

accounted for 74 percent of the internal discharges of selenium 

to the Bay-Delta; in May 1988, they accounted for 96 percent 

(Cutter and San Diego-McGlone, 1990). Selenium discharges 

from refineries are relatively constant through the year, so they 

are of greatest influence on selenium concentrations in the 

Bay-Delta during the low river inflow season. 

As a result of regulations imposed by the State, refinery 

discharges to the Bay-Delta declined after July 1998. The 

annual selenium load ranges reported by the State from 

•

1986 to 1992 for the five major refineries are listed in table 

10, along with loads measured in 1999 (San Francisco Bay 

Board, 1993). Using these estimates, refinery inputs declined 

by about two-thirds (to about 1,100 lbs selenium per year), 

from the amount measured from 1986 to 1992. On the other 

hand, refinery effluents also are regulated to a concentration 

of 50 μg/L selenium and to the volumes discharged in the late 

1980s. If the volume of effluent (5,000 acre-ft) remains what 

it was in the late 1980s, the resulting selenium load would 

be 1,400 lbs selenium per year. Monitoring programs have 

not yet been implemented that are capable of reliably evaluating whether 1,400 lbs or 1,100 lbs selenium per year best 

describes refinery discharges, but the difference is relatively 

small considering the variability within years and within refineries (table 10).

Historic selenium discharges were > 50 percent selenite 

(Cutter and San Diego-McGlone, 1990). Recently instituted 

treatment technologies in the refineries have changed the 

proportions of selenium species. Recent data suggest the 

selenite concentration peak near the refineries has declined 

after the treatment technologies were implemented and selenate 

concentrations have increased (Cutter and Cutter, 2004).

Table 10. Ranges of annual and daily selenium loads from oil 

refineries located in the North Bay for the period 1986 to 1992 and 

1999.

 [Cleanup of discharges and further permitting was required by 1998.] 

Oil refinery

Selenium load (lbs)

1986– 92a 1999b

Annual Daily Annual Daily

Equilon Enterprises 

LLC at Martinez

(formerlyShell Oil)

1,203−2,595 3.3−7.1 440 1.20

Tosco Corporation 

at Avon

180−482 0.49−1.3 118 0.32

Tosco Corporation

 at Rodeo 

(formerly Unocal)

1,045−1,938 2.9−5.3 98 0.27

Valero Refining 

Company 

(formerly Exxon 

Corporation)

321−755 0.88−2.1 132 0.36

Chevron Corporation354−1,687 0.97−4.6 327 0.90

Total 3,103−7,457 8.5−20.4 1,115 3.05

a

Data sources: San Francisco Bay Board (1992b and 1993).

b

Johnson Lam, San Francisco Bay Board, personal commun., September, 

19, 2000.
36 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Selenium from the Sacramento River

Most of the river inflow to the Bay-Delta comes from the 

Sacramento River (fig. 4 ). The San Joaquin River (at Vernalis) 

inflow is usually about 10 to 15 percent of the inflow of the 

Sacramento River (at Freeport). Dissolved selenium concentrations in the Sacramento River at Freeport are consistently 

and comparatively low, averaging 0.06 ± 0.02 μg/L (Cutter 

and San Diego-McGlone, 1990). Thus, the Sacramento River 

represents a comparatively low concentration/high volume 

source of selenium. Using a concentration of 0.04 μg/L selenium (a conservative estimate) and the inflows given below, 

the projected annual selenium loads conveyed by the Sacramento River to the Bay-Delta are:

32 million acre-ft, wet year: 3,482 lbs selenium per year

17 million acre-ft, median year: 1,850 lbs selenium per 

year

10 million acre-ft, dry to critically dry year: 1,088 lbs 

selenium per year

5 million acre-ft, most critically dry year: 544 lbs selenium per year

Selenium loads increase with volume of inflow from the 

Sacramento River, because selenium concentrations in the 

river are relatively low, but constant. Therefore, the Sacramento River inflow establishes a baseline flow and selenium 

concentration entering the estuary. 

Summary 

In the Bay-Delta selenium model (fig. 2), four sources of 

selenium in different proportions determine selenium loads to 

the Bay-Delta. Sacramento River loads vary purely as function 

of inflow volumes (1,850 lbs selenium per year, median precipitation year). Potential loads from an extension of the San Luis 

Drain vary widely. Projected supply-driven loads are lowest; 

demand-driven loads with management and treatment capabilities fall within the range of 15,000 to 45,000 lbs selenium 

per year. Loading rates escalate steeply if treatment strategies 

are not applied. Projected loads from the Grassland subarea or 

drainage basin, as regulated concentrations in the San Joaquin 

River, vary from approximately 1,400 to 6,547 lbs selenium per 

year. However, the load from the San Joaquin River entering 

the Bay-Delta is ultimately constrained by the quantity of river 

water that reaches the estuary. Oil refinery loads are assumed 

to remain at post-1998 values reflecting regulation and treatment technology (about 1,400 to 1,100 per year). The sums of 

combinations of these loads represent different management 

and hydraulic condition scenarios. A few specific, and most 

likely, scenarios for the Bay-Delta are considered in detail for 

forecasting selenium concentrations in water, sediment, and 

food webs; and for subsequent evaluation of ecological effects 

on predators (birds and fish) in the Bay-Delta. 

•

•

•

•

Hydraulic Connections and 

Conveyance of Selenium to the BayDelta

Selenium loads from the San Joaquin Valley can be 

conveyed to the Bay-Delta either through the San Joaquin 

River or a proposed extension of the San Luis Drain. As 

discussed earlier, the originally planned valleywide drain or 

San Luis Drain was a proposed canal that would collect irrigation drainage valleywide or from the San Luis Unit (Westlands 

subarea and parts of what is now the Grassland subarea) and 

transport it directly into Suisun Bay at Chipps Island (see also 

table 1; figs. 3 and 4; and appendix A). If extensions of the 

San Luis Drain are constructed, the drain could potentially 

collect drainage from all five subareas of the western San 

Joaquin Valley; or, as currently proposed and configured, from 

Westlands subarea and Grasslands subarea only and release it 

directly into the Bay-Delta (figs. 3 and 4).

The San Joaquin River is the only natural outlet from the 

San Joaquin Valley. A substantial proportion of the freshwater 

flowing toward the Bay-Delta from its watershed is diverted 

(exported) for agricultural and urban uses. Before the 1990s, 

the San Joaquin River was almost completely diverted and 

recycled back south (fig. 4). That meant little or none of the 

selenium discharged into the San Joaquin River as agricultural drainage reached the Bay-Delta. After the 1994 BayDelta Water Accord (State Board, 1994), water management 

changed; more selenium will reach the Bay-Delta as less recycling of the San Joaquin River occurs. However, not all water 

that remains in the San Joaquin River at Vernalis enters the 

Delta or the Bay. The merging of the Sacramento River and 

San Joaquin River systems in the estuary and exports or water 

diversions (figs. 8 and 9) add complexity to likely scenarios. 

The amount of potentially selenium-laden San Joaquin River 

inflow reaching specific locations in the Bay-Delta is influenced by (State Board, 1999a; Monsen, 2000):

tidal cycles;

variable inflows of the Sacramento River and San Joaquin River due to seasonality and upstream withdrawals;

quantity of water diverted (pumped) from the Delta 

to the Central Valley Project, State Water Project, and 

local water users through the California Aqueduct, 

Delta Mendota Canal, and Contra Costa Canal;

discharge of agricultural drainage from the San Joaquin 

Valley and within the Delta itself;

channel configurations and capacity; and

artificial barriers which periodically are constructed to 

route flows in the Delta 

Changes in both the channel configurations and barrier system 

are being proposed (CALFED, 1998a, b, 1999a, b, c, d). 

•

•

•

•

•

•
 37

Figures 8 and 9 show the balance of water for the BayDelta in a wet year (1996) and in a dry year (1994) among:

total river (Sacramento River and San Joaquin River) 

inflow; 

San Joaquin River inflow; 

water diversions [pumping at Tracy and Clifton Court 

Forebay (CCtF) south to the Delta-Mendota Canal and 

the California Aqueduct]; and

total outflow of the Bay to the Pacific Ocean.

Total inflows and San Joaquin River discharges are exceptionally high in the first five months of a wet year, far exceeding 

diversions. In the fall, however, water diversion can exceed 

total inflows. In September through November, San Joaquin 

River inflow at Vernalis can be a large proportion of total 

inflows. During this time of year, if San Joaquin River inflow 

•

•

•

•

is transported past the diversions, it can have a substantial 

influence on Bay-Delta waters. Manipulations of barriers, 

modification of the channels, or construction of alternative 

diversion facilities could all affect (or are affecting) whether 

or not San Joaquin River inflow reaches the Bay-Delta during this time of year. Better understanding of water movement from the San Joaquin River through the Bay-Delta and 

processes within the estuary are critical to future evaluations 

of selenium issues. Evaluations of the implications of water 

management decisions need to consider effects on selenium 

transport and residence time. A large range of residence times 

have been estimated for freshwater in various parts of the 

Bay-Delta (Walters and others, 1985). The estimated residence 

times for high flow and low flow periods are:

Suisun Bay: high flow, 0.5 day; low flow, 35 days

San Pablo Bay: high flow, 0.8 day; low flow, 25 days

•

•

Figure 9. For a wet year (1996), the balance among flow of the San 

Joaquin River at Vernalis, total river inflow (San Joaquin at Vernalis 

and Sacramento River at Freeport combined), water diversions 

(pumping at Tracy and Clifton Court Forebay), and outflow to the Bay.

Figure 8. For a dry year (1994), the balance among flow of the San 

Joaquin River at Vernalis, total river inflow (San Joaquin at Vernalis 

and Sacramento River at Freeport combined), water diversions 

(pumping at Tracy and Clifton Court Forebay), and outflow to the Bay.

200,000

5000

0

10,000

15,000

20,000

25,000

J F M A M J J A S O N D

Month

50,000

0

100,000

150,000

250,000

Flow, in cubic feet per second

Bay-Delta

flow schematic 

Calculated total

river inflow to Delta

Sacramento R. at Freeport

(measured)

San Joaquin R. at Vernalis

(measured)

Calculated outflow

to Bay

Tracy and

Clifton Court Forebay

(measured)

Total river inflow

Outflow

San Joaquin R. 

at Vernalis

Outflow

Diversions

J F M A M J J A S O N D

Month

200,000

5000

0

10,000

15,000

20,000

25,000

50,000

0

100,000

150,000

250,000 Flow, in cubic feet per second

Bay-Delta

flow schematic 

Calculated total

river inflow to Delta

Sacramento R. at Freeport

(measured)

San Joaquin R. at Vernalis

(measured)

Calculated outflow

to Bay

Tracy and

Clifton Court Forebay

(measured)

Total river inflow

Outflow

San Joaquin R. 

at Vernalis

Outflow

Diversions
38 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Northern reach: high flow, 1.2 days; low flow, 60 days

South Bay: high flow, 120 days; low flow, 160 days

South Bay (north of Dumbarton Bridge): high flow, 80 

days; low flow, 120 days

Extreme South Bay (south of Dumbarton Bridge): high 

flow, 40 days; low flow, 70 days

Concentrations of Selenium 

in the Bay-Delta

Effects of Source Water Selenium Loads on 

Receiving Water Selenium Concentrations

Interpretation of mass loads from individual sources 

requires understanding how load and volume in different 

source waters combine to produce concentrations in receiving 

waters. For the modeling approach used here, determining 

selenium concentrations in Bay-Delta receiving waters is the 

initial step in a series of linked steps that determines biological 

effects from selenium (fig. 2). So ultimately the interaction 

between source water load and receiving water concentration 

must be understood. 

In general, selenium loads in agricultural source waters 

from the western San Joaquin Valley may increase with 

increased applied water, given the characteristics of selenium 

concentrations in subsurface drainage and the massive storage 

of selenium in aquifers (fig. 5; appendices A and B). Loads 

also increase with the volume of inflow from the Sacramento 

River, because selenium concentrations in the river are relatively constant. On the other hand, concentrations in a mixture 

of waters where sources combine will be dependent on the 

sum of the volumes of the sources and the masses of selenium 

in each of those sources. Dissolved selenium constitutes 80 to 

93 percent of the total selenium (Cutter, 1989) in the BayDelta, so loads based on total selenium can be used to derive 

concentrations of dissolved selenium. 

The volume of water flowing into the Bay-Delta is 

determined by climate and water management. As a simplification, these inflows can be thought of collectively as the 

rivers, meaning the sum of the inflows of the Sacramento 

River and the San Joaquin River. Monitoring of selenium 

concentrations in Bay-Delta receiving waters must take into 

account the monthly, seasonal, and year-to-year variability of 

hydraulic discharge. A useful simplification is to consider the 

Bay-Delta watershed as characterized by a distinct seasonal 

cycle of high inflows from the rivers in January through 

about June, followed by lower inflows through the last six 

months of the calendar year (Conomos, 1979; Conomos and 

others, 1985).

In contrast to selenium loads dependent on water 

volumes, the mass of selenium from anthropogenic sources 

•

•

•

•

such as oil refineries is not highly variable because both 

effluent volumes and concentrations are relatively constant 

(State Board, 1992a, b). Permits include restrictions on both 

concentrations and loads to achieve environmental targets. 

Discharge from a San Luis Drain extension also could 

act as a traditional effluent that is regulated through volume, 

concentration, or load. Historically, the Westlands subarea 

during 1981 to 1985, discharged an average concentration of 

330 to 430 μg/L selenium, with an average volume of about 

570 acre-ft per month (appendix B, table B1). Monthly load 

targets for regulated discharge to the San Joaquin River in WY 

1997 varied from 348 to 1,066 lbs selenium, with the largest 

loads discharged during February (appendix B, table B9). 

Average volumes of agricultural drainage during that time 

varied from 1,274 to 4,867 acre-ft per month, with average 

monthly concentrations varying from 25 to 106 μg/L selenium 

to enable regulation. In all these cases, the degree of variability 

in volume of sources is small compared to the variability in 

river inflows. 

As a result of the mixing of variable inflows from the 

rivers (mostly with comparatively low selenium concentrations) and relatively constant anthropogenic inflows (with 

comparatively elevated selenium concentrations), strong 

seasonal fluctuations and year-to-year fluctuations of selenium 

concentrations would be expected. The general protocol for 

linking selenium load and concentration under the current 

hydraulic and inflow conditions in the Bay-Delta is:

[composite source load] = sum of loads from each 

source (six-month season or monthly) 

[composite source volume] = sum of volumes for each 

source (mainly inflows of Sacramento and San Joaquin 

Rivers) (six-month season or monthly) 

[composite source concentration] = [composite source 

load] ÷ [composite source volume] 

Specifically for Bay-Delta modeling, a composite freshwater endmember selenium concentration is calculated for 

a hypothetical location in the North Bay at the head of the 

estuary where all sources combine (all loads contribute to a 

freshwater endmember near the site of input) with instantaneous mixing. A selenium concentration also is calculated 

for Carquinez Strait, a point midway in the North Bay (at a 

salinity of 17.5 psu, practical salinity units).

In wet years (high precipitation), reduced selenium 

concentrations are expected in Bay-Delta receiving waters; in 

dry years and dry seasons, concentrations in receiving waters 

will increase. Therefore, evaluations of selenium effects must 

consider the time periods before, after, and during low flow 

periods, because this is when the highest concentrations of 

selenium will occur. Dry years and dry seasons will be times 

that govern ecological effects (that is, will be ecological 

bottlenecks) with regard to selenium. Factors such as residence 

times and exchanges within the Bay and Delta are also important, but models necessary to understand these smaller scale 

effects (such as elevated concentrations near sources of inflow; 

•

•

•
 39

detailed distribution within the Delta or Suisun Bay) are not 

adequately developed. Further development of hydrodynamic 

models (Cheng and others, 1993; Monsen, 2000; Monsen 

and others, 2002) multiple media mass balance models, and 

kinetic geochemical models are important to defining detailed 

ecological effects of selenium and to resolving future selenium 

problems. 

Existing Concentrations in the Bay-Delta

Regional baseline 

Dissolved selenium concentrations are 0.06 ± 0.02 μg/L 

in the Sacramento River (at Freeport) (Cutter and San DiegoMcGlone, 1990) and 0.02 to 0.08 μg/L in the seawater with 

which it mixes in all seasons (Cutter and Bruland, 1984). 

The regional selenium baseline for the Bay-Delta used here 

is defined by mixing selenium concentrations in these two 

endmembers, as determined by a salinity gradient through the 

estuary (fig. 10). A more complex case is one of a composite 

freshwater endmember comprised of the Sacramento River, 

the San Joaquin River, and refinery effluents. The regional 

baseline can be compared to a theoretical mixing line for 

which a selenium endmember concentration in a freshwater 

composite represents anthropogenic sources. In figure 10, 

the example mixing profile gives a selenium concentration of 

0.23 μg/L. This composite freshwater endmember concentration is calculated from annual selenium loads and volumes 

in the Sacramento River at 20 million acre-ft (typical conditions in a wet year before refinery cleanup) plus a refinery 

load of 4,400 lbs selenium per year (table 10). The gradient 

thus shows selenium concentrations through the estuary as 

an average composite endmember is diluted as a function 

of salinity. This type of mixing model, which is driven by 

salinity, can forecast a range of expected selenium concentrations in the Bay-Delta. This approach to modeling selenium 

discharges to the Bay-Delta illustrates that variation in selenium loads delivered by an endmember consisting only of the 

Sacramento River will not cause changes in average selenium 

concentrations in the Bay-Delta. This is because average 

selenium concentrations in the river are relatively constant 

(within the range of 0.04 to 0.08 μg/L). However, the sum of 

source selenium loads determines the selenium concentration of a composite freshwater endmember. Hence, adding a 

low volume/high concentration source of selenium to obtain 

a composite freshwater endmember selenium concentration 

will cause changes in the selenium concentrations in the 

estuary system.

The spatial details of observed selenium distributions 

can be compared to theoretical distributions in order to draw 

conclusions about internal sources or trapping of selenium 

within the estuary. The projected selenium concentration in 

the theoretical composite freshwater endmember used above 

(0.23 μg/L) is similar to the selenium concentration observed 

in surveys of the estuary (see discussion below and Cutter and 

Cutter, 2004). 

Concentrations observed in the Bay-Delta

Five studies have been conducted that employed a reliable methodology for the analysis of dissolved selenium 

distributions in the Bay-Delta. Cutter (1989) sampled the full 

salinity gradient of the North Bay in April and May 1986; 

Cutter and San Diego-McGlone (1990) repeated that study in 

October 1987, December 1987, March 1988 and May 1988. 

Cutter and Cutter (2004) (also see data quoted in Luoma and 

Fisher, 1997) sampled the salinity gradient again in May 1995 

and October 1996. Since its inception in 1993, the San Francisco Estuary Regional Monitoring Program also has analyzed 

selenium in the North Bay, although not as systematically 

along the salinity gradient (San Francisco Estuary Institute, 

1993, 1994, 1995, 1996). 

All surveys of the Bay-Delta report dissolved selenium 

concentrations less than the 1 μg/L criterion designated by 

Canada (Environment Canada/Health Canada, 1995; Outridge 

and others, 1999); the 2 μg/L USFWS recommended chronic 

criterion for protection of aquatic life for all waters within the 

range of listed endangered species in the State of California 

(USFWS and NMFS, 1998 and amended 2000); or the 5 μg/L 

USEPA chronic criterion for protection of aquatic life (derived 

from freshwater studies) (USEPA, 1992). The maximum 

concentrations of dissolved selenium in most surveys are 

less than those observed in the adjacent watersheds (Cutter, 

1989; Cutter and San Diego-McGlone, 1990; San Francisco 

Bay Board, 1992a , b, 1993) (tables 3 and 5). Slightly higher 

concentrations are sometimes observed near the Golden Gate 

Bridge, but these appear to originate from the South Bay 

(Cutter, 1989). The highest dissolved selenium concentration 

observed in any North Bay survey was 0.44 μg/L in August 

1993 (San Francisco Estuary Institute, 1994). The lowest 

0

0

0.1

0.2

Landward Suisun Bay San Pablo Bay Seaward Carquinez

Strait

(17.5 psu)

Composite freshwater

endmember at head

of estuary

Sacramento R. endmember

Mixing

0.3

10 20 30

Salinity, in practical salinity units (psu)

Selenium concentration,

in micrograms per liter

Seawater

endmember

Regional selenium baseline

Figure 10. Hypothetical dilution profiles for selenium in the 

Bay-Delta: (1) the regional baseline profile shows selenium 

concentrations through the estuary as concentrations in the 

Sacramento River are diluted by concentrations in the Pacific 

Ocean as indicated by salinities; (2) the example mixing profile 

shows the selenium concentration in a hypothetical average 

freshwater endmember as it is diluted by concentrations in the 

Pacific Ocean.
40 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

concentrations were observed in the Sacramento River in 

September 1986 and June 1995 (0.048 to 0.052 μg/L). Few 

surveys have been conducted of selenium concentrations in the 

Delta, although a recent CALFED supported study has begun 

some data collection in this area (see for example, Lucas and 

Stewart, 2005).

 The spatial features of the selenium gradient in the 

North Bay (fig. 11) were initially described by Cutter (1989). 

Surveys done between 1986 and 1996 show that selenium 

concentrations are (1) highest in Suisun Bay, in the midsalinity ranges near Carquinez Strait; and (2) lowest in river 

and oceanic endmembers. This suggests a source of selenium 

exists in the middle of the estuary. Cutter (1989) determined 

that oil refineries were that source, an observation consistent with the distribution of biologically available selenium 

reported by Johns and others (1988). 

Seasonal and year-to-year variations in river inflows 

influence dissolved selenium concentrations in the Bay-Delta. 

Higher concentrations appear to occur during periods of low 

inflow than during periods of high inflows (fig. 11). Spatial 

distribution also changes with inflows from the rivers. In 

April 1986, after a large flood in February, dissolved selenium 

declined linearly from freshwater to seawater, correlating 

with salinity. Estimates of fluxes indicate that the export of 

selenium from the Bay-Delta to the ocean was controlled by 

riverine sources during this month. During low flow seasons, 

dissolved selenium concentrations increase and a peak in 

Suisun Bay becomes more distinct. Cutter (1989) and Cutter 

and San Diego-McGlone (1990) showed that in September 

1986, total input from the rivers was 2.45 lbs selenium per day 

(or extrapolated, 894 lbs per year) and from internal sources 

was 17.9 lbs selenium per day (or extrapolated, 6,534 lbs per 

year). Flux calculations from different sources indicated that 

the selenium load from refineries was 2- to 8-times that from 

the rivers in this month, and was the cause of the shape of 

the gradient. In March of 1987, during a drought, refineries 

accounted for 74 percent of the selenium flux; in May 1987 

they accounted for 96 percent. Recent data suggest that selenium fluxes have changed since regulatory limits took effect in 

July 1998, but the relative proportion of source waters remain 

approximately the same (Cutter and Cutter, 2004).

Thus, while estuarine waters in the Bay-Delta are 

enriched in selenium compared to the regional baseline, 

selenium concentrations in estuarine waters are low compared 

to many contaminated freshwater environments. The concentration of dissolved selenium among rivers and estuaries in 

England (Measures and Burton, 1978) and several rivers 

in eastern North America (Takayanagi and Cossa, 1985) 

range from 0.049 μto 0.39 μg/L. Presumably some of these 

sites also are anthropogenically contaminated. This range of 

dissolved selenium is the same range as seen in the Bay-Delta. 

It is possible that physical or biogeochemical conditions in 

estuaries are the cause of these relatively low values. The 

challenge is to understand how these relatively low dissolved 

selenium concentrations result in the degree of food web 

contamination described next. 

Chemical Forms of Selenium 

(Speciation)

Concentrations of waterborne selenium are not sufficient 

to predict the biological implications of selenium contamination. The geochemical speciation of selenium is a critical 

consideration. Speciation of dissolved selenium ultimately 

controls transformation reactions between dissolved and 

particulate forms (such as sediments, detrital particles, and 

primary producers). Transformations and particulate concentrations are important factors determining the biological 

effects of selenium; but they cannot be forecast without 

consideration of speciation. 

Selenium is a natural trace element, number 34 on the 

periodic table, just below sulfur. Selenium can occur in three 

oxidation states in the dissolved phase: 

 Organo-Se (-2 or -II) substituting for S-2 in proteins 

seleno-methionine and seleno-cysteine 

Selenite (+4 or IV) the oxyanion selenite (SeO3

-2), an 

analog to the sulfur compound sulfite 

Selenate (+6 or VI), the oxyanion selenate (SeO4

-2), an 

analog to the sulfur compound sulfate 

Equilibrium thermodynamic calculations do not accurately predict the speciation of selenium in oxidized natural 

waters because of the influences of biological processes 

(Luoma and others, 1992). In such waters, selenium exists 

in a variety of oxidation states. Biological accumulation by 

microorganisms, reductive bioproduction of organoselenium 

and, release of the latter contribute to the disequilibrium. 

Dissolved selenium in aerobic waters can sometimes occur 

predominantly as organo-Se and this species may be important 

seasonally (Takayanagi and Wong, 1984; Cutter and Bruland, 

1984; Presser and others, 2004b). However, selenate and 

selenite usually are the common dissolved forms.

•

•

•

0 0

0.12

0.24

10

9/86

Low flow

10/96

Low flow

4/86

High flow

4/95

High flow

20 30

Salinity, in practical salinity units

Selenium concentration,

in micrograms per liter

Figure 11. Dissolved selenium concentration profiles as function of 

salinity in the Bay-Delta during high and low flow seasons in 1986 

and in 1995 – 96.
 41

In nature, bioaccumulation of selenium into food webs 

can be more proficient and biotic consequences to birds and 

fish more severe when a source water is selenite-dominated, 

than when it is selenate dominated (Skorupa, 1998a). However, 

generalizations about effects based on comparative toxicity 

and bioavailability of different selenium species in water (for 

example, Maier and others, 1993) must be used with caution. 

As illustrated in the approach used here, overall conclusions 

about bioavailability are dependent on linking receptors to 

foodweb components using very detailed species-specific 

analysis.

Examples exist in nature where each of the three major 

species of selenium is predominant: (1) selenate predominates in most irrigation drainage inputs to wetlands (Presser 

and Ohlendorf, 1987; Zhang and Moore, 1996, 1997a, b); (2) 

selenite can predominate in systems affected by industrial 

wastes, especially those associated with wastes from fossil fuel 

products or consumption (Cutter and San Diego-McGlone, 

1990; Skorupa, 1998a); and (3) organo-Se can predominate 

where selenium is strongly recycled (Takayanagi and Wong, 

1984). In the Bay-Delta, speciation differed among the source 

waters in 1980s (Cutter and Diego-McGlone, 1990): 

Sacramento River inflow was 30 to 70 percent selenate, 

depending on season; organo-Se was the other main 

component. 

San Joaquin River inflow was 70 percent selenate and 

22 percent organo-Se.

refinery wastewaters averaged 62 percent selenite.

in the late 1980s, during low flow in Carquinez Strait, 

as much as 50 percent of the selenium was selenite, 

reflecting the predominance of refinery inputs.

in the late 1990s, preliminary studies in Suisun Bay 

showed less selenite, but selenite plus organo-Se could 

constitute 60 percent of the mass of selenium. 

Particulate and Sediment-Associated 

Selenium

Processes Affecting Particulate Selenium

Partitioning

One of the most important biogeochemical steps or links 

controlling the bioavailability and effects of selenium is the 

partitioning reactions that determine the distribution between 

dissolved and particulate phases, where particulate phases 

include primary producers (such as phytoplankton), bacteria, 

detritus, suspended inorganic material, and sediments. There 

are several reasons these reactions are important: 

The pathway for nearly all selenium transfer to the second trophic level in an ecosystem is through particulate 

•

•

•

•

•

•

forms (animals bioaccumulate selenium from their 

food to a much greater extent than they take up selenium from water, at the distributions typical of nature 

(Luoma and others, 1992; Luoma and Rainbow, 2005). 

The transformation efficiency from dissolved to particulate selenium ultimately determines foodweb concentrations of the element (higher particulate material 

selenium concentrations means greater contamination 

in the food web, although the form of the selenium in 

the particulate also can be important);

Particulate selenium concentrations can differ by as 

much as 100-fold at the same dissolved concentration 

depending on biogeochemical transformation reactions 

governing dissolved particulate interactions. Thus, 

forecasts of effects depend on understanding what 

transformations will occur. 

The largest inventory of selenium in a contaminated 

ecosystem usually occurs in sediments. For example, 90 

percent of the inventory of selenium in Kesterson National 

Wildlife Refuge was deposited in sediments (Tokunaga 

and others, 1996). However, the proportion of selenium in 

suspended particles, at any one time, may be only a small 

fraction of the total quantity of selenium in the water column. 

For example, in April 1986, Cutter (1989) found that only 7 

percent of total selenium in the water column of the North 

Bay was particulate; in September 1986, only 13 ± 7 percent 

was particulate. The large inventory of selenium in sediments results either because suspended particulate selenium is 

progressively deposited in sediments over time and/or because 

reactions within the sediments progressively strip selenium 

from solution. 

The concentration per unit mass in the particulate 

material is more critical than the mass in suspension (per 

unit volume of water). In fact, the most important measure 

of selenium in any environment may be the concentration 

of selenium per unit mass of suspended particulate material. This concentration determines the exposure of the many 

species that feed on such material. Exposure for each species 

to selenium is partly determined by how that species samples

the complex water/sediment/particulate/organism milieu that 

composes its environment. Many species are able to efficiently 

gather large quantities of particulate material from the water 

column, even when particulate concentrations themselves are 

relatively low. Bioaccumulation is then determined from the 

concentration of selenium in food or particulate material (μg/

g), along with the efficiency with which that concentration is 

assimilated (Luoma and others, 1992). Assimilation efficiency 

(AE) is the proportion of ingested selenium that is taken up 

into tissues (for example, into the tissues of prey organism 

such as bivalves); and AE varies with the type of food or the 

form of particulate selenium that is ingested. 

Direct determination of selenium concentrations per unit 

mass on suspended sediments is rare. This is at least partly 

a result of the difficulty in collecting a sufficient mass of 

suspended material for direct analysis.

•

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42 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Transformation

Several different primary reactions can transform (or 

affect transformation of) dissolved species of selenium to 

particulate selenium. Transformation reactions include biological, redox (reduction/oxidation), and physical processes. The 

more important reactions are:

Assimilatory biological uptake and transformation.

In an oxygenated water column, a primary transformation is the biochemical transformation of Se(IV), Se(VI) 

and/or dissolved organo-Se [Se(-II)] to particulate Se(-

II) through uptake by plants or, perhaps microorganisms. 

Microbes, plants, and microflora (phytoplankton) reduce 

the selenium they concentrate to Se(-II). Most biochemically transformed selenium is found within the cell solution, at least in phytoplankton (Reinfelder and Fisher, 

1991), and it is highly bioavailable to animals that consume the microorganisms for food. When cells die and 

breakdown the plants release both Se(IV) and Se(-II) 

back to the water column in dissolved form. Biotransformed Se (-II) can also be sequestered in sediments or 

suspended particulate material, as detrital Se(-II). 

Dissimilatory (extra-cellular) biogeochemical 

reduction. When selenium in water contacts reduced 

particles or reduced sediments, sequestration onto or 

into sediments by bacteria can occur. The most important microbial transformation reaction under these 

conditions is dissimilatory reduction (Oremland and 

others, 1989). Dissimilatory reduction of either Se(IV) 

or Se(VI) predominantly generates elemental selenium 

[Se(0)] in sediments; but it may also generate some 

operationally defined organo-Se [Schlekat and others, 

2000]. Elemental selenium can be further transformed 

within the sediments by reactions such as precipitation 

as ferroselite (FeSe2); incorporation into solid phases 

such as pyrite (Velinsky and Cutter, 1991); or uptake 

by plants to ultimately form detrital organo-Se (Zhang 

and Moore, 1997a, c). 

Oxidation state. Particulate selenium generated by 

transformation reactions can occur in different oxidation states depending on the transformation reaction 

and subsequent exposure to geochemical conditions. 

Understanding the form of particulate selenium is critical to evaluating effects of selenium contamination, 

because each form has a different biological availability (Luoma and others, 1992). Reduction/oxidation 

status, determined by the balance of redox couples, is 

especially important in determining particulate form. 

Possible particulate forms include: adsorbed/coprecipitated (SeIV) and (SeVI), organic selenides [either in 

the form of intracellular Se(-II) or detrital Se(-II)], or 

elemental selenium [(Se(0)]. 

Adsorption. Geochemical adsorption can occur in the 

water column if reduced sediments are mixed back into 

•

•

•

•

an oxygenated water column and oxidized (Dowdle 

and Oremland, 1999); or, perhaps, at the boundary of 

oxygenated and de-oxygenated conditions (the redox 

interface) (Tokunaga and others, 1997, 1998; Myneni 

and others, 1997). 

Volatilization. Biogeochemical volatilization of selenium has been documented in wetland soils (Cooke and 

Bruland, 1987; Thompson-Eagle and Frankenburger, 

1992) and in evaporation ponds (Fan and Higashi, 

1998). Volatilization rates depend on physical/chemical conditions, vegetation, water management, or other 

rate limiting factors (Flury and others, 1997; Zhang 

and Moore, 1997a, c; Hansen and others, 1998). The 

influence of volatilization on selenium concentrations in 

sediments (the relevance to this discussion) is determined by the mass of selenium volatilized, compared 

to that in sediments. A careful mass balance including 

determination of selenium inputs, outputs, and internal 

inventories is the only way to verify effects of volatilization on selenium inventories Presser and Piper, 1998). 

Studies that present a full complement of such analyses 

are rare; so significant uncertainties remain about the 

role of volatilization. Cooke and Bruland (1987) originally observed from limited data that about 30 percent 

of the incoming selenium was volatilized at Kesterson 

Reservoir. Zhang and Moore (1997d) and Hansen and 

others (1998) reported results consistent with that figure 

for other wetland systems. If 30 percent is typical, it 

is possible to calculate the effect of volatilization on 

selenium concentrations in a wetland that receives a 

continuous influx of selenium. If 90 percent of incoming dissolved selenium is trapped in the sediments, and 

if 30 percent of that is volatilized, then the net effect of 

volatilization is to reduce the progressive accumulation 

of selenium in particulate material to: 0.90 trapped × 

0.30 volatilized = 0.63 trapped × 100 = 63 percent of 

incoming selenium retained. Thus, volatilization could 

slow selenium accumulation to a rate less than would 

otherwise be achieved. However, in no known case has 

volatilization eliminated selenium contamination or 

alleviated water quality problems. Wetland trapping can 

remove selenium from contaminated waters, but most 

of the selenium remains in the sediments; efforts to 

completely volatilize selenium to the atmosphere have 

not proven successful. If selenium inputs to the wetland 

were eliminated, eventual removal by volatilization is a 

theoretical possibility. However, this also has never been 

observed in natural sediment with a high selenium load 

(see, for example, Flury and others, 1997). 

Range of distribution coefficients (Kd's)

The distribution coefficient (Kd) is a way to quantitatively 

describe the partitioning of total selenium between dissolved 

and particulate states. The Kd is the ratio of selenium per unit 

•
 43

mass particulate material to selenium per unit volume water, in 

equivalent units. An example of a calculated Kd for the BayDelta from typical 1986 data (Cutter, 1989) is:

[700 μg particulate Se/kg particulate] ÷ [0.315 μg dissolved Se/L] = 2.2 × 103 L/kg.

Speciation of dissolved selenium and transformation 

reactions have a combined influence on the distribution coefficient of selenium. The Kd oversimplifies both with the result 

that Kd's based on total concentrations in natural waters vary 

by as much as two orders of magnitude. Nevertheless, the 

Kd is a first order measure of partitioning and the measure 

uses the types of data most widely available from a variety 

of systems. Table 11 lists Kd's typical of a variety of ecosystems from which reliable geochemical data are available. 

The Kd's in various field studies range from 0.2 × 103 to 4 × 

104, reflecting the complicated transformation reactions and 

processes described above. Laboratory studies (Reinfelder 

and Fisher, 1991) show a range of 4.0 ×103 to 1.1 × 105, with 

the maximum extending somewhat above 4 × 104. Skorupa 

(1998a) also summarized the range of dissolved and sediment 

data found in various field studies. Median Kd's from that list, 

although not calculated by Skorupa (1998a), show a similar 

range. Knowing the range of Kd's in nature allows understanding of the potential range of particulate selenium concentrations that could occur in the Bay-Delta under different 

partitioning conditions in the absence of site-specific biogeochemical models. 

Sources of Particulate Selenium in the Bay-Delta 

General sources of particulate selenium in the Bay-Delta 

include:

Autochthonous (internal) sources in the San Joaquin River or the Delta Selenium could be transformed to particulate forms in the marshes of the San 

Joaquin River and the wetlands/lakes of the Delta by 

either dissimilatory reduction to Se(0) or biotransformation to Se(-II). Little is yet known about selenium 

trapping or transformation within the Delta itself. 

Allochthonous (external) sources It is possible that 

selenium contaminated particles produced in the San 

Joaquin River could be transported to and trapped in 

the Delta. Particulate selenium transformed within the 

Delta may be transported to the Bay-Delta, although 

the conditions under which such transport would occur 

are not well known. Any drain carrying drainage water 

to the Bay-Delta will transport externally and internally produced particulate selenium. 

Autochthonous (internal) sources in Suisun Bay

Long hydraulic residence times occur in Suisun Bay, as 

inflows recede or during low inflows. Longer residence times progressively increase the likelihood for 

biotransformation by local microflora and microbes in 

•

•

•

the water column, on surface sediments, or within sediments (Lemly, 1997a).

Long residence times and contact between the water 

column and the redox interface in sediments are critical 

factors in progressively accumulating selenium in the sediments of wetlands or shallow-waters (Zhang and Moore, 

1997a, b). Thus, the times of greatest vulnerability in the Bay 

or Delta are low inflow seasons and low inflow years when 

residence times are longest. The places most likely to generate 

particulate selenium are wetlands and shallows with long 

residence times. Restoration activities could affect selenium 

contamination in the San Joaquin River/Bay-Delta system if 

hydraulic residence times change or a larger area of the kind 

of systems that trap selenium are generated, without remediating selenium inflows.

Particulate selenium in the San Joaquin River

Discharge of agricultural drainage to the San Joaquin 

River through canals and wetlands has long occurred. Since 

1996, a 28-mile portion of the existing San Luis Drain also has 

discharged drainage from districts of the Grassland subarea 

to the river. Difficulties arise in drawing generalizations about 

temporal trends or spatial distributions of particulate selenium in 

the San Joaquin River, however, because there are few consistent, extensive or systematic surveys. Where such surveys exist, 

sampling methodologies do not allow elimination of biases 

caused by changes in river discharge; amounts of suspended 

material; selenium concentrations in suspended material in 

different seasons; or bed sediment characteristics such as particle 

size and differences in organic carbon concentrations. A detailed, 

systematic and carefully designed study of particulate selenium 

occurrence and trends is a critical need. Data from 1987 through 

1997 (appendix E, tables E1 and E2) show the following: 

Upstream of San Luis Drain Concentrations of selenium were 0.01 to <0.18 μg/g dry weight in sediments 

from upstream of the San Luis Drain discharge at the 

San Joaquin River at Lander Avenue in 1987– 89. These 

are probably baseline concentrations of selenium for the 

system. In 1993 – 96 and 1997, concentrations upstream 

of the San Luis Drain discharge at Mud Slough, were 

within the range 0.10 to 0.44 μg/g dry weight; these 

higher values probably reflect contamination from 

historic selenium discharges when the slough transported 

drainage. 

Downstream of San Luis Drain, before 1996 discharges The range of selenium concentrations, among 

several studies, in sediments of the San Joaquin River 

downstream of the inactive discharge site (pre-1996) 

was 0.3 to 1.9 μg/g dry weight. One value of 5.2 μg/g 

dry weight was reported from the San Joaquin River 

near Vernalis. 

Downstream after current operations began In 

September 1996, after operation of the San Luis Drain 

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44 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

began, selenium concentrations of 0.1 to 0.76 μg/g 

dry weight were determined in sediments immediately 

below the discharge, in Mud Slough. Concentrations 

6.6 miles downstream from the discharge were 0.7 to 

1.9 μg/g dry weight. Recent data (2002 to 2003) show 

selenium increasing to 8.5 μg/g dry weight in sediments in a seasonal backwater tributary of Mud Slough 

where residence time increases (USBR and others, 

1998 and ongoing).

Suspended sediments Several surveys also have analyzed suspended sediments in the San Joaquin River 

or adjacent marshes or sloughs. In all cases, concentrations in suspended sediments exceeded concentrations in bed sediments. The range of concentrations in 

suspended sediments was 0.91 to 6.7 μg/g dry weight. 

Systematic studies of suspended sediment in relation 

to seasonality, hydrology, or forms of selenium could 

be instructive with regard to sources and the causes of 

variability.

•

Particulate selenium in the Delta

Little is known about selenium concentrations in the 

Delta, but studies of specific areas of the Delta recently have 

been completed (see for example, Lucas and Stewart, 2005). 

In 1986 – 88, Johns and others (1988) sampled bivalves and 

sediments (fine-grained oxidized surface sediments, <100 

μm) monthly at a station in the Old River channel near Clifton 

Court Forebay. At that time and location, selenium concentrations in both indicators (Corbicula sp., mean 3.1 μg/g dry 

weight and particulates grand mean, 0.19 ± 0.03 μg/g, dry 

weight) were significantly lower than found within Suisun 

Bay (Corbicula sp., range of means, 3.9 to 5.2 μg/g dry 

weight and particulates range of grand means 0.23 to 0.53 

μg/g dry weight); and similar to concentrations found in the 

un-enriched Tuolumne River, which drains the selenium-poor 

geologic units of the eastern San Joaquin Valley. No systematic selenium studies have been done in the Delta after San 

Joaquin River inflows to the Delta increased in the mid-1990s. 

The lack of study of Delta wetlands or shallow waters leaves 

Table 11. Partitioning (Kd) between dissolved selenium and particulate or sediment selenium in 

ecosystems for which reliable analytical data is available.

[Two experimental values from Reinfelder and Fisher (1991) also are included.]

Ecosystem or organism

Selenium

Reference Dissolved 

(μg/L)

Particulate 

(μg/g)

Distribution 

coefficient (Kd)

Kesterson Reservoir

 Pond 2 330 55–165 0.2 – 0.5 × 103 Presser and Piper, 1998

 Terminal pond 14 13–24 0.9 –1.7 × 103 Presser and Barnes, 1998

Belews Lake ~11 ~15 1.3 × 103 Lemly, 1985

Benton Lake

 Pool 1 channel 4 10 2.5 × 103 Zhang and Moore, 1996

 Pool 2 10.4 3.5 0.34 × 103 Zhang and Moore, 1996

 Pool 5 0.74 0.35 0.5 × 103 Zhang and Moore, 1996

Constructed wetland 5.0–9.8 2.1−6.7 0.2 –1.2 × 103 Hansen and others, 1998

San Luis Drain 330 84 0.25 × 103 Presser and Piper, 1998

Grassland Bypass

Channel Project

62.5 30 0.5 × 103 Appendix E

Delaware River

(tidal freshwater)

0.17−0.35 0.6−1.5 4 × 103 Riedel and Sanders,1998

Diatoms – – 1.1 × 105 Reinfelder and Fisher, 1991

Dinoflagellate – – 4 × 103 Reinfelder and Fisher, 1991

Great Marsh, Delaware 0.01−0.06 0.3−0.7 3 × 103−1 × 104 Velinsky and Cutter, 1991

Bay-Delta (suspended

particulate matter 

1986, 1995, 1996) 

0.1−0.4 1−8 1−4 × 104 Cutter and Cutter, 2004;

Doblin and others, 2006

Bay-Delta sediment 0.1−0.3 0.2−0.5 1−5 × 103 Johns and others, 1988
 45

open the question of whether selenium can be sequestered 

there, at least in some locations.

Particulate selenium in the existing length of the 

San Luis Drain

Transport, re-suspension, and re-oxidation of particulate 

material from the existing portion of the San Luis Drain, if 

extended, might also be a source of bioavailable particulate 

selenium to the Bay-Delta. Transformation of dissolved 

Se(VI) into particulate selenium has been demonstrated within 

the existing San Luis Drain. Early surveys done when the 

San Luis Drain was conveying drainage from the Westlands 

subarea to Kesterson National Wildlife Refuge determined a 

maximum sediment selenium concentration of 210 μg/g dry 

weight and an average of 84 μg/g dry weight in the San Luis 

Drain (Presser and others, 1996; appendix E, table E1). A 

compilation of data from surveys in 1994, after the Grassland 

Bypass Channel Project had begun, showed a maximum of 

110 μg/g dry weight and an average of 44 μg/g dry weight 

in San Luis Drain sediment samples (appendix E, table E1). 

In whole core samples collected in 1997 from the San Luis 

Drain, the range of selenium concentrations was 2.9 to 100 

μg/g with a mean of 30 μg/g dry weight (USBR and others, 

1998). The elevated selenium concentrations and the wide 

range of concentrations documented in bed sediment of the 

San Luis Drain are consistent with observations from wetlands 

(including Kesterson Reservoir) where microbial dissimilatory 

reduction and biotransformation by primary producers stripped 

dissolved selenium from the water and converted it to particulate Se(0) and particulate Se(-II). Martens and Suarez (1997) 

showed that selenium in San Luis Drain sediment was probably about 90 percent elemental selenium, also suggestive that 

microbial dissimilatory reduction was especially important in 

that environment. Contact may occur within the drain between 

oxidized water and a sharp redox gradient in sediments, which 

is apparently sufficient to transform a significant quantity of 

incoming selenium to particulate form (Presser and others, 

1996; Presser and Piper, 1998). Re-suspension and transport 

of sediments from the San Luis Drain, therefore, must be 

considered as a source of selenium for the San Joaquin River, 

deserving of further study. Similarly, re-suspension of sediments in a San Luis Drain extension to the Bay-Delta could 

provide a direct source of highly contaminated particulate 

selenium to the Bay-Delta. The hydraulic residence time of the 

North Bay at low flows is about 60 days (Walters and others, 

1985). Substantial oxidation of Se(0) could occur if fine particles and plant detritus generated in the San Luis Drain were 

transported to the Bay-Delta. Elemental selenium might also 

be expected in sediments in the Bay-Delta where conditions 

favor biogeochemical deposition (anoxic sediments). Such 

conditions might be present in marshes near a discharge point 

for a San Luis Drain extension or within sediments deposited 

within the San Luis Drain itself. 

None of the sampling protocols referenced above 

included sampling of algal mats as part of the suspended 

or bed sediment fraction. Seasonal algal blooms occur in 

drainage canals and sloughs receiving agricultural drainage. 

Data collected during the discharge of the San Luis Drain into 

Kesterson National Wildlife Refuge showed that selenium was 

concentrated in algal mats associated with evaporation ponds 

(Presser and Ohlendorf, 1987). Thus, algal mats and blooms 

may represent a significant fraction of total selenium in an 

aquatic ecosystem from a mass balance basis that has not been 

systematically documented during surveys of suspended or 

bed sediment. The surficial layer of bed sediment may be the 

most affected by accumulations of decaying organic material 

(Presser and others, 1996)

Sedimentary selenium in Suisun Bay and San 

Pablo Bay 

Transformation of selenium in wetlands in the Bay-Delta 

has not been well studied, nor have surveys of marsh sediments been done systematically. Zawislanski and McGrath 

(1997) reported concentrations of 1.0 to 1.25 μg/g dry weight 

in the sediments of a marsh on Carquinez Strait. Concentrations were similar in core samples collected down to 15 

centimeters depth in the sediment. Using a range of dissolved 

concentrations in Carquinez Strait of 0.1 to 0.3 μg/L, the Kd

for the marsh sediments ranges from 3.33 × 103 to 1.25 × 104. 

Zawislanski and McGrath (1997) also reported pore water 

concentrations of 2 to 10 μg/L, but further verification of such 

elevated values is necessary. 

Bed sediments that have been studied to date in shallowwater habitats of the Bay-Delta are not heavily contaminated 

with selenium. For example, selenium concentrations were 

determined in fine-grained sediments from a core collected in 

Richardson Bay, near the mouth of the estuary (Hornberger 

and others, 1999). Concentrations of selenium (0.2 to 0.4 μg/g 

dry weight) were similar throughout the length of the core, 

with no clear anthropogenic signal accumulating in recent 

sediments. 

Zawislanski and McGrath (1997) reported selenium 

concentrations of 0.5 to 1.0 μg/g dry weight in mudflat 

sediments adjacent to a marsh in Carquinez Strait. Johns 

and others (1988) found mean concentrations of 0.31 μg/g 

dry weight in repeated analyses of sediments (fine-grained 

oxidized surface sediments, <100 μm) from four locations in 

Suisun Bay in the late 1984 to 1986. Concentrations in New 

York Slough, where the San Joaquin River enters Suisun Bay, 

were the highest in the region (0.53 ± 0.28 μg/g dry weight) 

and varied, the most widely of any station, from 0.2 to 1.0 μg/

g dry weight. Recent studies by Cutter and Cutter (2004) and 

Doblin and others (2006) show results across a range similar 

to those reported by Johns and others (1988). In summary, 

concentrations of selenium in fine-grained Suisun Bay 

sediments are about 0.3 to 0.5 μg/g dry weight and median 

concentrations of dissolved selenium are 0.2 μg/L. These data 

show that the Kd is about 1.5 to 2.5 × 103, within the range 

reported for other ecosystems. 
46 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Suspended particulate selenium in Suisun Bay 

and San Pablo Bay

Water column biogenic transformation of dissolved to 

particulate selenium is well known and is especially important in determining exposures of detrital and filter-feeding 

consumer organisms. Selenium concentrations per unit mass 

suspended material exceed concentrations in bed sediments, 

based on several analyses conducted in April and September 

1986 (Cutter, 1989); June 1995; and October 1996. Selenium 

concentrations in suspended material can vary widely.

In April 1986, after an episode of extremely high river 

inflow, the maximum concentration of particulate selenium near Carquinez Strait was 0.64 μg/g dry weight, 

with an average concentration throughout the North 

Bay of 0.33 μg/g dry weight. 

In September 1986, during low inflows, the concentration of particulate selenium averaged 0.75 μg/g 

dry weight, with a maximum of about 1.25 μg/g dry 

weight. The particulate selenium concentrations were 

about 5 × 103 to 1 ×104 greater than the concentration 

per unit mass dissolved in the water column. 

In June 1995, during a prolonged period of very high 

inflows, particulate selenium concentrations ranged 

from 0.53 to 0.99 μg/g dry weight, with an average 

concentration among six samples of 0.68 μg/g dry 

weight. The Kd for median concentrations in this sampling was:

 [750 μg/kg dry weight] ÷ [0.075 μg/L] = 1 × 10 [750 μg/kg dry weight] ÷ [0.075 μg/L] = 1 × 10 g/kg dry weight] ÷ [0.075 μg/L] = 1 × 10 g/kg dry weight] ÷ [0.075 μg/L] = 1 × 10 g/L] = 1 × 10 = 1 × 10 = 1 × 104.

In October 1996, during low flows, particulate selenium concentrations were more than twice the concentrations in September 1986 (fig. 12). A concentration of about 7.70 μg/g dry weight was observed in 

suspended material in the Sacramento River channel 

at Rio Vista and 3.57 μg/g dry weight was found in the 

San Joaquin River channel. The two are interconnected 

at that time of year, so the San Joaquin River was the 

likely source of this material. Concentrations declined 

down the estuary, further suggesting a delta/riverine 

source. Elsewhere in the Bay-Delta, suspended material selenium concentrations were about 1.54 to 2.51 

μg/g dry weight, with an average concentration in eight 

bay samples of 1.98 μg/g dry weight [more than two 

times higher than the mean (0.75 μg/g dry weight) in 

September 1986]. The Kd's for the median Suisun Bay 

selenium concentrations for the October 1996 survey 

were therefore:

 [2,100 μg/kg dry weight] ÷ [0.18 μg/L] = 1.17 × 104 

For the landward sites, highly elevated particulate 

concentrations yielded a Kd of:

 [5,600 μg/g dry weight] ÷ [0.18 μg/L] = 3.1 × 10 [5,600 μg/g dry weight] ÷ [0.18 μg/L] = 3.1 × 10 g/g dry weight] ÷ [0.18 μg/L] = 3.1 × 10 g/g dry weight] ÷ [0.18 μg/L] = 3.1 × 10 g/L] = 3.1 × 10 = 3.1 × 10 = 3.1 × 104.

•

•

•

•

Summary

Concentrations >1 μg/g dry weight in suspended materials 

are common and concentrations as high as 7.7 μg/g dry weight 

are observed in a few instances. The sources and frequency of 

the highest concentrations are not clear. Kd's in these surveys are 

consistently ≥1 × 104. The roles of factors such as particle size, 

organic content, and different transformation processes need to 

be better understood to resolve causes of the differences between 

concentrations of selenium in suspended and sedimentary material and the differences in Kd's between these two reservoirs of 

selenium. Time-intensive studies and continued assessment of 

the sources of the highest selenium concentrations transported in 

suspended material to the Bay-Delta also are needed.

Bioaccumulation of Selenium by 

Invertebrates

Processes 

Bioaccumulation by lower trophic level invertebrates 

(such as zooplankton and bivalves) is a critical step in determining effects of selenium. These are the animals that provide 

the vector (food) that is the source of selenium exposure to 

higher trophic level predators such as fish and birds. Estuarine 

invertebrates are exposed to selenium through: 

direct uptake of dissolved selenium; 

primary producers taking up selenium and they themselves being consumed by animals: and/or 

direct uptake of detrital or sedimentary selenium 

enriched particles via filter-feeding or deposit feeding. 

In laboratory studies of the mussel Mytilus edulis, dissolved 

selenite is the most bioavailable form of inorganic selenium 

taken up from solution, but the uptake rate is slow compared 

to many trace elements (Wang and others, 1996). Luoma and 

•

•

•

0

0

1

2

3

4

September 1986

October 1996

7

8

10 20

Salinity, in practical salinity units

Particulate selenium concentration,

in micrograms per gram dry weight

30

Figure 12. Particulate selenium profiles as a function of salinity in 

the Bay-Delta during high and low flow seasons in 1986 (9/86) and in 

1996 (10/96).
 47

others (1992) showed that the uptake rate of dissolved selenite 

explained less than 5 percent of the tissue burden of selenium 

accumulated by the clam Macoma balthica at concentrations 

typical of the Bay-Delta. The role of dissolved organic selenides 

in selenium bioaccumulation is not as well understood as availability of inorganic selenium, but it is unlikely that the rate of 

uptake is sufficient to be greater than uptake rates from food. 

The evidence is strong that uptake of dissolved selenium 

(dissolved selenite plus dissolved organo-Se) by invertebrates is 

not as important as uptake from diet (Luoma and others, 1992; 

Lemly, 1993a). Dissolved selenium speciation strongly influences uptake by primary producers (such as phytoplankton) and 

microbes. Uptake of selenite by phytoplankton is substantially 

more efficient than uptake of selenate. But if selenate concentrations are 10 times those of selenite, and uptake rates differ by 10 

times, then the two forms could be equally important. Concentration factors by phytoplankton, for selenite, can be as high as 

about 104

 or 105 (see, for example, Butler and Peterson, 1967; 

Fowler and Benayoun, 1976; Wrench and Measures, 1982). 

Once taken up, selenite is incorporated into seleno-amino acids 

within phytoplankton (Wrench, 1978; Wrench and Campbell, 

1981), which are then transferred to the next trophic level with 

great efficiency. Assimilation efficiencies for phytoplanktonassociated selenium range from 55 to 90 percent among 

different invertebrates (see, for example, Reinfelder and others, 

1997). Selenium uptake from non-living particulate material 

or detritus has not been well studied. In general, it is probably 

less efficient than uptake from living plant material; although 

some fraction of most natural forms appears to be bioavailable (Wang and others, 1996; Luoma and others, 1992). For 

example, Luoma and others (1992) studied uptake of particulate 

elemental selenium produced from the microbial reduction of 

75Se-selenate M. balthica. The particulate Se(0) was formed by 

simulating the biogeochemical transformation process thought 

to be predominant in wetlands. The assimilation efficiency of 

elemental selenium was 22 percent by this bivalve. 

Selenium in Invertebrates from the Bay-Delta

Fish and birds are the two taxa of greatest concern 

(the most sensitive) with regard to selenium contamination 

(Ohlendorf and others, 1989a; Skorupa, 1998c; Hamilton, 

2004). However, fish and birds are mobile, impractical to 

sample in large numbers, and difficult to monitor routinely. 

On the other hand, consumption of prey comprised of primary 

and secondary consumer species is the route by which these 

predators are exposed to selenium. Consumer species such 

as bivalves, polychaetes, amphipods, or zooplankton can be 

practical to employ as resident bioindicators of selenium exposure (Phillips and Rainbow, 1993; Brown and Luoma, 1995b; 

Luoma and Rainbow, 2005). As discussed below, predators 

with the highest tissue concentrations of selenium in the 

Bay-Delta are benthivores that consume bivalves in their diet. 

Therefore, the most relevant bioindicators for these sensitive 

predator species are bivalves.

Interpretations are least ambiguous when selenium 

concentrations in bioindicator species are compared to clearly 

defined reference concentrations. For our model, we assume 

that a location is an adequate reference if soils or source 

geologic units are not selenium-enriched, if no anthropogenic 

sources of selenium are known, and if concentrations in the 

indicator organism are in the lowest quartile of all available 

data. Concentrations of 1.70 to 2.66 μg/g dry weight were 

reported during 1993 to 1995 for the clam C. fluminea transplanted from a clean environment to the Sacramento River 

(San Francisco Estuary Institute, 1994, 1995, 1996). Johns and 

others (1988) found a mean reference concentration and 95 

percent confidence limits of 3.08 ± 0.28 μg/g dry weight in C. 

fluminea from apparently uncontaminated sites near Clifton 

Court Forebay and in the Tuolomne River (fig. 13a). 

Bivalves from the Bay-Delta have elevated selenium 

concentrations compared to these reference sites (Risebrough 

and others, 1977; Johns and others, 1988; Urquhart and 

Regalado, 1991) (fig. 13a). Risebrough and others (1977) 

reported concentrations of 10.0 to 11.4 μg/g dry weight in a 

single deployment of transplanted mussels (Mytilus sp.) in 

Carquinez Strait, and concentrations of 5.0 to 7.4 μg/g dry 

weight near Mare Island in Suisun Bay. Anderlini and others 

(1975) reported concentrations of 4.5 to 6.7 μg/g dry weight 

in the clam M. balthica near Mare Island in 1974. Although 

done more than 20 years ago, both these studies analyzed 

their samples by neutron activation, which is a relatively 

insensitive but reliable analytical technique. Johns and others 

(1988) collected C. fluminea from resident populations at six 

locations in Suisun Bay, between January 1985 and October 

1986. Figure 13a compares the frequency distribution in 129 

composite samples of C. fluminea collected from the sites 

nearest Carquinez Strait (Roe Island and Middle Ground) 

to the reference values reported by Johns and others (1988). 

The mean concentration and 95 percent confidence limits 

among the Suisun Bay data was 5.08 ± 0.17 μg/g dry weight, 

significantly different than the reference values (p<0.001). 

These historic data show that the habitat in Carquinez Strait 

was contaminated twofold or more with selenium compared 

to reasonable reference locations, and that contamination was 

present since at least 1974.

In 1986, the bivalve P. amurensis invaded the Bay-Delta. 

This species was previously known only in the estuaries of 

Northeastern China, Korea, and Japan. P. amurensis eventually replaced several other resident species in Suisun Bay 

after the invasion, and is probably now the dominant food of 

benthivore predators in the ecosystem (Nichols and others, 

1990). Figure 13b shows the C. fluminea reference site distribution and the frequency distribution of selenium among 62 

composite samples of P. amurensis collected from Carquinez 

Strait between May 1995 and June 1997 (Linville and others, 

2002). The mean concentration and 95 percent confidence 

limits among all data for P. amurensis was 12.94 ± 0.75 μg/g 

dry weight. A wide distribution of concentrations was also 

observed, reflecting substantial temporal variability. 
48 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Thus, the mean concentration of selenium in the dominant resident bivalve in Suisun Bay (C. fluminea in 1985 – 86 

compared to P. amurensis in 1996) (fig. 14) has more than 

doubled since 1985– 86. It is therefore likely that the total 

amount of selenium exposure of birds and fish that feed on 

bivalves has similarly doubled. The 1995– 97 mean concentration in P. amurensis exceeds a dietary guideline with a high 

certainty of producing adverse effects in predators (see later 

discussion). During 1995– 97, 32 percent of P. amurensis

samples from Carquinez Strait contained selenium > 15 μg/g 

dry weight (Linville and others, 2002), thus creating an even 

greater potential for biotic consequences during some times of 

the year.

Selenium concentrations in P. amurensis from Carquinez 

Strait vary seasonally (fig. 14). Concentrations varied approximately threefold with time during 1995– 97. The highest 

concentrations were observed in October 1996 (20 ± 1 μg/g 

dry weight) and the lowest concentrations were observed 

in May 1995 (7.13 ± 0.34 μg/g) and May 1997 (6.2 ± 0.2 

μg/g). The changes in concentrations coincided with seasonal 

changes in mean monthly river inflows to the North Bay. The 

lowest concentrations occurred after two episodes of highest 

river inflows. The greatest increase in selenium occurred after 

prolonged periods of low inflow. Inflows from the San Joaquin 

River and/or inflow-driven differences in residence times of 

local waters also could be important, because the highest ratios 

of San Joaquin River to total Delta outflow occur in the fall 

(figs. 8 and 9).

An extensive spatial survey was done in October 1996 

to determine how concentrations of selenium in P. amurensis

compare among different locations in the North Bay. Selenium concentrations were determined in replicate composite 

samples of P. amurensis at 22 locations (Brown and Luoma, 

1995a; Linville and others, 2002) (fig. 15). The October 

1996 sampling included an extensive investigation of shallow 

habitats adjacent to marshes and mudflats of San Pablo Bay 

and Suisun Bay, as well as deeper channel stations. Selenium 

enrichment, compared to historic concentrations in previously 

dominant benthos, was widespread throughout the North Bay, 

with all concentrations in P. amurensis in excess of those in 

C. fluminea observed by Johns and others (1988). Among the 

stations, the highest concentrations of selenium were found in 

resident P. amurensis located (1) in Carquinez Strait; (2) in the 

deeper, westward channel of Suisun Bay; and (3) towards the 

mouth of the San Joaquin River. Selenium concentrations in P. 

amurensis from the shallows, adjacent to marshes in Honker 

Bay were higher than concentrations in Grizzly Bay and San 

Pablo Bay. The two sites with the lowest mean selenium 

concentrations were found in Grizzly Bay, in particular in 

association with inflows of Sacramento River water through a 

location called Suisun Cutoff.

Summary of Exposure

In summary, selenium bioaccumulation data from invertebrates show the following: 

Selenium enrichment in primary consumer species 

(bivalves) has been evident in Suisun Bay since the 

1970s. 

The spatial pattern of historic contamination is consistent with an origin from refinery effluents (as shown by 

water column analyses). 

•

•

0

20 4 6 8 10

Reference

Reference

C. fluminea

C. fluminea

P. amurensis

Bay-Delta

Bay-Delta

Selenium concentration, in micrograms per gram dry weight

12 14 16 18 20

10

20

Percentage of samples

30

40

0

10

20

30

40

a

b

Figure 13. Frequency distributions of selenium concentrations in 

(a) composite samples of C. fluminea from references sites (see 

text for definition) and from Carquinez Strait collected between 

January 1985 and October 1986; and (b ) composite samples of P.

amurensis from reference sites (see text for definition) and from 

Carquinez Strait collected between May 1995 and June 1997.

0

5

10

15

20

25

Carquinez

Straits

San Pablo

Bay

San Joaquin R.

 discharge

J MF MA J S O N DAJ J MF MA J S O N DAJ J MF MA J

1995

Selenium concentration in P. amurensis,

in microgramss per gram dry weight

0

100

200

300

Average monthly Delta outflow,

in thousands of cubic feet per second

1996 1997

Figure 14. Selenium concentrations in replicate composite 

samples of P. amurensis and Delta outflows on a monthly basis 

from 1995 through 1997
 49

The highest selenium concentrations in a species of 

bivalve that is now the dominant benthic species in 

Suisun Bay were found in the 1995 to 1997 studies of 

Linville and others (2002). No systematic studies of 

selenium concentrations in clams are available since 

that time. 

Selenium enrichment was apparently spread through all 

of Suisun Bay and all of San Pablo Bay by 1996. 

Temporal variability was not significant in monthly 

samples of C. fluminea in 1985– 86; but threefold 

seasonal variability in selenium concentrations is now 

observed in P. amurensis near Carquinez Strait. Concentrations in P. amurensis increased during low river 

inflow regimes, decreased during higher river inflow 

regimes

 In the most recent survey, selenium concentrations in 

P. amurensis near Carquinez Strait exceed 10 μg/g dry 

weight in most months of the year (all months of some 

years), and 32 percent of values measured between 

October 1995 and June 1997, exceed 15 μg/g dry 

weight. Thus, concentrations in P. amurensis exceed a 

dietary guideline for predators that has a high certainty 

of producing adverse effects in predators (see later 

discussion). 

It is not yet clear whether the elevated selenium contamination in P. amurensis is unique to this species; 

represents greater selenium inputs (probably from the 

Delta and San Joaquin Valley through the San Joaquin 

River) than occurred historically; or both. 

•

•

•

•

•

Modeling Selenium Bioaccumulation in 

the Bay-Delta: Dynamic Multi-Pathway 

Bioaccumulation (DYMBAM) Model 

Bioavailability of selenium is affected by a variety of 

factors. Models are the most effective forecasting tool to 

encompass a range of factors involving a range of assumptions. Realistic exposure models need to be geochemically 

robust (include consideration of geochemical form), biologically specific, and flexible in order to handle a variety of 

environmental circumstances. Predictions from a model should 

be verifiable in nature.

An approach used by USEPA (Peterson and Nebeker, 

1992) uses the following simple ratio:

Bioaccumulation = [concentration in organism] 

 [concentration in environment],

where environmental concentrations are either those in water 

[bioaccumulation (BAF) or bioconcentration (BCF) factors] 

or sediment [sediment accumulation factor (BSAF)]. The flaw 

of this approach is that it does not allow consideration of the 

effects of speciation in water or of particulate material on bioaccumulation. Thus, bioaccumulation factors can vary by as 

much as 50-fold for a given species in different environments, 

and much more than that among species. An alternative modeling approach, the Dynamic Multi-pathway Bioaccumulation 

(DYMBAM) Model uses different experimentally established 

uptake rates for different forms of dissolved and particulate 

selenium, along with environmental concentrations of these 

forms, to determine bioaccumulation in tissues (Luoma and 

others, 1992). The advantages of this approach are discussed 

extensively in Luoma and Fisher (1997), Schlekat and others (2002 and 2004), and Luoma and Rainbow (2005). One 

advantage for the Bay-Delta forecasts developed here is that 

bioaccumulation in prey (bivalves) can be derived for different 

speciation regimes. The speciation consideration is important 

because speciation will change as sources change, and relations with total selenium or individual species of selenium 

will also change (see, for example, San Francisco Bay Board, 

1992a). Another substantial advantage of the approach is 

that predictions can be verified by comparison to analyses of 

selenium in tissues of resident species, such as clams. The 

DYMBAM model is used here in all forecasts of bioaccumulation in prey derived from different selenium load scenarios.

The mathematics of the simplest kinetic model with food 

and water pathways illustrates the necessary data:

dCm/dt = (If

 + Iw) – Cm(ke + g) (1)

Cm,t = [If + Iw/(ke + g)] [1 – e-(kt + g)t] (2)

Cm,ss = If/ke (3)

where, Cm is the tissue concentration in an animal, t is time, 

If is gross influx rate from food, Iw is gross influx rate from 

water, ke is the proportional rate constant of loss (slowest compartment), and g is growth. For Cm,ss or concentration at steady 

state, the equation can simplify to:

Chipps I.

Suisun Bay

Honker Bay

Grizzly Bay

San Pablo

Bay

Carquinez

Strait

DELTA

San Luis Drain

(proposed)

Selenium concentrations,

in micrograms

per gram dry weight

4 – 8

8 – 14

14 – 20

7.9

7.5 7.3

6.7

6.1 8.2

6.9 8.1

8.1

8.3

8.7 8.9

10.3 10 7.5

9.2

9.6

5.7

20

11 16.8

0 10 km

0 10 mi

Figure 15. Selenium concentrations in replicate composite 

samples of P. amurensis at 21 locations in the Bay-Delta during 

October 1996.
50 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Cm,ss = If + Iw/ke (4)

if we assume that growth is not important. Mechanistically, 

the mathematics state that bioaccumulation in an organism 

results from a combination of gross influx rate as balanced by 

the gross efflux rate. Gross efflux is an instantaneous function 

of the concentration in tissues and the rate constant(s) of loss 

(equations 1 and 2). Gross influx can come from water or from 

food and is a species-specific function of the concentration of 

a bioavailable element. 

For influx rate from food alone, in μg/g of selenium in 

tissue per day: 

If

 = FR × Cf × AE (5)

where FR is feeding rate in grams of food per gram of tissue 

per day; Cf

 is concentration in food (particulate material in 

the case of bivalves) in grams of selenium per gram food (dry 

weight), and AE is assimilation efficiency of the food eaten 

by the animal. Influx rate from water can be broken into its 

components similarly (Wang and others, 1996), but because 

the influx rate from water was determined experimentally 

for specific species by Fowler and Benayoun (1976), Wang 

and others (1996), and Luoma and others (1992), the rate is 

employed directly here as μg selenium/g tissue per day. 

From Reinfelder and others (1997), the ultimate concentration of selenium that a bivalve would bioaccumulate under 

each environmental condition can be calculated from: 

Css = [Iw + (FR × Cf

 × AE)]/ke (6)

Bioaccumulation of Selenium by 

Predators

Numerous studies have demonstrated that a small 

increase in waterborne selenium will result in a disproportionately large elevation of selenium concentrations in fish and 

wildlife (Skorupa, 1998a). Several attributes affect selenium 

uptake by these organisms:

Processes that affect selenium retention and inter-organ 

distribution are important considerations for fish and 

birds that range and feed widely over areas with varying selenium exposure pathways.

Dietary exposure and, in most cases, with progressive 

biomagnification through the food web, is the pathway 

that leads to disproportionately large bioaccumulation 

of selenium in upper trophic levels. 

Some implications of dietary uptake are: 

waterborne selenium concentrations are poorly 

linked to predator bioaccumulation because 

environmental factors affect transformation of 

selenium and uptake by invertebrates; 

where data on predators is difficult to obtain 

directly, invertebrates may be the best indicator 

for monitoring predator exposures; 

•

•

•

o

o

a predator’s choice of food, which varies widely 

among species, could result in some trophic pathways being more efficient accumulators of selenium than others. For example, long-term studies 

of the terrestrial environment created by burial of 

the contaminated evaporation ponds at Kesterson 

Reservoir show that invertebrate carnivorous and 

scavenger species provide an elevated route of 

vertebrate exposure as compared to herbivorous 

species (CH2M HILL, 1996, 1999a). 

Dietary Exposure 

Lemly (1982, 1985) was one of the first to show that 

dietary uptake was responsible for the largest proportion of 

bioaccumulated selenium in fish. This study was at a reservoir 

(Belews Lake, North Carolina) contaminated by wastes from a 

coal-fired power plant (Cumbie and Van Horn, 1978). Lemly 

compared concentrations of selenium in bluegill and largemouth bass collected from the lake, with concentrations of 

selenium in those species when exposed to sublethal concentrations of selenium in water alone in a laboratory study. 

A lower concentration factor was found from water alone 

than from bioaccumulation through dietary plus waterborne 

sources. This finding was corroborated by the observation that 

piscivorous fish (fish that feed on other fish), at the highest 

trophic level, accumulated the most selenium in the lake. All 

piscivores and omnivores eventually succumbed to selenium 

poisoning, while a few lower trophic level fish survived. Other 

studies have since verified directly and indirectly the overwhelming importance of selenium bioaccumulation from food, 

as compared to direct uptake from water. 

If the primary source of selenium to wildlife is dietary, 

then it should not be surprising that waterborne or dissolved 

selenium is an imprecise predictor of the selenium exposure 

of birds and fish (Luoma and others, 1992; Presser and others, 

1994; Schlekat and others, 2002; Luoma and Rainbow, 2005). 

Differences in dissolved species, transformation to particulate 

form(s), particulate species, and invertebrate bioaccumulation 

all influence how waterborne selenium is transferred to predators. These processes are affected by the nature of the source 

and the environmental conditions in receiving waters (for 

example, selenium in agricultural drainage water can be in a 

different form than the selenium in industrial sources; selenium discharged to a wetland is transformed differently than 

selenium discharged to an estuarine water column). Physical 

processes such as hydraulic residence time also are important. Particulate transformation of selenium in a river (such as 

the San Joaquin River) may occur far downstream from the 

source; while transformations in a wetland or an estuary with 

a long residence time may occur near the source. Biological 

processes that affect exposure of a predator include differences 

among species in feeding, behavior, and physiology. 

An example of the influence of confounding processes 

among these links can be found in data from the Bay-Delta 

watershed. Black-necked stilts (wading birds), averaged about 

o
 51

the same exposure to selenium (20 to 30 μg/g dry weight 

found in eggs) at Chevron Marsh in the Bay-Delta as at 

Kesterson Reservoir (25 to 37 μg/g dry weight in eggs), but the 

source water in Chevron Marsh contained about 10 percent the 

concentration of selenium found at Kesterson Reservoir (maximums: 20 μg/L compared to 300 μg/L) (Skorupa, 1998a). The 

reason for the difference was that the transfer of selenium 

from water to aquatic invertebrates was greatly enhanced at 

Chevron, compared to Kesterson, because the source form of 

the element was selenite. 

Because of such complexities, the strongest correlative 

predictor of selenium concentrations in predator tissue that 

reflects selenium exposures is probably selenium concentrations in invertebrates (prey). Invertebrates may be the optimal 

indicator to use in monitoring selenium in an ecosystem 

because they are practical to sample and are most closely 

linked to predator exposure (prey are the primary source of 

selenium for the predators). Few investigators have fully 

explored feeding relationships and resultant correlations with 

selenium bioaccumulation in food webs.

One repeated observation in contaminated ecosystems 

is that predator species differ in their bioaccumulation of 

selenium. In general, this variable accumulation seems to be 

related to the diet of the predators. In Belews Lake, concentrations followed the ranking: piscivores (bass and perch) > 

omnivores > planktivores. These feeding groups were probably too broad, however. In Lake Oltertjarn, Sweden, after 

treating the lake with selenite for two years, selenium tissue 

concentrations in northern pike (Esox lucius) averaged 4.6 μg/

g dry weight, whereas in perch (Perca fluviatilis) the average 

was 23 μg/g dry weight (Paulsson and Lundbergh, 1991). The 

perch had disappeared by the second year, but the pike had 

not. One explanation of the results was that perch ate invertebrates with elevated selenium concentrations, whereas pike ate 

water-column-feeding fish with low selenium concentrations.

Differences in selenium exposure among predators also 

seem to be the case in the Bay-Delta. Fish (such as white sturgeon, starry flounder, and probably Sacramento splittail) that 

ingest benthos, and especially bivalves, have higher selenium 

concentrations (see, for example, Urquhart and Regalado, 

1991) than predators that feed from the water column, like 

striped bass (Morone saxatilis) (Saiki and Palawski, 1990). 

Further systematic study of such hypotheses is important 

because it could focus attention on the species most likely to 

disappear first from excessive selenium contamination. It is 

likely that the species experiencing the highest exposure of 

selenium are at the greatest risk of extinction or of population 

damage. It also should be remembered that biomagnification is 

sufficient to eliminate species at the top of the trophic structure, 

even when waterborne selenium concentrations are in the 2 to 5 

μg/L range (Lemly, 1985, 1997b, d). Therefore, some selenium 

contaminated systems may already have lost vulnerable links in 

the food web, even though populations of some species remain. 

Study of systems with less extreme contamination may be one 

way to understand where those vulnerable links occur. 

Existing Selenium Concentrations in Tissues of 

Birds and Fish in the Bay-Delta

The Department of Fish and Game conducted extensive 

sampling of a variety of bird and fish species in the BayDelta between 1986 and 1990 through a Selenium Verification Study for the State Board (White and others, 1987, 1988, 

1989; Urquhart and Regalado, 1991). This effort was one of 

the most extensive surveys of selenium contamination in a 

food web ever conducted. Fish samples from the Bay-Delta 

were compared to fish from Humboldt Bay (table 12), an area 

with no known source of selenium. The greatest differences 

between the two ecosystems occurred in bottom-feeding fish 

[such as English sole (Parophrys vetulus) with 3.05 ± 0.2 

compared with 1.78 ± 0.2 μg/g dry weight in flesh, respectively; and starry flounder with 9.2 ± 2 compared with 3.6 μg/g 

dry weight in liver, respectively]. Although the sampling was 

limited in number, Dungeness crab from Suisun Bay contained 

a mean selenium concentration of 14 μg/g dry weight tissue, 

compared to a mean concentration of 5 μg/g dry weight tissue 

in Humboldt Bay. Selenium concentrations in Pacific herring 

(Clupea pallasi), speckled sanddab (Citharichthys stigmaeus)

and longfin smelt (Spirinchus thaleichthys) were not different 

between the two ecosystems. Uptake of selenium by striped 

bass in the North Bay also did not appear problematic in 

samplings in 1986 (average, 1.3 to 1.9 μg/g dry weight) (Saiki 

and Palawski, 1990). Thus, some bottom-feeding fish bioaccumulated selenium in excess of the reference area, but fish 

(such as herring, striped bass) that were primarily herbivorous, 

or fed from the water column, showed little difference in selenium tissue concentrations between the two ecosystems. 

The highest concentrations of selenium were found in 

white sturgeon in the Bay-Delta (fig. 16). However, white 

sturgeon were not found for comparison in Humboldt Bay. 

White sturgeon is a long-lived benthic predator that spends 

its life in the Bay-Delta, the Sacramento River, and to a small 

extent, the San Joaquin River (Kohlhorst and others, 1991). 

White sturgeon are voracious consumers of P. amurensis. This 

raises the possibility that selenium trophic transfer via bivalves 

is a critical pathway of selenium exposure in the Bay-Delta. If 

so, it would be expected that selenium concentrations in white 

sturgeon should probably have increased after P. amurensis

invaded the estuary in 1986. In 1986, the average concentration of selenium in livers from ten white sturgeon was 9.2 ± 

2.9 μg /g dry weight (White and others, 1987, 1988, 1989; 

Urquhart and Regalado, 1991). In 1989– 90, the average 

concentration of selenium in livers from 42 white sturgeon 

was 30 ± 21 μg/g dry weight. Although variability was high 

(as expected for animals that move over large areas), the 

average selenium concentration after the P. amurensis invasion 

was more than double that before the invasion. 

White sturgeon were analyzed more recently in two 

surveys conducted to determine exposure of sport fisherman 

to contaminants (Davis and others, 1997; Fairey and others, 

1997; San Francisco Estuary Institute, 1999). The number of 

white sturgeon analyzed were many fewer than determined for 
52 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

the Selenium Verification Study, and therefore the ability to 

detect differences or trends (the statistical power) was weak. 

Locations of sampling and fish size were also highly variable. 

From this data it is not possible to draw conclusions about 

selenium contamination of white sturgeon in the late 1990s. 

The contrast is interesting between selenium concentrations in white sturgeon and those in striped bass, another major 

resource species in the system. Striped bass, like white sturgeon, 

are anadromous fish, but they feed primarily on crustaceans 

from the water column. Contaminants in juvenile striped bass 

were studied in detail in 1986 by Saiki and Palawski (1990). 

They analyzed whole body fish samples from 22 stations from 

the upper San Joaquin River downstream through San Pablo 

Bay. Some of their observations about selenium concentrations 

in whole-body samples of striped bass included:

• The highest selenium concentrations were found in the 

main channel of Mud Slough and in the San Joaquin 

River immediately downstream from Mud Slough.

• The mean selenium concentration among the six most 

contaminated sites was 5.3 μg/g dry weight.

• Selenium concentrations were low above Mud Slough and 

also downstream in the San Joaquin River, as tributary 

dilution increased (range of 1.03 to 2.9 μg/g dry weight 

in the lower San Joaquin River, below the Merced 

Table 12. Selenium concentrations in fish from the Bay-Delta (North Bay including Suisun, San Pablo, Grizzly and Honker Bays) and 

Humboldt Bay. 

[Data from Selenium Verification Study: White and others (1987, 1988, 1989); Urquhart and Regalado (1991). Tissue data in dry weight; std. dev. = standard 

deviation; n = number of samples.]

Location (date)

and species

Selenium (dry weight)

Flesh (μg/g) Liver (μg/g) Whole-body (μg/g)

Average Std. dev. n Average Std. dev. n Average Std. dev. n

North Bay (January −June, 1986)

white sturgeon 7.8 3.1 10 9.2 2.9 10 − − −

English sole 3.0 0.2 4 − − − − − −

starry flounder 4.6 1.0 7 9.2 2.2 7 − − −

longfin smelt − − − − − − 1.5 0.4 8

Pacific staghorn sculpin 2.5 0.2 8 6.7 1.0 8 − − −

Pacific herring − − − − − − 3.0 0.7 4

speckled sanddab − − − − − − 1.8 0.03 2

northern anchovy − − − − − − 2.1 0.08 4

yellowfin goby − − − − − − 2.4 0.2 7

North Bay (March−May, 1987) 

white sturgeon 10 3.7 13 − − − − − −

North Bay (December, 1987 and January, 1988) 

white sturgeon 7.2 4.4 14 − − − − − −

North Bay (February, 1989 to March, 1990)

white sturgeon 15 11 62 30 21 42 − − −

yellowfin goby 2.0 − 1 4.3 − 1 3.1 − 1

Humboldt Bay (February and June, 1986)

English sole 1.8 0.22 3 7.8 − 1 − − −

starry flounder 0.9 − 1 3.6 − 1 − − −

longfin smelt − − − − − − 1.2 0.08 2

Pacific staghorn sculpin 1.6 0.13 4 3.9 0.46 3 − − −

Pacific herring 1.6 0.08 2 − − − 4.5 − 1

speckled sanddab − − − − − − 1.6 0.3 4
 53

River). So bioaccumulation was responsive to expected 

inputs of contamination.

• Mean selenium concentrations in the North Bay were 1.3 

to 1.9 μg/g dry weight. These values are at least fivefold 

lower than the average concentration in white sturgeon 

from the North Bay, at that time (table 12, when selenium in flesh is converted to selenium in whole-body 

samples).

In summary, striped bass do bioaccumulate more selenium in environments where more selenium is present. 

However, these animals are not exposed to as much selenium 

in their food web as are sturgeon, resulting in less bioaccumulation than in white sturgeon. Striped bass are therefore 

less likely to be adversely affected by selenium than are white 

sturgeon, suggesting that links between bioaccumulation and 

adverse effects need to be studied, perhaps comparatively, in 

these species.

Eleven species of waterfowl also were analyzed in the 

Selenium Verification Study (White and others, 1987, 1988, 

1989; Urquhart and Regalado, 1991) (fig. 17). In addition 

to fish tissue data, bird tissue data also suggest that the most 

contaminated aspect of the food web is in those species that 

consume bivalves. Data from California reference areas 

(Humboldt Bay, Gray Lodge Wildlife Area, and the Sacramento National Wildlife Refuge) showed the following 

average selenium concentrations in liver tissue: dabbling 

ducks, 3 to 8 μg/g dry weight; shorebirds, 4 to 12 μg/g dry 

weight; and cormorants 18 μg/g dry weight (White and others, 

1987, 1988, 1989; Urquhart and Regalado, 1991). Average 

concentrations in greater and lesser scaup liver were 9 μg/g 

dry weight and in surf scoter liver were 17 μg/g dry weight. 

These values are typical of uncontaminated areas elsewhere in 

the world, as well (Goede, 1994). Concentrations of selenium 

in mallard (Anas platyrhynchos), American bittern (Botaurus 

lentiginosus), northern shoveler (Anas clypeata), and doublecrested cormorant (Phalacrocorax auritus) were not different 

between the Bay-Delta and the reference areas. Mean 

concentrations in two species of shorebird– willet (Catoptrophorus semipalmatus) and American avocet (Recurvirostra 

americana)– were about 20 percent higher in the Bay-Delta 

than in reference areas. Mean selenium concentrations in livers 

of American coot and scaup from Suisun Bay and San Pablo 

Bay were 2 to 4 times those in samples from reference areas. 

The highest concentrations of selenium in aquatic birds in the 

Bay-Delta were found in surf scoter (range 13 to 368; average 

134 μg/g dry weight range in liver) from Suisun Bay and San 

Pablo Bay. Annual averages from Suisun Bay range from 80 to 

240 μg/g dry weight for the period 1986 to 1990. These annual 

averages in surf scoter liver are from 7 to 11 times those 

averages in samples from Humboldt Bay for the period 1986 

to 1989 (annual averages, 11 to 16 μg/g dry weight). These 

concentrations also exceeded concentrations found in surf 

scoter from Morro Bay, the Central Bay and the South Bay 

(White and others, 1987, 1988, 1989; Urquhart and Regalado, 

1991). Concentrations in surf scoter livers from the North Bay 

were also two to threefold higher in 1988, 1989, and 1990, 

than in 1986. 

Concentrations of selenium varied remarkably among bird 

species with different food preferences in San Pablo and Suisun 

Bay. The most contaminated birds (surf scoters) had selenium 

concentrations in their livers that were up to two orders of 

magnitude higher than the selenium concentrations in mallards 

and American bittern. Because of feeding habits, it seems that 

vegetarians exhibited some of the lowest selenium concentrations among bird species, whereas benthic predators had the 

highest concentrations. More specifically, animals whose prey 

included bivalves were most contaminated. Surf scoter, for 

example, are benthic feeders whose prey include bivalves, 

gastropods and crustaceans, with some plants, macroalgae, 

insects, polychaetes and fish (Henny and others, 1995; 

English soleHerringSmeltAnchovyFlounderSanddabSculpinGobySturgeon

0

4

8

Selenium concentration,

in micrograms per gram dry weight 12

Whole

Liver

Flesh

0 40 80 120

Average selenium concentration in bird liver tissue,

in micrograms per gram dry weight

Mallard (*)

American coot

Northern shoveler (*)

American bittern (*)

Black-necked stilt

Willet

American avocet

Double-crested cormorant

Canvasback

Greater and lesser scaup

Surf scoter

3.8

7.2

7.4

3.3

5.7

7.6

9.6

18.7

11.4

36.4

134

Figure 16. Average selenium concentrations in fish collected from 

the North Bay during 1986. (Data from White and others, 1987)

Figure 17. Average selenium concentrations in bird liver tissue 

collected from 1986 to 1990 in: (1) Suisun Bay and San Pablo Bay; 

and (2) Suisun Marsh (denoted by asterisk), a large area of brackish 

wetland located north of Suisun Bay (fig.2), not subject to the 

same direct selenium sources as Suisun Bay [Data from White and 

others, 1987; 1988; 1989; Urquhart and Regalado, 1991].
54 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Hoffman and others, 1998). In general, scaup obtain about 40 

percent of their diet from animal food sources compared to 

scoter, which obtain about 95 percent of their diet from animal 

food sources. 

In 74 samples from an array of studies, Skorupa and 

Ohlendorf (1991) reported mean selenium concentrations 

in bird eggs from reference sites as 1 to 3 μg/g dry weight. 

More than 90 percent of values were below 3 μg/g dry weight. 

The authors concluded that concentrations above 3 μg/g dry 

weight in eggs represent contamination (Skorupa and Ohlendorf, 1991). Thus, data exist to compare selenium concentrations in bird eggs in the Bay-Delta. However, only limited 

studies in the broader Bay-Delta ecosystem are available 

(see, for example, Lonzarich and others, 1992; Ohlendorf and 

Marois, 1990).

Effects of Selenium on Predators

Selenium is an essential element in animals necessary for 

the formation and proper functioning of glutathione peroxidase, an important antioxidant enzyme. The difference between 

required concentrations and toxic concentrations of this 

element is narrow compared to other toxins (see, for example, 

National Research Council, 1976; Luckey and Venugopal, 

1977; Wilbur, 1983; Hodson and Hilton, 1983; Presser and 

Ohlendorf, 1987; Drainage Program, 1990b). In amounts just 

slightly above those need for nutrition, selenium is erroneously substituted for sulfur in selenium-containing amino acids 

(methionine and cysteine). This substitution disrupts the structure of proteins and enzymes, which results is malformations 

during critical stages of development and growth. In birds, 

reproductive failure (inviability of eggs) and/or teratogenesis 

(deformities in developing young) are early and dramatic 

manifestations. However, egg hatchability in birds has proven 

to be the more sensitive endpoint (Skorupa, 1998b and 1999). 

Effects endpoints in birds can be generally grouped in terms 

of sensitivity from least to greatest (adult mortality, juvenile mortality, teratogenesis, mass wasting in adults, embryo 

mortality, reduced juvenile growth, immunosuppresssion), 

although some endpoint have been studied more than others. 

In fish, reproductive impairment occurs to reduce production 

of viable eggs due to ovarian pathology in spawning females 

(necrotic and ruptured mature egg follicles) and post-hatch 

mortality due to metabolism of egg selenium by developing 

larval fish (teratogenic deformities and biochemical dysfunction) (Lemly, 2002). Hatchability of eggs in fish is not affected 

by elevated selenium. However, teratogenesis is induced when 

larval fish are relying on their attached yolk sac for nourishment and development. Once external feeding begins, selenium 

will not cause further deformities in the juvenile fish. Thus, 

the vulnerable pathway is mother to egg to developing larvae 

and fry. Further detail is added to interpretation of effects by 

guidance measured against either an effect concentration or 

lethal concentration and its relation to the percentage of effects 

tolerated (tables 13, 14, and 15). 

Deformities in themselves may not always be lethal, but 

they lower the probability that a deformed individual will 

survive. In fish, deformed larvae either die or quickly fall prey 

to predators and thus are rare in the juvenile or adult populations (Lemly, 1993c). This circumstance was evidenced in 

Belews Lake, North Carolina by a decreased incidence of 

deformities in juveniles, but not fry, when more predators were 

present. Thus, in assessing prevalence of teratogenic effects in 

fish it is important to focus on newly emerging larvae and fry. 

In addition to the sensitivity of life stages, studies of birds 

demonstrate the sensitivity of different species and forms of 

dietary selenium. Selenomethionine is considered the relevant 

dietary supplement (Heinz and Hoffman, 1996; Heinz and 

others, 1996 a, b). Diets supplemented with inorganic selenium result in selenium concentrations in eggs that are only 

0.1 to 0.18 times dietary concentrations, whereas those supplemented with selenomethionine are in the range of 1 to 4 times 

dietary selenium (Heinz and others, 1989; Ohlendorf, 1989). 

Field studies of ducks, stilts, and avocets comprise the largest 

database (Skorupa, 1998a, b), with the order of sensitivity 

(duck > stilt > avocet) helping to determine protective guidelines on both a national scale and site-specific scale.

O’Toole and Raisbeck (1998) in studies of the effects of 

selenium at Kesterson National Wildlife Refuge argue that 

tissue residues should be interpreted flexibly, and used mainly 

as an index of exposure. They suggest that it is necessary to 

examine all possible causes of lesions before attributing cause 

and effect. They also suggest that field-observed effects levels 

should be consistent with those experimentally induced (the 

basis for the thresholds). 

Other considerations in determinative studies for interpretation of guidelines include use of eggs as a metric. Selenium 

concentrations in eggs reflect changes in reproductive success 

and thus are a sensitive indicator of biological response (Lemly 

2002). Bird eggs especially provide unbiased exposure-response 

data in field studies because the health of embryo inside does 

not influence a scientist’s probability of sampling the egg 

(Skorupa, 1998b). Eggs also are not subject to survivor bias; 

that is, samples of free-living birds and fish are self-selected to 

be insensitive (biased) measures of biotic response because only 

survivors (live specimens) are sampled. For example, complete 

reproductive failure can occur in the absence of observable toxic 

effects on adults. Adult fish can survive and appear healthy 

despite the fact that extensive reproductive failure is occurring (that is, toxicity in fish can be invisible) (Lemly 2002b). 

Committing type II error (acceptance of a false negative) 

also can be common in bird studies, if eggs are not collected. 

Bird populations can be abundant and diverse at the time of 

sampling, but without demonstration of embryotoxic effects 

through use of bird egg selenium concentrations, these exposure 

surveys, not exposure-response studies, have a low power to 

detect a biotic response (Skorupa, 1998b).

Additionally, most field studies have been completed 

in off-stream environments (ponds, lakes, reservoirs) that 

in terms of fish have dealt with demographically closed 

populations (Skorupa, 1998b). Here, population collapse is 
 55

relatively easy to detect as a response. In in-stream studies of 

effects, measurements can be taken on biased survivors from 

demographically open populations replenished by outside 

immigrants. Thus, such studies can report the counterintuitive 

combination of elevated levels of selenium in fish and what 

is viewed as normally abundant and diverse fish assemblages. 

These type studies are of low statistical power for detecting 

toxicity because they neither meet the closed-population or 

unbiased exposure-response sampling criteria. 

Community simplification (including local extinction 

of some species) is ultimately the result of excessive selenium contamination. Sixteen of the twenty fish species that 

originally inhabited Belews Lake disappeared when selenium 

contamination increased. Kesterson Reservoir was thought to 

contain a multi-species assemblage of warm water fish before 

discharges of irrigation drainage waters began (Skorupa, 

1998a). Only mosquitofish (Gambusia affinis) persisted after 

selenium contamination was introduced (Saiki, 1986; Saiki 

and Lowe, 1987; Saiki and others, 1991; Skorupa, 1998a). 

Hamilton (1999) presented the hypothesis that selenium 

contamination of the Colorado River Basin in the 1890 to 

1910 period caused the decline of native endangered fish 

species [particularly razorback sucker (Xyrauchen texanus) 

and Colorado pikeminnow (Ptychocheilus lucius)] and it 

continues to inhibit their recovery. Hamilton (1999) concluded 

that reservoir construction and introduction of exotic species 

have undoubtedly contributed to the decline of endangered fish 

species in the Colorado River, but that selenium also must be 

included as an important contributing factor. Hamilton (1999) 

cited four lines of evidence linking selenium as a causative 

factor in simplifying this fish community:

selenium concentrations in the Colorado River (water, 

invertebrates and fish) are strongly elevated as a result 

of irrigation drainage discharges, which began in the 

1890s;

adverse effects on the endangered species and other 

species have been demonstrated at the level of contamination that occurs presently;

disappearance of large Colorado pikeminnow and 

razorback sucker was documented in 1910 to 1920 

before disturbances (such as dam building) other than 

substantial input of irrigation drainage; and

absence of young razorback suckers in historic collections suggest reproductive failure (lack of recruitment) 

was the cause of the population collapse.

Restoring native species in the Bay-Delta and its watershed 

is an important goal of the CALFED Ecosystem Restoration 

Plan (CALFED, 1998a, b, 1999a, b, c, d). The lessons from the 

Colorado River suggest that selenium cannot be ignored as an 

issue that can inhibit accomplishment of that goal. 

Fish eggs (unfertilized in a female or fertilized), developmental stages of fish (alevins or yolk-sac fry, larvae), and 

offspring of live-bearing fish species collected in the field 

also are valuable as unbiased measures of reproductive status 

•

•

•

•

(Lemly, 2002). A combination of field collected eggs and 

laboratory fertilization is productive in detecting and quantifying effects based on field diets. Sensitive life-stages such 

as larvae, fry, and juveniles can be studied. Holm and others 

(2003), Palace and others (2004), and Muscatello and Janz 

(2004) have studied effects in coal and uranium mining areas 

of Canada using this technique for rainbow trout (Oncorhynchus mykiss), brook trout (Salvelinus fontinalis), northern pike 

(Esox lucius), and white sucker (Catostomus commersoni). 

Hamilton and others (2005b) also used this technique with 

razorback sucker studies related to selenium contamination 

in the Colorado River basin. Effects studied were fertilization 

rate, time to hatch, percent hatchability, time to swim-up, and 

frequency of deformities. Care must be taken in interpretation 

of larval fish studies in that rapid growth is occurring that may 

lead to large variations in tissue selenium concentrations. 

Selenium concentrations in food and in tissues (tables 

13, 14, and 15) both have been employed to evaluate how the 

exposure of selenium experienced by an animal is linked to 

effects on reproduction or teratogenesis. Links to concentrations in food or in tissue both have the advantage that critical 

exposures can be determined from field data (unlike toxicity 

tests which require extrapolation from independent lab waters 

to field exposures). To determine effects in ecosystems like 

the Bay-Delta, selenium concentrations in invertebrates can 

be monitored to estimate concentrations in food and critical 

exposure in the predator itself can be determined from concentrations in liver, flesh, or eggs. Compiled studies reported for 

determining concentration guidelines (tables 13, 14, and 15) 

show the many considerations (selection of species, endpoint, 

life-stage, exposure mechanism, effect level, translation to dry 

weight) influence effect studies and their outcomes. 

Relating Selenium Concentrations in Food 

(Prey) to Effects in Predators

Fish 

Threshold and concern levels encompass a range of 

dietary selenium of 2 to 8 μg/g dry weight, with effects a 

certainty if the upper limit is exceeded (table 13). The range 

of concern has narrowed to 2 to 5 μg/g dry weight because of 

studies involving sensitive species, life-stages, and endpoints 

(table 13). Concentrations of selenium > 3 μg/g dry weight in 

the diet of fish result in deposition of elevated concentrations 

in developing eggs, particularly in the yolk (Lemly, 2002). 

Studies of effects in sensitive life stages and during increased 

stress (reduced temperatures) show a range in diet of 4.6 to 

5.2 μg/g dry weight (table 13). Terata in fry of recovering fish 

were recorded at diets of 2 to 5 μg/g dry weight at Belews Lake 

(Lemly, 1993b; 1997b). Dietary selenium concentrations of 5 

to 20 μg/g dry weight load eggs beyond teratogenic guidelines 

(Lemly, 1997a, 1998a, and 2002). Complete reproductive 

failure is associated with dietary concentration of 30 to 35 

μg/g dry weight (Skorupa, 1998b; Woock and others, 1987; 

Coyle and others, 1993). Extinctions of fish species occurred 
56 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

in Belews Lake, when selenium concentrations in invertebrates 

were in the concentration range of 15 to 57 μg/g dry weight. 

Concentrations in invertebrates in Kesterson National Wildlife 

Refuge were > 100 μg/g dry weight in the presence of seleniuminduced bird deformities and disappearance of most species 

of fish (Saiki and Lowe, 1987; Presser and Ohlendorf, 1987; 

Ohlendorf, 1989).

Birds 

Concern levels range from 2 to 7 μg/g dry weight in diet 

(table 15). The range of concern has narrowed to 2 to 5 μg/g 

dry because of studies involving sensitive species, life-stages, 

and endpoints (table 15). Lemly rates 2 to 4 μg/g dry weight as 

a diagnostic residue range that indicates ecosystem contamination sufficient to cause reproductive impairment. Heinz 

and others (1989) showed that selenium in eggs of mallards 

(experimental exposure) was closely related to hen’s dietary 

exposure to selenium (fed seleno-methionine). Average egg 

Table 13. Dietary selenium exposure guidelines for fish and selenium concentrations in the most abundant benthic prey organism in the 

North Bay (Suisun Bay and San Pablo Bay). 

[Focus is on sensitive endpoints and life stages; diet as selenomethionine; and parental exposure. Values are in dry weight with conversion from wet weight and 

percent moisture given, if applicable. The example of Kesterson Reservoir, California also applies to aquatic birds.]

Diet (μg/g 

selenium 

dry weight)

Approach or site Effects and Species Reference(s)

2−4 Synthesis Threshold ranges for reproductive failure Engberg and others, 1998

3 Synthesis Maximum allowable concentrations (protective of reproduction) Lemly, 2002a

2−4 Synthesis Diagnostic residues; ecosystem contamination sufficient to cause 

reproductive impairment

Lemly, 1998b

3– 7 Synthesis Range of concern; toxicological and reproductive effects a 

certainty if upper limit exceeded; impaired development and 

survival in larval fish. 

Engberg and others, 1998; USBR and 

others 2004; Hamilton and others, 

1996, 2004; Presser and others, 2004

3−8 Synthesis Reproductive impairment threshold (LOAEL)a

 via lethal larval 

exposure (salmon, bluegill, razorback sucker)

Skorupa, 1998b

2– 5.9 Belews Lake, 

North Carolina

Teratogenesis in fry of four recovering fish species [common carp 

(Cyprinus carpio), bluegill (Lepomis macrochirus), largemouth 

bass (Micropterus salmoides), mosquitofish (Gambusia affinis)]

Lemly, 1997b; 2002a; 2002b

4.6 Lab Mortality in razorback sucker (Xyrauchen texanus) larvae Hamilton, 2004; Hamilton and others, 

2002, 2005d

3.2– 5.3 Lab Reduced growth in chinook salmon (Oncorhynchus tshawytscha) 

swim-up larvae 

Hamilton and others, 1990

5.1 Lab 40% overwinter mortality (winter stress) in juvenile bluegill Lemly, 1993b

5−20 Synthesis Sufficient to load eggs beyond teratogenic threshold Lemly, 1997a, 1998a, 2002

30– 35 Synthesis Complete reproductive failure (100% effect level) in bluegill; 

parental exposure

Skorupa 1998a based on Coyle and others, 1993; Woock and others, 1987

15– 57 Belews Lake, 

North Carolina 

(1973– 84)

Massive poisoning of fish community (16 of 20 species disappeared; two species rendered sterile, but persisted as aging 

adults; one occasionally re-colonized as adults; and one unaffected; deformities in survivors; some recovery after selenium)

Cumbie and Van Horn, 1978; Lemly, 

1985; 1997b; 1998a

155– 290 Kesterson Reservoir (pond 2), 

California

Massive poisoning of fish and birds and deformities in coots, 

grebes, ducks, and stilts. 

Saiki and Lowe, 1987; Ohlendorf, 

1989; Presser and Ohlendorf, 1987.

4– 20 North Bay 

1985−86 and 

1995−96

Range in predominant bivalve as diet for Bay-Delta predators 

such as sturgeon, scoter, and scaup

White and others, 1987; 1988; 1989; 

Urquhart and Regalado, 1991; Johns 

and others, 1988; Linville and others, 

2002 

a

LOAEL = lowest observable adverse effect level.
 57

concentrations were 2.5 to 4.0 times dietary concentrations. 

Ohlendorf (1989) reported that bird eggs generally contain 1 

to 3 times the dietary selenium of breeding females. Skorupa 

and Ohlendorf (1991) concluded that, if assimilation of selenium in the wild is similar to seleno-methionine in the laboratory, then dietary selenium of 5 μg/g dry weight would yield 

15 μg/g dry weight in eggs. This level in eggs was the lowest 

mean concentration associated with embryo teratogenesis at 

Kesterson Reservoir. 

Heinz and others (1989) and Heinz (1996) cited 3.3 μg/g 

dry weight in diet as threshold for reproductive impairment 

from a synthesis of data. Ohlendorf (1989) concluded that 

hatchability of eggs is reduced when dietary concentrations are 

6 to 9 μg/g dry weight. In a compilation of data for mallards, 

4.87 μg/g dry weight in diet was associated with a 10 percent 

hatchability effect (Ohlendorf, 2003). The upper confidence 

level was 5.74 mg/g dry weight and lower confidence level 

was 3.56 mg/g dry weight (table 15). Stanley and others 

(1996) showed that 7.7 μg/g dry weight in diet was associated 

with a range of effects in mallards (reduced hatching success, 

reduced growth and weight in hatchlings, reduced number 

of surviving ducklings produced per female). Based on a 

synthesis of data, Stanley and others (1996), concluded that 

the threshold range in mallards for teratogenesis and mortality 

in ducklings (both less sensitive endpoints) was 7.7 to 8.8 μg/g 

dry weight. Adverse effects on body condition (thought to 

be an endpoint of intermediate sensitivity) of male American 

kestrels (Falco sparverius) occurred at 6 μg/g dry weight 

(Yamamoto and Santolo, 2000). Seleno-methionine in food 

at concentrations of 16 μg/g (as selenium) caused complete 

reproductive failure in mallards (Heinz and others, 1989). 

So, as with fish, concentrations of 2 to 6 μg/g dry 

weight in food encompass critical dietary levels for birds. As 

mentioned previously, a small range encompasses what level 

is nutritional and what level represents a certainty of effects 

if that limit is exceeded (that is, an upper limit essential for 

ensuring ecosystem health). Thus, field and laboratory studies 

all suggest that selenium concentrations typical of bivalves in 

Suisun Bay and San Pablo Bay (6 to 20 μg/g, table 13 and figs. 

13 through 15) are beyond guidelines of selenium concentrations in food that have a high degree of certainty of causing 

reproductive damage and teratogenesis in bivalve predators. 

Relating Selenium Concentrations in Tissue to 

Effects in Predators 

Fish 

A number of studies have related tissue concentrations of 

selenium in fish to reproductive or teratogenic effects (table 14). 

Reproduction has the advantage of being a sensitive endpoint to 

study. But, other environmental factors as well as selenium can 

affect reductions in reproductive success in nature. Short-term 

studies always suffer from the difficulties of separating causes 

of changes in reproductive success. Long-term studies can be 

more effective, in that environmentally caused effects on reproductive success tend to fluctuate, whereas contaminant-caused 

changes are more likely to be uni-directional with exposure to 

the contaminant. No long-term studies are available from the 

Bay-Delta, however. Teratogenesis is a less sensitive measure of 

selenium effects, but has the very attractive advantage of being 

a more selenium-specific outcome (many fewer factors cause 

teratogenesis than affect reproductive success). 

The range of concern for selenium concentrations in 

whole-body fish tissue has narrowed from 4 to 12 μg/g dry 

weight to 1.5 to 6 μg/g dry weight because of studies involving 

sensitive species, life-stages, and endpoints (table 14). This 

range of whole-body values translates to 1.2 to 4.6 μg/g dry 

weight in muscle using a translation factor of 0.83. Although 

a consensus has not been reached on this factor for selenium, 

the overall lowering of the concentration in flesh is due to 

the exclusion from the sample of organs such as liver which 

contain elevated concentrations of selenium compared to flesh. 

The range of concern in fish eggs is 5 to 10 μg/g dry weight 

and in liver 12 to 15 μg/g dry weight. Deformities increase 

rapidly in prevalence once selenium in fish eggs exceeds 10 

μg/g dry weight. Only a few fish species have been studied in 

detail, however, and species undoubtedly vary in tolerance. 

Although the universality of a critical tissue level is difficult 

to evaluate, the guidance values are in agreement with case 

studies from Belews Lake, North Carolina; Sweitzer Lake, 

Colorado; and lakes in Sweden (Skorupa, 1998a, b). In the 

Bay-Delta in 1989– 90, the mean selenium concentration 

found in 62 samples of white sturgeon muscle was 15 μg/g 

dry weight and in 42 samples of liver was 30 μg/g dry weight 

(table 12 and fig. 16). Both means are above the range of 

guidance concentrations at which reproductive effects and 

deformities in larvae and fry are likely to occur (table 14). 

Some concentrations (range 6 to 80 μg/g, dry weight liver; 2 

to 50 μg/g, dry weight muscle) in individual fish exceed tissue 

guidelines for producing extinction of fish species. However, 

the relation of reproduction and selenium-induced teratogenesis has never been studied in white sturgeon. A limited study 

of white sturgeon caught in San Pablo Bay and the Sacramento 

River showed selenium concentrations in ovaries and egg yolk 

components are above guidelines for effects (Kroll and Doroshov, 1991) (table 14). 

Birds 

Guidelines for selenium in tissue of birds are not too 

different from those in tissues of fish. The range of concern 

for selenium concentrations in egg tissue in birds is from 

3 to 6 μg/g dry weight (table 15). Heinz (1996) stated that 

the embryo is the avian life stage most sensitive to selenium 

poisoning. Skorupa (1998a, b, c) concluded that selenium 

concentrations in eggs are a good choice for a risk metric to 

determine avian embryonic exposure and response. Hatchability is more sensitive an endpoint than teratogenesis, but 

it is more ambiguous to interpret in the field because it is 

also sensitive to non-contaminant perturbation. Comparing 

Kesterson National Wildlife Refuge and a reference site, 
58 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Table 14. Tissue selenium guidelines for fish and selenium concentrations in tissues and eggs of white sturgeon from the North Bay 

(Suisun, San Pablo, Grizzly, and Honker Bays). 

[Focus is on sensitive endpoints and life stages; and parental exposure. Values are in dry weight with conversion from wet weight and percent moisture given, 

if applicable.]

Fish tissue (μg/g

selenium dry weight) Approach or site Effects, species, or North Bay fish Reference(s)

4– 12 (whole-body) Synthesis Range of concern; toxicological and reproductive effects a certainty if upper limit 

exceeded.

Engberg and others, 1998

4 (whole-body)

8 (muscle)

12 (liver)

10 (egg)

Synthesis Maximum allowable concentrations (protective of reproduction)Lemly, 2002a

5– 7 (whole-body) 

6– 8 (muscle) 

15– 20 (liver)

5– 10 (egg) 

8– 12 (larvae and fry) 

Synthesis Diagnostic residues for reproductive impairment (deformity or mortality of larvae/fry); 

applies to centrarchids, fathead minnows, 

salmonids, percichthyids

Lemly, 1998b

4– 6 (whole-body)

7– 13 (gonad/egg)

Synthesis Reproductive impairment (10% effect 

level) in sensitive species (perch, bluegill, 

salmon)

Skorupa, 1998b; Presser and others, 2004 

4– 6.5 (whole-body) Lab and synthesis Growth and survival (swim-up Chinook 

salmon larvae)

Hamilton and others., 1990; Hamilton, 2002 and 2003 

3.6– 8.7 (whole-body) Field Survival (razorback sucker larvae) Hamilton and others, 1996, 2005c, 

d; Hamilton 2002, 2004

5.85 (whole-body) Lab 40% overwinter mortality in juvenile bluegill 

(winter stress)

Lemly, 1993b

6 coldwater (whole-body)

9 warmwater (whole-body)

17 (ovary)

Synthesis Recommended toxicity guidelines (10% effect level)DeForest and others, 1999

10 (egg); 6– 17 (egg) Synthesis Rapid rise in deformities (terata) 

for centrarchids

Lemly, 1993b

12.5 (egg based on 52% moisture)

4.3 (muscle translation)

Field (eggs and milt)

Lab (rearing of fish)

Rapid rise in edema and deformities in 

rainbow trout (Oncorhynchus mykiss) 

and brook trout (Salvelinus fontinalis) fry 

(parental exposure)

Holm and others, 2003

18−22 (egg based on 52% 

moisture); 6.4−7.6 (muscle 

translation)

Field (eggs and milt)

Lab (rearing of fish)

Range of 15% effect level (edema, skeletal or 

craniofacial deformities) in rainbow trout 

swim-up fry

Holm and others, 2005

40– 125 (whole-body)

25– 200 (muscle)

20– 170 (egg)

Field 16 fish species extirpated; 10– 70% rates of 

teratogenesis

Cumbie and Van Horn, 1978; 

Lemly, 1985, 1997b, 1998a, 

2002 

30 (liver, average; n=42; range 

6– 80)

15 (flesh, average; n=62; range 

2−50)

North Bay

(1989– 90) 

white sturgeon (Acipenser transmontaus) Urquhart and Regalado, 1991

3– 29 (ovary); 5– 9 (plasma)

3– 90 (egg yolk components) 

North Bay

(no date)

white sturgeon Kroll and Doroshov, 1991
 59

Ohlendorf and others (1986) showed a strong correlation between embryonic selenium exposure and embryonic 

viability (hatchability). Hatching failure started increasing 

rapidly above 10 μg/g dry weight egg. Skorupa (1998a) 

suggested the critical exposure concentration causing reduced 

hatchability, for sensitive birds, is 6 to 7 μg/g dry weight in 

eggs. His conclusion is based on a variety of case studies 

around the world and a body of work in the Tulare Basin, California. Not all species are of equal sensitivity, of course. The 

threshold (3 percent effect level) of hatchability in a sensitive 

species of aquatic bird (stilt) is 6 μg/g dry weight (Skorupa, 

1998a,b; 1999). Ohlendorf (2003) calculated a 10 percent 

effect concentration of 12.5 μg/g dry weight in eggs from a 

compilation of data from laboratory studies of mallards. The 

upper confidence level was 16.5 μg/g dry weight and lower 

confidence level was 6.4 μg/g dry weight. Data from the coal 

mining areas of Canada concerning American dippers and 

spotted sandpipers show a 15 to 16 percent depression in egg 

viability at 5.1 and 8.2 μg/g dry weight egg selenium. 

Hepatic (liver) concentrations may be a less precise 

indicator of pathological conditions than are egg concentrations (table 15). Selenium concentrations quickly buildup or 

decline in the liver when birds are introduced to or removed 

from a selenium-contaminated diet (Heinz, 1996). Using selenium concentrations in adult females to predict reproductive 

impairment in birds is not as good as using selenium concentrations in eggs, because it is the selenium in the egg that 

actually harms the embryo. Livers of female mallards contain 

less selenium than livers of males because the egg is a route 

of excretion for females. The range of concern for selenium 

concentrations in liver tissue in birds is from 9.9 to 20 μg/g dry 

weight (table 15). Heinz (1996) suggested a hepatic threshold 

for reproductive impairment for laying females of 9.9 μg/g 

dry weight (converted from wet weight using 70 percent 

moisture), with a somewhat higher concentration range (12 

to 18) for non-breeding mallards. Skorupa (1998b) suggested 

a 30 μg/g dry weight hepatic threshold for juvenile and adult 

toxicity. 

Loss rates of selenium are another important consideration for migratory waterfowl or fish. Surf scoter, greater 

and lesser scaup, and white sturgeon may experience high 

selenium exposures during their residence time in the BayDelta, but selenium exposures may decline as the animals 

move to less contaminated breeding grounds. Many aspects 

of the reproductive effects specific to the Bay-Delta remain 

unstudied, especially in the species that are most threatened. 

Mean liver tissue concentrations of greater and lesser scaup 

and canvasbacks approach or exceed guidelines for producing 

adverse effects (fig. 17 and table 15). From 1986 to 1990, 

individual and mean annual average selenium concentrations 

in liver of surf scoter far exceed guidelines during their residence in Bay-Delta (table 15). Concentrations in liver of surf 

scoter in the North Bay are in the range of selenium concentrations in livers of ducks, coots, grebes, and stilts sampled 

at Kesterson Reservoir in 1983– 84 (table 15). Hoffman and 

others (1998) in a study of adult male surf scoter (n = 11) and 

greater scaup (n = 11) in Suisun Bay in 1989 found a mean of 

67 μg/g dry weight in greater scaup and 119 μg/g dry weight 

in surf scoter. Mercury was also measured in this study as it 

has been suggested that mercury contamination at selenium 

contaminated sites can be a confounding factor in interpreting 

tissue concentrations. Surf scoter populations also are rapidly 

declining in North America and they remain one of the least 

understood of the migratory waterfowl species (Henny and 

others, 1995). Selenium concentrations seem to rise extraordinarily in scoter in response to selenium exposures. Henny and 

others (1995) have suggested that caution should be exercised 

in linking tissue concentrations to effects in animals with 

strong bioaccumulative capabilities. For example, in other 

ecosystems bottle-nosed dolphins (Tursiops truncates), Risso’s 

dolphins (Grampus griseus), and cormorants seem to bioaccumulate high concentrations of selenium compared to other 

species. Mineral granules rich in selenium are common in 

these species (Nigro and Leonzio, 1996). It could be speculated that some species concentrate selenium in non-toxic 

forms, and, in such species, thresholds for adverse effects 

may be higher than in other species. This hypothesis remains 

untested, but points to the great need to better understand 

the links between internal selenium exposure and effects of 

selenium across a range of species. Those species exposed to 

elevated selenium concentrations as a result of their dietary 

choices should be of special interest in such studies. 

Because of the difficulties associated with studies of 

migratory fauna, no current data are available to help prove 

that white sturgeon, surf scoter, or greater and lesser scaup are 

suffering from selenium toxicity or impaired reproduction in 

the Bay-Delta. However, data both from food exposures and 

tissue residues strongly indicate that these animals are at or 

near significant risk. Despite the complexities, planning an 

effective restoration of the Bay-Delta ecosystem depends on 

studies of the effects of selenium on reproduction, population 

biology, and life histories of migratory waterfowl and anadromous fish that are important components of the Bay-Delta 

ecosystem.

Selenium Hazard Rating

Lemly (1995, 1996a, b) defined hazard as a toxic threat to 

birds and fish that can be characterized by selenium concentrations in the environment (water, sediment, diet) and exposure 

of fish and birds to that hazard (measured by selenium concentrations in eggs or tissues). This systematic approach can be 

applied to data compiled for the Bay-Delta from 1986 to 1996. 

Lemly (1995, 1996a) defined five categories of hazard:

High hazard: Imminent, persistent threat sufficient to 

cause complete reproductive failure in most species of 

birds and fish. 

Moderate hazard: Persistent toxic threat sufficient 

to substantially impair, but not eliminate reproductive 

success. Some species will be severely affected; others 

will not be affected.

•

•
60 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Table 15. Tissue and dietary selenium guidelines for birds, selenium concentrations in ducks, grebes, and stilts from Kesterson 

National Wildlife Refuge, and selenium concentrations in surf scoter, greater scaup, and lesser scaup from the North Bay (Suisun and 

San Pablo Bays).

[Focus is on sensitive endpoints and life stages; diet as selenomethionine; and parental exposure. In general, reproductive endpoints are more sensitive than 

toxicity and mortality. Within reproductive endpoints, hatchability is the more sensitive endpoint in comparison to deformity. Values are in dry weight with 

percent moisture given, if applicable.] 

Diet or avian tissue 

(μg/g selenium dry weight) Approach or 

site

Effects, species, or North Bay birds Reference(s)

3−7 (diet); 3−8 (egg) Synthesis Range of concern; toxicological and reproductive 

effects a certainty if upper limit exceeded.

Engberg and others, 1998

3−7 (diet); 6−10 (egg) Synthesis Reproductive impairment threshold (populationbased for diet; individual based for eggs)USBR and others, 2004; 

Presser and others, 2004

3 (diet); 10 (liver); 7 (egg) Synthesis Maximum allowable concentrations (protective 

of reproduction)

Lemly, 2002a

2−4 (diet); 20−30 (liver);

6−15 (egg)

Synthesis Diagnostic residue for reproductive impairment 

(deformity or mortality of embryos)

Lemly, 1998b

3.3 (diet based on 10% moisture); 

9.9 (liver based on 70% moisture); 

13.5 (egg based on 78% moisture)

Synthesis Thresholds for reproductive impairment; liver of 

egg-laying mallard (Anas platyrhynchos) female associated with reproductive impairment

Heinz and others, 1989; Heinz, 

1996

12– 18 (liver based on 70% moisture)Synthesis Threshold for reproductive impairment for nonbreeding mallards Heinz and others, 1989; Heinz, 

1996

4.87/3.56−5.74 (diet); 

12.5/6.4−16.5 (egg) 

Lab and synthesisHatchability in mallards (10% effect level/ 95% 

confidence boundaries)

Ohlendorf, 2003

3.85−7.7 (diet based on 10% moisture)Lab Reduced hatching success in mallards (33% 

at 7.7 μg/g); reduced growth and weight in 

hatchlings

Stanley and others, 1996

7.7 (diet based on 10% moisture) Lab Reduction in number of surviving mallard ducklings produced per female Stanley and others, 1996

8.8 (diet based on 10% moisture) Lab Reduction (17%) in survival of mallard ducklings; mean decrease (43%) in number of 

6-day-old ducklings

Heinz and others, 1989

6 (diet) Lab Adverse effect on body condition of male American kestrels (Falco sparverius)Yamamoto and Santolo, 2000

7.7−8.8 (diet based on 10% moisture)Synthesis Dietary threshold of teratogenic effects in mallards; above upper threshold, rate of deformity 

rises sharply

Stanley and others, 1996

7.7−8.8 (diet based on 10% moisture)Synthesis Dietary threshold of mallard duckling mortality 

(parental exposure)

Stanley and others, 1996

6 (egg) Synthesis of 

field data

Threshold (3% effect level) of hatchability in sensitive species (stilts, Himantopus mexicanus) Skorupa, 1998a, b; Skorupa, 

1999

8.2 (egg based on 73% 

moisture)

Field 16% depression in egg viability of spotted sandpiper (Actitus macularia)Harding and others, 2005

5.1 (egg based on 78.4% moisture) Field 15% depression in egg viability of American dipper (Cinclus mexicanus)Harding and others, 2005

9.0 (mallard egg); 14.5 (stilt egg) Synthesis Impaired clutch viability (8.2% effects level for 

mallard; 11.8% effect level for stilt)

Lam and others, 2005

30 (liver) Field Approximate threshold for juvenile/adult toxicity Skorupa, 1998b

2−180 (egg)

3−360 (liver)

Kesterson 

Reservoir

1983–1984

Massive deformities and toxicity in aquatic birds Ohlendorf and others, 1986a; b; 

Presser and Ohlendorf, 1987; 

Skorupa, 1998a
 61

Low hazard: Periodic or ephemeral toxic threat that 

could marginally affect reproductive success of some 

sensitive species, but most species will be unaffected.

Minimal hazard: No toxic threat identified but 

concentrations of selenium are slightly elevated as 

compared to uncontaminated reference sites.

No hazard: Selenium concentrations are not elevated in 

any ecosystem component compared to reference sites. 

A scoring method was developed in which points were 

assigned to define selenium hazard in specific systems: no 

hazard = 5; minimal hazard = 6 to 8; low hazard = 9 to 11; 

moderate hazard = 12 to 15; high hazard = 16 to 25 (Lemly, 

1995, 1996a). The scores represented summation for the 

lines of evidence (sampling of water, sediment, invertebrates, fish eggs, and bird eggs). The aggregate rather than 

the average was chosen as the best representation of hazard 

because any component (or habitat route), alone, can cause 

toxicity. 

Defined here are four levels of certainty associated with a 

statement of hazard:

•

•

•

The greatest certainty occurs if waterborne, particulate, 

bioaccumulation, and predator lines of evidence are 

accompanied by direct observations of teratogenesis or 

reproductive impairment.

A strong level of certainty is possible if data are available from all links in the chain of processes, but no 

observations of reproductive impairment are available.

 Moderate certainty results if more than one line of 

evidence from a chain of evidence is available. 

Low certainty results if the hazard evaluation is based 

on one line of evidence. 

Table 16 shows selenium concentrations and the results 

of hazard analysis from several ecosystems (Lemly, 1985, 

1995, 1996a, 1997c; Kroll and Doroshov, 1991) compared to 

conditions in the Bay-Delta using data collected from 1986 to 

1996. These hazard ratings from different ecosystems illustrate the diversity of conditions that can occur in ecosystems 

receiving selenium discharges. Most notably, high dissolved 

selenium concentrations in some rivers (such as the LaPlata, 

Mancos, Animas Rivers in Colorado, New Mexico, and Utah, 

•

•

•

•

Table 15. Tissue and dietary selenium guidelines for birds, selenium concentrations in ducks, grebes, and stilts from Kesterson 

National Wildlife Refuge, and selenium concentrations in surf scoter, greater scaup, and lesser scaup from the North Bay (Suisun and 

San Pablo Bays)—Continued.

Diet or avian tissue 

(μg/g selenium dry weight) Approach Effects, species, or North Bay birds Reference(s)

Avg/range (liver n=71; grand avg=145)

80/37−113 (liver)

84/13−167 (liver)

193/134−244 (liver)

240/137−368 (liver)

127/78−190 (liver)

20.9/3.6–58.6 (flesh n=81)

Suisun Bay 

(1986)

(1987)

(1988)

(1989)

(1990) 

surf scoter (Melanitta perspicillata), greater 

scaup (Aythya marilla), and lesser scaup 

(Aythya affinis)

White and others, 1987; 1988; 

1989; Urquhart and Regalado, 1991

Avg/range (liver n=62; grand avg=123)

74/ 4−148 (liver)

113/65−196 (liver)

135/62−176 (liver)

162/81−217 (liver)

130/84−192 (liver)

20.5/4.5–50 (flesh n=64)

San Pablo Bay

(1986)

(1987)

(1988)

(1989)

(1990)

surf scoter White and others, 1987; 1988; 

1989; Urquhart and Regalado, 1991

Avg/range (liver n=39; grand avg=41)

−/14−86 (liver)

−/8−48 (liver)

85/35−114 (liver)

12.8/2.6–34.6 (flesh n=38)

Suisun Bay 

(1986)

(1987)

(1988)

greater and lesser scaup White and others, 1987; 1988; 

1989

Avg/range (liver n=31; grand avg=32)

−/12−23 (liver)

−/11−47 (liver)

46/26−87 (liver)

12.9/2.5–35.9 (flesh n=38)

San Pablo Bay

(1986)

(1987)

(1988)

greater and lesser scaup White and others, 1987; 1988; 

1989

67 (geometric mean, liver)

119 (geometric mean, liver)

41 (geometric mean, liver)

Suisun Bay

(1989)

greater scaup

surf scoter 

ruddy duck (Oxyura jamaicensis)

Hoffman and others, 1998
62 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

respectively) can be accompanied by low concentrations in 

sediments. Invertebrates are moderately contaminated in some 

of those systems and not in others. Nevertheless, moderate to 

high contamination was noted in fish eggs. Obviously, selenium 

cycling, selenium speciation, as well as form and concentration in suspension are not sufficiently known from many 

of the surveys to identify the factors critical to determining 

selenium hazard. In all the reservoirs and pond environments 

surveyed by Lemly (1995, 1996a, b, 1997a, b, c), elevated 

dissolved selenium concentrations are accompanied by 

selenium contamination in sediments, substantial contamination of invertebrates, and a high hazard to fish and bird eggs. 

Lemly (1997c) suggested that long retention times in reservoirs contributed to the contamination of all media and a high 

hazard. As residence times increased, the potential increased 

for selenium to be bioaccumulated, to be deposited in and 

recycled from sediment, and to adversely affect fish and birds 

Lemly (1997c). For hazard evaluations, Lemly (1995, 1996a) 

suggested that sampled nesting birds should be those feeding 

locally, and that coots, grebes and dabbling ducks were 

good choices. Suggested choices of fish for hazard evaluation 

included minnows, sunfish (centrarchids), suckers, catfish, and 

trout. For the Bay-Delta, however, these species are not the most 

sensitive because their exposure to selenium is less than that of 

species that feed on bivalves. In the Bay-Delta, the best choices 

are benthivores based on feeding habits of species at risk. 

Suisun Bay seems to be typical of a system with high 

residence times subjected to selenium contamination. A 

ranking of Suisun Bay under the conditions of 1986– 96 

is possible using the protocol of Lemly. The results of the 

Table 16. Selenium hazard ratings for various U.S. sites and for the Bay-Delta.

[Selenium concentrations for each media (water, sediment, invertebrates, fish eggs, and bird eggs) are stated within each cell (μg/L for water and μg/g dry 

weight for solids). Hazard ratings for each set of concentrations are stated within each cell (as defined by Lemly, 1995 and 1996b). The individual scores and 

total score are compared to listed evaluation criteria to determine a hazard rating (high, moderate, low, minimal, or none identified) (Lemly, 1995). For the 

Bay-Delta, bird egg concentrations are converted from bird liver concentrations. Data sources are Lemly, 1995; 1996a, b; 1997a, b, c for western U.S. sites and 

this report. 

Site or hazard rating Water (μg/L)/

Hazard

Sediment (μg/g)/ 

Hazard

Invertebrates 

(μg/g)/ Hazard

Fish Eggs (μg/g)/ 

Hazard

Bird Eggs (μg/g)/ 

Hazard

Score/ Hazard

Ouray Refuge (Leota), 

Utah

<1– 3/low 0.7– 1/none 1– 3/minimal 2– 4/minimal 2– 7/low 11/Low

Ouray Refuge (Ponds), 

Utah

9– 93/high 7– 41/high 12– 72/high 75– 120/high 12– 120/high 25/high

Ouray Refuge (Sheppard), 

Utah

3– 4/moderate 0.6– 3/low 3– 33/high 8– 27/high 1– 17/moderate 21/high

Belews Lake North Carolina (pre-1986)

5– 20/high 4– 12/high 15– 57/high 40– 159/high – 20/high

Belews Lake, North Carolina (1996)<1/none 1– 4/moderate 2– 5/moderate 5– 20/moderate 2– 5/minimal 15/moderate

Animas River, Colorado 

and New Mexico

1– 20/high 0.1– 2.3/low 1.8– 2.9/minimal 3– 16/moderate – 14/moderate

 La Plata River, Colorado 

and New Mexico

1– 12/high 0.1– 0.95/none 1.1– 2.2/minimal 2.6– 39.6/high – 13/moderate

Mancos River, Colorado 

and New Mexico

2– 29/high 0.2– 0.8/none 1.8– 11/high 5.6– 46/high – 16/high

Ridges Basin Reservoir, 

Colorado/New Mexico

1– 10/ high 1– 8/high 5– 75/high 5– 100/high 5– 100/high 25/high

Southern Ute Reservoir, 

Colorado/New Mexico

1– 6/high 1– 5/high 5– 50/high 5– 80/high 5– 80/high 25/high

Bay-Delta, Suisun Bay, 

1990– 1996

<1/none 0.5– 2 (8)/low to 

moderate

4– 20/high 3– 29a/high moderate to high 17/high

None <1 <1 <2 <3 <3 5

Minimal 1– 2 1– 2 2– 3 3– 5 3– 5 6– 8

Low 2– 3 2– 3 3– 4 5– 10 5– 12 9– 11

Moderate 3– 5 3– 4 4– 5 10– 20 12– 20 12– 15

High >5 >4 >5 >20 >20 16– 25

a

Kroll and Doroshov (1991).
 63

here for a hypothetical location in the North Bay at the head of 

the estuary where all sources combine (all loads contribute to 

a freshwater endmember near the site of input) with instantaneous mixing. A second calculation gives selenium concentrations at Carquinez Strait, a point midway in the North Bay at a 

salinity of 17.5 psu, (practical salinity units).

Four major sources make up a composite freshwater 

endmember load: agricultural drainage from direct discharge 

to the Bay-Delta, effluents from the North Bay refineries, San 

Joaquin River inflows, and Sacramento River inflows. The 

composite input volume in the Bay-Delta is most affected by 

inflows from the Sacramento River and San Joaquin River 

(figs. 8 and 9). Each of the loads and volumes is constrained 

here to a given set of conditions to construct feasible scenarios 

for selenium loads to the Bay-Delta. 

Forecasts from the model are presented here by season, 

where a season is defined as six months of predominantly 

high river inflows (high flow season, December through 

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

flow season, June through November). Seasonal presentation 

(high and low flow seasons) is the least complicated approach 

to account for riverine influences which are very different 

in different seasons. Flows also are variable on time scales 

shorter than season. To illustrate the effects of these shorter 

time scale changes, (and to further illustrate the methodology), 

several forecasts are additonally determined from monthly 

loads.

Riverine influences also depend on water-year type. In 

combination with flow seasons, forecasts also are presented 

here based on climatic regime. Two regimes are illustrated: a 

critically dry year and a wet year. 

A wide range of agricultural selenium input loads are 

possible, depending on which management strategies are 

chosen, as described earlier (also see appendices A and 

B). Several factors influence agricultural loads of selenium 

discharged directly to Bay-Delta:

choice of drainage conveyance, either the San Joaquin 

River or a San Luis Drain extension;

demand by agriculture for drainage or a selenium load 

targeted by considering environmental safeguards; 

hydraulic discharge in the San Joaquin River or a San 

Luis Drain extension;

selenium concentration in the San Joaquin River or a 

San Luis Drain extension; and

proportion of the conveyance discharge that reaches the 

Bay-Delta.

Potential ranges of annual loads were derived earlier 

(tables 6 and 7) assuming selenium discharge is continuous. 

Load scenarios are presented here as discharged load per six 

months (one-half the annual load under a constant rate of 

loading). Forecasts are constrained to selected scenarios within 

the three general ranges of San Joaquin Valley loads described 

earlier (tables 8 and 9).

•

•

•

•

•

aquatic hazard assessment and a hazard rating for the BayDelta (table 16) are: 

Total score = 17

Hazard rating = High

Direct observation of reproductive processes in the most 

sensitive predators is not possible in the Bay-Delta because 

the most contaminated species are migratory. This lack of data 

adds some uncertainty to the hazard rating. Nevertheless, the 

certainty, as defined previously, is high. Selenium data were 

available from water, particulate material, bioaccumulation 

in invertebrates, and predator bioaccumulation (in the latter 

case, more than one species). Furthermore, toxicity threshold/

extinction information, in general, can be related to the selenium data for both birds and fish. So the high hazard rating 

can be made with relatively high certainty. It is possible that 

the hazard level declined after 1998, when refinery discharges 

declined. Studies underway may help determine further sitespecific ratings. (CALFED Bay-Delta Program 1999b, c, and 

d; and for example, Lucas and Stewart, 2005).

Scenarios and Forecasts

A major goal of this report is to present a systematic 

approach, the Bay-Delta selenium model (fig. 2), for forecasting 

the effects of selenium on predators. Several feasible future 

conditions (scenarios) of selenium loading are used to develop 

forecasts. The choices of conditions are not nearly as important 

as the process of evaluating those choices. However, the forecasts that result from chosen scenarios provide guidance to help 

narrow the range of possible management alternatives. 

The approach presented here can be used with any 

set of explicitly stated conditions, including assumed load 

scenarios. From each set of assumed conditions, progressive 

forecasts show:

loads, volumes, and waterborne concentrations;

speciation and transformation to particulate material; 

bioaccumulation in generic bivalves (prey); and

tissue concentrations of predators.

Scenarios of Composite Loads and Volumes to 

the Bay-Delta 

As noted previously, the general protocol for linking 

selenium load and selenium concentration under assigned 

hydraulic conditions and time duration is:

[composite freshwater endmember concentration] =

[composite source load] ÷ [composite source volume]

Using volumes and source concentrations, composite 

freshwater endmember selenium concentrations are calculated 

•

•

•

•
64 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Targeted loads conveyed by the San Joaquin River 

(3,400 or 3,590 lbs selenium discharged in six months). 

The values used here for targeted loads are toward the 

maximum projected by the TMDL/TMML process (6,547 

lbs per year or 3,274 lbs in six months). This load is 

assumed delivered through the San Joaquin River with 

full conveyance to the Bay-Delta (no recycling of the San 

Joaquin River). A San Joaquin River inflow of 0.5 million 

acre-ft is assumed during the low flow season of both wet 

and critically dry years. During the high flow season of a 

wet year, 1.1 million acre-ft is assumed allowed to enter 

the Bay-Delta. 

San Joaquin River used, in effect, as a drain (range of 

381 to 15,300 lbs in six months). If the TMDL/TMML 

process resulted in management of a constant concentration of selenium in the San Joaquin River year-around, a 

different load would result than if management is based on 

load targets. The selenium load delivered to the Bay also 

would depend on how much of the load is passed through 

the Delta. Little is presently known about water movement 

within and through the Delta; a value for transport (percentage of San Joaquin River that reaches the Bay-Delta) 

is necessary, but it should be recognized as hypothetical. 

Effects of selenium on the San Joaquin River ecosystem 

are not included in this analysis. Examples of selenium 

loads that could be transported through the San Joaquin 

River are given below (also see examples in table 9). 

Load managed at the USEPA selenium criterion of 5 μg/L in a wet year. A constant selenium 

concentration of 5.0 μg/L is maintained in the San 

Joaquin River, with an annual river discharge at 

Vernalis of 3 million acre-ft. If it is assumed that 

75 percent of flow and load reaches the Bay-Delta, 

then the annual selenium load would be 30,600 lbs 

(15,300 lbs selenium in six months).

Load managed at the USFWS recommended selenium criterion of 2 μg/L in a wet year. In this case, 

an annual load of 12,240 lbs of selenium is released 

to the Bay-Delta if a constant selenium concentration 

of 2.0 μg/L is maintained in the San Joaquin River; 

annual flow is 3 million acre-ft; and 75 percent of it 

passes through the Delta (6,120 lbs in six months).

Dry years. If annual discharge from the San Joaquin 

River is 1.1 million acre-ft and 25 percent reaches 

the Bay-Delta, as might be expected in below normal 

precipitation, then the annual selenium load would 

be 9,262 lbs from the San Joaquin River at a 5 μg/L 

selenium criterion; and 3,705 lbs at a 2 μg/L selenium 

criterion (1,852 or 4,631 lbs selenium in six months).

Restored ecosystem. A constant selenium concentration of 0.5 μg/L is maintained in the San Joaquin 

River, with 75 percent of the annual San Joaquin 

River flow and load delivered to the Bay-Delta during 

1.

2.

a.

b.

c.

d.

the high flow season; and 25 percent allowed to enter 

in the low flow season. A concentration of 0.5 μg/L is 

lower than both the USEPA criterion (5 μg/L) and the 

USFWS recommended criterion (2 μg/L). In this case, 

an annual load of 4,080 lbs (3,060 lbs during the high 

flow season; 1,020 lbs during the low flow season) 

is conveyed by the San Joaquin River assuming an 

annual flow of 3 million acre-ft in a wet year. In a dry 

year, an annual load of 1,496 lbs (1,115 lbs during 

the high flow season; 381 lbs during the low flow 

season) is conveyed by the San Joaquin River assuming an annual flow of 1.1 million acre-ft. This type of 

forecast typifies a scenario that considers restoration 

of the San Joaquin River during proposed increases in 

flow of the river to aid fish passage.

Demand-driven loads with management of drainage 

quantity and quality in an extension of the San Luis 

Drain. Assumptions used here are (a) demand for drainage 

is met by construction of a San Luis Drain extension which 

discharges directly to the Bay-Delta; (b) drainage discharge is either 0.05 million acre-ft each six months (half 

design flow capacity of existing San Luis Drain, 150 ft3/s) 

or 0.11 million acre-ft each six months (full design flow 

capacity of San Luis Drain, 300 ft3/s); and (c) selenium 

concentrations will vary with the success of treatment. 

Specific forecasts are:

Demand-driven loads with priority given to management of quality and quantity (6,800 or 18,700 

lbs selenium discharged in six months). Two load 

scenarios are calculated for this condition. One scenario is calculated assuming a condition of 150 ft3/s 

in the San Luis Drain (0.05 million acre-ft of drainage or half capacity) with a selenium concentration 

of 50 μg/L. Under this condition, 6,800 lbs selenium 

is discharged in six months. In a second scenario, 

62.5 μg/L drainage is assumed discharged at full 

capacity (0.11 million acre-ft); the load discharged 

is 18,700 lbs selenium per six months. These two 

loads bracket the lowest end of the range of cumulative potential loads from the different subareas (or 

combinations of subareas) of the San Joaquin Valley 

(tables 5 through 7). 

Demand-driven loads with low priority given 

to management of quality and quantity (44,880 

and 89,760 lbs selenium in six months). Two load 

scenarios are calculated for this condition. Minimal 

treatment could result in direct (unblended) discharge of existing shallow ground water and no control on the quantity of discharge. Thus, this forecast 

assumes a 150 μg/L selenium concentration in a San 

Luis Drain extension with the drain running at full 

capacity (0.11 million acre-ft in six months) (44,880 

lbs selenium discharged in six months). The second 

case assumes 300 μg/L and 0.11 million acre-ft of dis3.

a.

b.
 65

charge in six months (89,760 lbs selenium discharged 

in six months), assuming little regional management 

(as described earlier). These two loads bracket the 

high end of the range of potential loads from a valleywide system draining most potential problem lands, 

with minimal management (tables 6 through 8). 

 Calculation of total selenium loads to the Bay-Delta 

and resulting selenium concentrations consider climate, oil 

refinery loads, San Joaquin River recycling, and Sacramento 

River condition as follows:

As noted previously, the magnitude and fate of selenium 

loads are highly dependent on climatic regime. Climate 

regimes are derived from existing data:

Critically dry year. Eight critically dry years in the 

Bay-Delta watershed occurred between 1978 and 

1998, so this is an important factor to consider. Data 

for this condition are from 1994.

Wet year. Data from 1997, a wet year as designated 

by the Department of Water Resources, are used.

In all scenarios, oil refineries are assumed to meet the 1998 

permit requirements of approximately 1,360 lbs selenium 

per year or 680 lbs per six months. Oil refinery loads measured in 1999 totaled 1,115 lbs selenium (table 10), similar 

to the assumed amount. 

In demand-driven load scenarios during critically dry 

years, selenium loads from the San Joaquin River are 

assumed to be low. These scenarios implicitly assume 

that use of a San Luis Drain extension could relieve the 

pressure for discharge of drainage to the San Joaquin 

River. These scenarios also assume continued substantial 

recycling of the San Joaquin River, so only 500 to 1,000 

acre-ft of San Joaquin River flow reaches the Bay-Delta 

in critically dry years during high or low flow seasons. If 

selenium concentrations of 1 or 2 μg/L are assumed to be 

maintained in the river, then the San Joaquin River delivers 

3 to 5 lbs selenium in six months. 

During wet years in periods of high flow, less recycling of 

the San Joaquin River occurs, with substantially more San 

Joaquin River throughput to the Bay-Delta. To accurately 

reflect this condition in demand-driven load forecasts, 2 

million acre-ft of San Joaquin River flow is assumed to 

reach the Bay-Delta. A concentration of 1 μg/L is assigned 

for this inflow (5,440 lbs selenium in six months).

Loads from the Sacramento River are calculated using 

measured hydraulic discharge and assuming a selenium 

concentration of 0.04 μg/L.

A summary of feasible future conditions and selenium loads for the Bay-Delta is shown in table 17. Specific 

load scenarios employed in modeling bioaccumulation and 

predicting effects on predators are highlighted in summary 

tables that follow (tables 18 through 22). The compilation is 

not exhaustive in its coverage of all conditions; but the choices 

1.

a.

b.

2.

3.

4.

5.

bracket the wide range of loads possible in the future from 

western San Joaquin Valley acreage that is in need of drainage 

(tables 8 and 9, and appendix B).

Comparison of forecasted selenium 

concentrations to observed conditions prior to 

refinery cleanup

To initially test the validity of the approach, an average 

composite freshwater endmember selenium concentration is 

calculated for conditions resembling those that were documented in the North Bay prior to refinery cleanup (table 18). 

Forecasts are for the high flow season during a wet year; and 

for the low flow season during both a wet and critically dry 

year, similar to conditions selected for projections of future 

conditions (see tables 19 through 21). Sacramento River 

inflow for six months of high flow was taken from 1997 data 

(17 million acre-ft). Sacramento River inflows during six 

months of low flow in 1997 and 1994, respectively, provide 

the two other cases (2.3 and 1.62 million acre-ft). San Joaquin 

River inflow was 3 million acre-ft for high flow in 1997 and 

0.1 million acre-ft in the latter two low-flow cases. Refinery 

discharges (2,040 lbs in six months) are in the range measured 

before refinery cleanup (average 1986– 92; 2,505 lbs per six 

months) (table 10) (San Francisco Bay Board, 1992a, b, 1993). 

No San Luis Drain discharge is included for these forecasts.

The forecasted average composite freshwater endmember 

concentration of selenium during six months of high flow in 

a wet year is 0.22 μg/L (table 18). The forecasted concentration is comparable to a selenium concentration of 0.16 μg/L 

determined after high flows in April 1986 (Cutter, 1989). The 

contrasting influences of the San Joaquin River and the Sacramento River are interesting to note in this example. Selenium 

concentrations in the San Joaquin River are much higher than 

concentrations in the Sacramento River (1 μg/L and 0.04 μg/L, 

respectively). The load of selenium from the San Joaquin 

River also is substantial compared with the load from the 

Sacramento River (8,160 lbs compared with 1,850 lbs per six 

months, respectively). Concentrations of selenium are as low 

as 0.22 μg/L at the head of the estuary because of dilution by 

the high volume of lower-selenium water from the Sacramento 

River. A selenium concentration of 0.11 μg/L is projected at 

the selected seaward location of Carquinez Strait. 

The concentration of selenium at 17.5 psu (approximate 

location of Carquinez Strait) during the six months of low 

flow in a wet year is projected as 0.20 μg/L; in a critically 

dry year it is 0.27 μg/L (table 18). The composite freshwater 

endmember concentrations for these two forecasts are 0.39 

and 0.53 μg/L, respectively. Selenium concentrations are 

highest during periods of low flows, because dilution from 

the Sacramento River is reduced in years of low rainfall. The 

forecasted concentrations are remarkably close to the range of 

values found within the estuary by Cutter (1989) (0.15 to 0.44 

μg/L selenium). The correspondence of these calculations with 

observed data confirms that the basic foundation of the model 

and forecasts are reasonable. 
66 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Table 17. Selenium loads employed in forecasts of selenium effects. 

[Loads are calculated per six month. Annual loads would be two times higher if selenium discharge is continuous (at a constant rate). Agricultural inputs fall into three groups depending on management strategy: supply-driven management (3,000 to 8,000 lbs selenium per year); 

demand-driven load with management of land and/or drainage quality (15,000 to 45,000 lbs selenium per year); and demand-driven load with 

minimum management (45,000 to 128,000 lbs selenium per year).]

Inputs to Bay-Delta 

Wet year/high flow 

(lbs selenium 

per six months)

Wet year/low flow

(lbs selenium

per six months)

Critically dry/low flow 

(lbs selenium

per six months)

San Luis Drain extension

50 μg/L, 150 ft3

/s, 0.05 MAF/season

6,800 6,800 6,800

San Luis Drain extension

62.5 μg/L, 300 ft3

/s, 0.11 MAF/season

18,700 18,700 18,700

San Luis Drain extension

150 μg/L, 300 ft3/s, 0.11 MAF/season

44,880 44,880 44,880

San Luis Drain extension

300 μg/L, 300 ft3

/s, 0.11 MAF/season

89,760 89,760 89,760

San Joaquin River (targeted load) 3,400– 3,600 3,400– 3,600 3,400– 3,600

San Joaquin River (maximum recycling) 3– 5 3– 5 3– 5

Oil Refineries 680 680 680 

Sacramento River 141 250 1,850 

Table 18. Calculation of selenium concentrations for a composite freshwater endmember at the head of the estuary and at Carquinez Strait 

(a point midway in the North Bay at a salinity of 17.5 practical salinity units) under conditions simulating those prior to refinery cleanup.

[Inputs are from the Sacramento River, San Joaquin River, and oil refineries, with no input from a proposed San Luis Drain extension. Forecasts contrast wet 

and dry years; and high and low seasons. Table is a representation of a spreadsheet. Carqinez Strait location at 17.5 psu]

Conditions prior to refinery cleanup

Volume

(million 

acre-ft)

Volume

(billion liters)

Selenium

Concentration

(μg/L)

Load 

(billion μg)

Load (lbs per six 

months)

Freshwater

endmember (μg/L)

Carquinez Strait 

(μg/L)

Wet year (1997 data), high flow season (six months, December through May)

Sacramento River 17 20,961 0.04 838 1,850

San Joaquin River 3 3,699 1 3,699 8,160

San Luis Drain 0 0 0 0 0

Refineries 0.005 6 150 925 2,040

0.22 0.11

Wet year (1997 data), low flow season (six months, June through November)

Sacramento River 2.3 2,836 0.04 113 250

San Joaquin River 0.1 123 1 123 272

San Luis Drain 0 0 0 0 0

Refineries 0.005 6 150 925 2,040

0.39 0.20

Critically dry year (1994 data), low flow season (six months, June through November)

Sacramento River 1.62 1,998 0.04 80 176

San Joaquin River 0.1 123 1 123 272

San Luis Drain 0 0 0 0 0

Refineries 0.005 6 150 925 2,040

0.53 0.27
 67

Table 19. Forecasts of selenium concentrations for a composite freshwater endmember at the head of the estuary and at 

Carquinez Strait (a point midway in the North Bay at a salinity of 17.5 practical salinity units) for a wet year in a high flow 

season under load scenarios for conveyance of agricultural drainage either through a San Luis Drain extension or the San 

Joaquin River.

[Inputs from the Sacramento River and oil refineries also are considered. Refinery cleanup is assumed in all scenarios. Scenarios using a San Luis 

Drain extension for conveyance assume a 2 million acre-ft inflow reaches the Bay-Delta. The scenario using the San Joaquin River for conveyance 

assumes no San Luis Drain inflow and a 1.1 million acre-ft inflow reaches the Bay-Delta. This table is a representation of a spreadsheet.]

Wet year (1997 data); high flow season (six months, December through May); refinery cleanup

Volume

(million acre-ft)

Volume

(billion liters)

Selenium

Concentration 

(μg/L)

Load 

(billion μg)

Load

(lbs per six 

months)

Freshwater

endmember

(μg/L)

Carquinez

Strait 

(μg/L) 

Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; refinery cleanup

Sacramento River 17 20,961 0.04 838 1,850

San Joaquin River 2 2,466 1 2,466 5,440

San Luis Drain 0.05 62 50 3,083 6,800

Refineries 0.005 6 50 308 680

0.28 0.14

Load scenario: San Luis Drain extension at 300 ft3

/s and 62.5 μg/L for a load of 18,700 lbs per six months; refinery cleanup

Sacramento River 17 20,961 0.04 838 1,850

San Joaquin River 2 2,466 1 2,466 5,440

San Luis Drain 0.11 136 62.5 8,477 18,700

Refineries 0.005 6 50 308 680

0.51 0.26

Load scenario: San Luis Drain extension at 300 ft3

/s and 150 μg/L for a load of 44,880 lbs per six months; refinery cleanup

Sacramento River 17 20,961 0.04 838 1,850

San Joaquin River 2 2,466 1 2,466 5,440

San Luis Drain 0.11 136 150 20,345 44,800

Refineries 0.005 6 50 308 680

1.02 0.51

Load scenario: San Luis Drain extension at 300 ft3

/s and 300 μg/L for a load of 89,760 lbs per six months; refinery cleanup

Sacramento River 17 20,961 0.04 838 1,850

San Joaquin River 2 2,466 1 2,466 5,440

San Luis Drain 0.11 136 300 40,689 89,760

Refineries 0.005 6 50 308 680

1.88 0.94

Load scenario: Targeted San Joaquin River load of 7,180 lbs annually (3,590 lbs per six months); refinery cleanup

Sacramento River 17 20,961 0.04 838 1,850

San Joaquin River 1.1 1,356 1.2 1,628 3,590

San Luis Drain 0 0 0 0 0

Refineries 0.005 6 50 308 680

0.12 0.06
68 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Table 20. Forecasts of selenium concentrations for a composite freshwater endmember at the head of the estuary and at 

Carquinez Strait (a point midway in the North Bay at a salinity of 17.5 practical salinity units) for a wet year in a low flow 

season under load scenarios for conveyance of agricultural drainage either through a San Luis Drain extension or the San 

Joaquin River.

[Inputs from the Sacramento River and oil refineries also are considered. Refinery cleanup is assumed in all scenarios. Scenarios using a San Luis 

Drain extension for conveyance assume little San Joaquin River inflow reaches the Bay-Delta. The scenario using the San Joaquin River for conveyance assumes no San Luis Drain extension inflow and a 0.5 million acre-ft inflow from the San Joaquin River reaches the Bay-Delta. This table is a 

representation of a spreadsheet.]

Wet year (1997 data); low flow season (six months, June through November); refinery cleanup

Volume

(million acre-ft)

Volume

(billion liters)

Selenium

Concentration 

(μg/L)

Load 

(billion μg)

Load

(lbs per six 

months)

Freshwater

endmember

(μg/L)

Carquinez

Strait 

(μg/L) 

Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; refinery cleanup

Sacramento River 2.3 2,836 0.04 113 250

San Joaquin River 0.001 1.2 1 1 3

San Luis Drain 0.05 62 50 3,083 6,800

Refineries 0.005 6.2 50 308 680

1.21 0.60

Load scenario: San Luis Drain extension at 300 ft3

/s and 62.5 μg/L for a load of 18,700 lbs per six months; refinery cleanup

Sacramento River 2.3 2,836 0.04 113 250

San Joaquin River 0.001 1.2 2 2 5

San Luis Drain 0.11 136 62.5 8,477 18,700

Refineries 0.005 6.2 50 308 680

2.99 1.49

Load scenario: San Luis Drain extension at 300 ft3

/s and 150 μg/L for a load of 44,880 lbs per six months; refinery cleanup

Sacramento River 2.3 2,836 0.04 113 250

San Joaquin River 0.001 1.2 2 2 5

San Luis Drain 0.11 136 150 20,345 44,880

Refineries 0.005 6.2 50 308 680

6.97 3.49

Load scenario: San Luis Drain extension at 300 ft3

/s and 300 μg/L for a load of 89,760 lbs per six months; refinery cleanup

Sacramento River 2.3 2,836 0.04 113 250

San Joaquin River 0.001 1.2 2 2 5

San Luis Drain 0.11 136 300 40,689 89,760

Refineries 0.005 6.2 50 308 680

13.8 6.90

Load scenario: Targeted San Joaquin River load of 7,180 lbs annually (3,590 lbs per six months); refinery cleanup

Sacramento River 2.3 2,836 0.04 113 250

San Joaquin River 0.5 616 2.5 1,541 3,400

San Luis Drain 0 0 0 0 0

Refineries 0.005 6.2 50 308 680

0.57 0.28
 69

Table 21. Forecasts of selenium concentrations for a composite freshwater endmember at the head of the estuary and at 

Carquinez Strait (a point midway in the North Bay at a salinity of 17.5 practical salinity units) for a critically dry year in a low 

flow season under load scenarios for conveyance of agricultural drainage either through a San Luis Drain extension or the 

San Joaquin River. 

[Inputs from the Sacramento River and oil refineries also are considered. Refinery cleanup is assumed in all scenarios. Scenarios using a San Luis 

Drain extension for conveyance assume little San Joaquin River inflow reaches the Bay-Delta. The scenario using the San Joaquin River for conveyance assumes no San Luis Drain extension inflow and a 0.5 million acre-ft inflow from the San Joaquin River reaches the Bay-Delta. This table is a 

representation of a spreadsheet.]

Critically dry year (1994 data); low flow season (six months, June through November); refinery cleanup

Volume

(million acre-ft)

Volume

(billion liters)

Selenium

Concentration 

(μg/L)

Load 

(billion μg)

Load

(lbs per six 

months)

Freshwater

endmember

(μg/L)

Carquinez

Strait 

(μg/L) 

Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; refinery cleanup

Sacramento River 1.3 1,603 0.04 64 141

San Joaquin River 0.0005 0.6 2 1 3

San Luis Drain 0.05 62 50 3,083 6,800

Refineries 0.005 6.2 50 308 680

2.07 1.03

Load scenario: San Luis Drain extension at 300 ft3

/s and 62.5 μg/L for a load of 18,700 lbs per six months; refinery cleanup

Sacramento River 1.3 1,603 0.04 64 141

San Joaquin River 0.0005 0.6 2 1 3

San Luis Drain 0.11 136 62.5 8,477 18,700

Refineries 0.005 6.2 50 308 680

5.07 2.54

Load scenario: San Luis Drain extension at 300 ft3

/s and 150 μg/L for a load of 44,880 lbs per six months; refinery cleanup

Sacramento River 1.3 1,603 0.04 64 141

San Joaquin River 0.001 1.2 2 2 5

San Luis Drain 0.11 136 150 20,345 44,880

Refineries 0.005 6.2 50 308 680

11.87 5.93

Load scenario: San Luis Drain extension at 300 ft3

/s and 300 μg/L for a load of 89,760 lbs per six months; refinery cleanup

Sacramento River 1.3 1,603 0.04 64 141

San Joaquin River 0.0005 0.6 2 1 3

San Luis Drain 0.11 136 300 40,689 89,760

Refineries 0.005 6.2 50 308 680

23.53 11.76

Load scenario: Targeted San Joaquin River load of 6,800 lbs annually (3,400 lbs per six months); refinery cleanup

Sacramento River 1.3 1,603 0.04 64 141

San Joaquin River 0.5 616 2.5 1,541 3,400

San Luis Drain 0 0 0 0 0

Refineries 0.005 6.2 50 308 680

0.86 0.43
70 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Forecasts of influence of selenium discharged 

through a San Luis Drain extension: seasonal 

waterborne selenium concentrations 

Four specific forecasts are constructed to evaluate effects 

on the Bay-Delta of direct discharge from an extension of the 

San Luis Drain (tables 19 through 21). Those forecasts are 

based on feasible loads under three different sets of climate 

and river inflows conditions (wet year, high flow season; wet 

year, low flow season; and critically dry year, low flow season) 

as described earlier.

6,800 lbs selenium discharged in six months if management of drainage quality and quantity are a high priority 

(half-capacity or 150 ft3

/s of drain water with a selenium 

concentration of 50 μg/L). The forecasted six-month average selenium concentrations at the head of the estuary (com1.

Table 22. Forecasts of selenium concentrations for a composite freshwater endmember at the head of the estuary and at 

Carquinez Strait (a point midway in the North Bay at a salinity of 17.5 practical salinity units) under a restoration scenario 

that assumes greater San Joaquin River inflows enter the Bay-Delta to aid fish migration and the concentration in the river 

maintained at 5 μg/L. 

[The high flow season is assumed to convey 75% of the San Joaquin River annual flow; and the low flow season conveys 25%. Refinery cleanup and 

no San Luis Drain extension is assumed in all scenarios. This table is a representation of a spreadsheet.]

Restoration scenarios

Volume

(million acre-ft)

Volume

(billion liters)

Selenium

Concentration 

(μg/L)

Load 

(billion μg)

Load

(lbs per six 

months)

Freshwater

endmember

(μg/L)

Carquinez

Strait 

(μg/L) 

Wet year (1997 data); high flow season; conveys 75% of San Joaquin River inflow (six months, December through May)

Sacramento River 17 20,961 0.04 838 1,850

San Joaquin River 2.25 2,774 0.5 1,387 3,060

San Luis Drain 0 0 0 0 0

Refineries 0.005 6.2 50 308 680

Total 19.25 5,590 0.11 0.05

Wet year (1997 data); low flow season; conveys 25% of San Joaquin River inflow (six months, June through November)

Sacramento River 2.3 2,836 0.04 113 250

San Joaquin River 0.75 925 0.5 462 1,020

San Luis Drain 0 0 0 0 0

Refineries 0.005 6.2 50 308 680

Total 3.055 1,950 0.23 0.12

Dry year (1994 data); high flow season; conveys 75% of San Joaquin River inflow (six months, December through May)

Sacramento River 5 6,165 0.04 247 544

San Joaquin River 0.82 1,011 0.5 506 1,115

San Luis Drain 0 0 0 0 0

Refineries 0.005 6.2 50 308 680

Total 5.825 2,339 0.15 0.07

Dry year (1994 data); high flow season; conveys 25% of San Joaquin River inflow (six months, June through November)

Sacramento River 1.6 1,973 0.04 79 174

San Joaquin River 0.28 345 0.5 173 381

San Luis Drain 0 0 0 0 0

Refineries 0.005 6.2 50 308 680

Total 1.885 1,235 0.24 0.12
 71

posite freshwater endmember concentration) during the low 

flow season range from 1.21 μg/L in a wet year (table 20) to 

2.07 μg/L during a critically dry year (table 21). A selenium 

concentration of 0.28 μg/L (table 19) is forecasted in the high 

flow season of a wet year. Forecasted selenium concentrations at the selected seaward location of Caquinez Strait are: 

the low flow season of a wet year, 0.60 μg/L; the low flow 

season of a critically dry year, 1.03 μg/L; and the high flow 

season of a wet year 0.14 μg/L (tables 19 through 21). 

18,700 lbs selenium discharged in six months if a San 

Luis Drain extension operates at full capacity (300 ft3/s), 

carrying drainwater with a selenium concentration 

similar to that in the Grassland Bypass Channel Project 

(reuse of the drain project, 62.5 μg/L). This forecast is 

one of the more likely demand-driven loads in the long-term 

if successful treatment technology is applied to drainage and 

the amount of problem land is that considered by the Drainage Program (table 6). Forecasted selenium concentrations 

at the head of the estuary are projected to average 2.99 μg/L 

during the low flow season of a wet year; and 5.07 μg/L during six months of low flow in a critically dry year. Selenium 

concentrations average 0.51 μg/L at the head of the estuary 

during six months of high flow in a wet year. 

44,880 lbs selenium discharged in six months if drainage contains 150 μg/L selenium and the drain operates 

at full capacity. This load would provide for drainage from 

problem lands without investment in management of drainage (such as direct discharge of shallow ground water). Even 

during high flow, selenium concentrations are projected to 

exceed 1 μg/L (1.02 μg/L) at the head of the estuary under 

these conditions. During low flow, six-month average concentrations (6.97 to 11.87 μg/L) always exceed the USEPA 

criterion of 5 μg/L no matter what the rainfall.

89,760 lbs selenium discharged in six months if the 

most severely salinized soils supply a drain at full 

capacity and no treatment technology is available. This 

scenario is not highly likely given expected emphasis on 

source control and treatment. However, if it should occur, 

extremely high selenium concentrations are found in the 

estuary under low flow conditions (13.8 to 23.5 μg/L, 

rounded off) (tables 19 through 21). Average concentration at the head of the estuary (1.88 μg/g ) approximately 

equals the USFWS recommended criterion (2 μg/L), even 

during the high flow season (table 21).

Forecasts of the influence of selenium 

discharged through the San Joaquin River: 

seasonal waterborne selenium concentrations 

Regulating load. This scenario assumes a selenium load 

limited for regulatory or environmental purposes at 7,000 

lbs selenium per year and 3,500 lbs selenium discharged in 

six months. Conveyance is fully through the San Joaquin 

2.

3.

4.

1.

River. The projected range of selenium concentrations in 

the freshwater endmember for the Bay-Delta during the 

low flow season scenarios is 0.57 to 0.86 μg/L selenium; 

concentrations range from 0.28 to 0.43 μg/L at Carquinez 

Strait (tables 20 and 21). These values are slightly enriched 

from the conditions that applied before refinery cleanup 

(0.39 to 0.53 μg/L selenium at the head of the estuary and 

0.20 to 0.27 μg/L selenium at Carquinez Strait) (table 18). 

So, in terms of affecting total selenium concentrations, 

this targeted load of selenium from the San Joaquin Valley 

would replace the selenium removed by investment in refinery waste treatment. If 3,590 lbs of selenium are discharged 

during a six-month high flow season of a wet year (table 

19), concentrations are twofold lower (0.12 μg/L at the 

head of the estuary and 0.06 μg/L at Carquinez Strait) than 

conditions prior to refinery cleanup (0.22 μg/L at the head 

of the estuary and 0.11 μg/L at Carquinez Strait, table 18). 

Regulating concentrations in the San Joaquin River: a 

restoration forecast. Environmental restoration is often 

vaguely defined. A specific restoration scenario for the 

San Joaquin River might place explicit limits on selenium 

concentrations in the river and emphasize increasing San 

Joaquin River inflows (less recycling of the San Joaquin 

River) to the Bay-Delta to aid fish movement in certain 

seasons of the water year (CALFED, 1998a, b, 1999a, b, c, 

d; EA Engineering, Science, and Technology, 1999). Managing concentration in the San Joaquin River contrasts to 

previous scenarios in which selenium load is managed. In 

calculating the effect of such restoration on selenium concentrations in the Bay-Delta, the concentration assigned 

in the restoration scenario is 0.5 μg/L for the San Joaquin 

River at Vernalis. It should be noted that this concentration 

has not been achieved in the recent past (table 5). Further, it is not implied here that the technology is available 

to achieve this concentration or that it would be easy to 

achieve by management decree. This is a specific condition done for illustrative purposes. Conditions and selenium loads for this restoration scenario (table 22) include:

no San Luis Drain discharge;

constrain concentrations in the San Joaquin River at 

Vernalis to 0.5 μg/L; 

convey 75 percent of the annual San Joaquin River 

flow and load to the Bay-Delta in the high flow season 

and 25 percent in the low flow season; 

assume the San Joaquin River inflow for a wet year is 3 

million acre-ft and for a dry year is 1.1 million acre-ft; 

control industrial discharges to meet the July 1998 

mandate of approximately 1,400 lbs selenium per year; 

vary Sacramento River inputs with river flow as is done 

now (0.04 μg/L at 19.3 million acre-ft annual inflow in 

a wet year and 0.04 μg/L at 6.6 million acre-ft annual 

inflow in a dry year).

2.

•

•

•

•

•

•
72 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Under a restoration scenario in the high flow season, 

composite freshwater endmember selenium concentrations 

are projected at 0.11 and 0.15 μg/L for a wet year and a 

dry year, respectively (table 22). In the low flow season, 

composite freshwater endmember selenium concentrations are projected at 0.23 and 0.24 μg/L, respectively 

(table 22). These selenium concentrations are less than 

those that occurred prior to refinery cleanup (compare 

tables 18 and 22). An improvement also is achieved over 

the targeted load scenario (compare tables 19, 20, and 21 

to table 22). Conditions are most improved, compared to 

before refinery cleanup, during the bottleneck period of the 

low flow season (that is, the defining period for selenium 

ecological effects) in both wet and dry years. Less increase 

in concentration occurs in the Bay-Delta during low flow 

seasons in a restoration scenario because selenium inputs 

decline as flows decline. In high flow seasons, selenium 

inputs increase, but the increase in dilution due to the 

higher inflows of the Sacramento River offset the higher 

loads from the San Joaquin River and concentrations in the 

Bay-Delta decline.

Regulating selenium concentrations in the San Joaquin 

River: effect of high flows and consequent high loads as 

a result of expanded selenium objectives. The advantage of discharging an increased selenium load during 

high flows under a concentration management scenario 

does have some limitations in the low flow season and if 

selenium concentrations in the San Joaquin River increase. 

The concentration objective at which the San Joaquin 

River is held constant by implementation of a management plan is increased in a series of scenarios illustrated in 

figure 18. If the selenium concentration in the San Joaquin 

River inflow is a constant 1 μg/L using the same conditions 

as defined above, the concentration at the head of the estuary is 0.36 μg/L during a wet year in the low flow season. 

During a dry year in the low flow season, the concentration 

is comparable at 0.32 μg/L. However, if the concentration 

is a constant 2 μg/L, the concentration at the head of the 

estuary is 0.60 μg/L during a wet year in the low flow season, as compared to 0.46 μg/L selenium during a dry year 

in the low flow season. In this case (above the crossover 

point, fig. 18), the estuary during the low flow season of 

a wet year is more at risk from higher concentrations than 

the low flow period of a dry year. This occurs because a 

higher selenium load discharged during a wet year is not 

offset as much by increased flows as occurs seasonally.

Forecasts of the influence of selenium 

discharges: monthly waterborne selenium 

concentrations

The six-month scenarios described above represent 

average seasonal selenium concentrations (low flow season 

compared to high flow season). Six-month averaged forecasts 

3.

could be misleading, however, because flows are variable over 

shorter time scales. To illustrate the effects of these shorter 

time scale changes, and to further illustrate the methodology, 

selenium concentrations are forecast that result from monthly 

loads. The forecasts are based on wet year flows (1997). The 

results of the monthly forecasts are presented graphically in 

figures 19 and 20 and supplemental data are given in appendix 

F, tables F1 and F2. Conditions used in the forecasts and 

results of the forecasts are: 

Operation of a San Luis Drain extension at full 

capacity (0.22 million acre-ft/yr) conveying drainage at 

quality levels typical of the present reuse of the drain by 

Grassland subarea (62.5 μg/L). The annual load of selenium 

is 36,720 lbs (or about 18,700 × 2 = 37,400 lbs, table 17). 

Although monthly drain discharge is constant (3,060 lbs per 

month) in this scenario, forecasted selenium concentrations 

at the head of the estuary increase progressively from 0.24 

μg/L in January to 4.5 μg/L in October (fig. 19). The range of 

concentration change is dramatic, because dilution declines 

through the year as river inflows decline. The peak concentration in October would be a permanent feature of monthly 

variability in selenium concentrations as long as a constant 

load is released from the drain throughout the year (fig. 19). 

The vulnerability of the estuary to adverse effects is generally greatest during the season of lower flows (June through 

November), but a detailed monthly analysis shows that vulnerability is at a maximum in the fall months when water exports 

most exceed river inflows (figs. 8 and 9). Figure 19 expresses 

this scenario as a function of both load and composite freshwater endmember selenium concentration. Figure 20 shows 

the composite freshwater endmember selenium concentration 

at the head of the estuary and the selenium concentration at 

Carquinez Strait for comparison. 

Management of the San Joaquin River at 2 μg/L selenium with full conveyance to the Bay-Delta during a wet 

year (6.06 million acre-ft/yr). It is also instructive to evaluate 

0

0

0.4

0.8

Wet year

Dry year

1.2

1 2

San Joaquin River input, in micrograms per liter

Selenium concentration,

in micrograms per liter

3 4 5

Figure 18. Forecasts of composite freshwater endmember selenium 

concentrations for a series of concentration management 

scenarios for the San Joaquin River in low flow seasons of both 

wet and dry years.
 73

the variation in monthly concentrations that might develop 

at the head of the estuary as a result of managing a constant 

San Joaquin River selenium concentration. The annual load of 

selenium discharged to the Bay-Delta from the San Joaquin 

River in this forecast is similar to that discharged by a San Luis 

Drain extension in the above scenario (32,936 lbs compared 

with 36,720 lbs for the San Luis Drain scenario, table 17). The 

highest loads (about 10,400 lbs each month) are discharged 

in January and February. The highest selenium concentration 

at the landward reach is 1.2 μg/L (appendix F, table F1). Two 

periods of maximum concentration occur, in March through 

June and in September through November (fig. 20). The latter 

period of elevated concentration coincides with that under 

constant discharge from the San Luis Drain (fig. 20). Selenium 

concentrations in the Bay-Delta are much lower from April 

through December if the San Joaquin River is the conveyance 

rather than if a San Luis Drain extension is the conveyance. 

This disparity in load is because monthly loads from the San 

Joaquin River decline as hydraulic discharges decline and 

most of the load is released with the highest flows. Weighting 

with flow prevents the extreme concentrations that build up as 

a result of high loads during periods of low inflow if load is 

constant. The fall build-up in selenium concentration illustrates 

an important problem with releasing selenium through an artificial conveyance facility. Additional limitations also exist when 

large loads are released during high flows (see fig. 18 and later 

discussion). 

Management of the San Joaquin River at 1 μg/L selenium with full conveyance to the Bay-Delta during a wet 

year. The annual load calculated for this condition is 16,468 

lbs in a high flow year. The monthly trends are the same as 

those under the 2 μg/L selenium scenario, but the amplitude of 

the fall peak is reduced (fig. 19). The highest concentrations 

in the landward reach of the estuary are 0.60 and 0.68 μg/L

in September and October (appendix F, table F2), respectively (about 1.5 times the maximum observed before refinery 

cleanup, table 18). Forecasted concentrations near Carquinez 

Strait in October (fig. 20) are about equal to the highest 

concentrations (0.30 to 0.34 μg/L) observed prior to refinery 

cleanup based on a seasonal analysis (table 18), although 

speciation would probably be different (see later discussion). 

Summary of forecasts 

Forecasts of selenium concentrations in a composite 

freshwater endmember entering the Bay-Delta as a result of 

loads discharged through a San Luis Drain extension and a 

targeted load discharged through the San Joaquin River overall 

show that the most vulnerable years are critically dry years

(table 23; figs. 21 and 22). The low flow season is the critical 

period of each year for the Bay-Delta. However, if selenium 

concentration in the San Joaquin River is regulated under a 

constant concentration management plan and San Joaquin 

River inflows are increased, wet years are more vulnerable 

than dry years, but only during the low flow season (fig. 18).

A generalized graphical tool presented in figure 22 can be 

used to forecast waterborne selenium concentrations resulting 

from a wide range of six-month hydraulic discharges (emphasizing lower flow seasons) and selenium loads. Each line 

represents a selenium concentration resulting from a different 

combinations of variables. From figure 22, the composite 

0

0

2

1

3

San Luis Drain

extension input 

(62.5 μg/L) 

Carquinez

Strait

(17.5 psu) 

San Joaquin R.

(1 μg/L) (2μg/L)

Freshwater

endmember

4

5

10 20 30

Salinity, in practical salinity units 

Selenium concentration,

in micrograms per liter

Figure 20. Forecasts of selenium concentrations for a composite 

freshwater endmember at the head of the estuary and at Carquinez 

Strait (a point midway in the North Bay at a salinity of 17.5 

practical salinity units) under three load scenarios (San Joaquin 

River at 1 and 2 μg/L selenium; San Luis Drain extension at 62.5 

μg/L selenium) based on dilution of selenium through the estuary 

as function of salinity in October, 1997.

1

0

2

3

4

5

2,400

0

4,800

7,200

9,600

12,000

J F M A M J J A S O N D

1994

32,936

16,468

San Joaquin R. San Luis Drain extension

Selenium load

(lbs per year)

Selenium concentration

(μg/L)

Selenium concentration, in micrograms per liter

Selenium load, in pounds

36,720 (3,060/month)

2

1

62.5

Figure 19. Forecasts of monthly composite freshwater endmember 

selenium concentrations under three discharge scenarios (San 

Joaquin River at 1 and 2 μg/L selenium; San Luis Drain extension at 

62.5 μg/L selenium) contrasted to input concentrations and loads.
74 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

freshwater endmember concentration of selenium (that 

concentration at the head of the estuary) can be estimated from 

any combination of climate (as indicated by differing total 

river inflows) and selenium load. The strong dependence of 

selenium contamination on weather and water demand (which, 

together, determine discharge to the estuary) is evident. Figure 

22 illustrates the extreme vulnerability of the estuary to selenium inputs during low flow seasons (cumulative discharges of 

1 to 2 million acre-ft over six months). For example, for total 

loads of approximately 7,700 lbs, 20,000 lbs, and 46,000 lbs 

selenium at defined cumulative volumes of 1.3 and 2.3 million 

acre-ft during low flow seasons, the range of estuary selenium 

concentrations is from 1.2 to 12 μg/L. 

Under the range of illustrated load scenarios, selenium 

concentrations in the Bay-Delta increase in all scenarios that 

include a San Luis Drain extension, and especially as the flow 

capacity of the San Luis Drain is achieved and/or if concentrations of selenium increase in the discharge (table 23 and 

fig. 21). A minimum estimate of loads from a San Luis Drain 

extension is 6,800 lbs per six months (or 13,600 lbs annually). 

This scenario can only be achieved if the drain is managed at 

a flow of 150 ft3/s and the most optimistic treatment technologies are invoked. Even under this load scenario, composite 

freshwater endmember selenium concentrations would 

increase two to fourfold over concentrations typical prior to 

refinery cleanup (also see table 18). Freshwater endmember 

selenium concentrations in the driest of years are projected to 

exceed 2 μg/L toward the head of the estuary. 

If a San Luis Drain extension is built to the Bay-Delta, 

pressure may be strong to maximize its potential to carry 

salt-laden waters. Under this condition, loads from a San Luis 

Drain extension may approach the level of 18,700 lbs per 

six months (37,400 lbs per year). Under this load scenario, 

average selenium concentrations in the Bay-Delta at the head 

of the estuary for the six-month low flow season of a wet or 

critically dry year are forecast to exceed the USFWS recommended criterion of 2 μg/L through all of Suisun Bay (table 22 

and fig. 21). This exceedance also occurs at Carquinez Strait 

during the low flow period of critically dry years. 

If treatment technologies are not developed or if demand 

becomes more important than load management, then the 

quality of discharged drainage could drop (that is, selenium 

concentrations could increase). If, on average, drainage quality 

becomes similar to that of subsurface drainage (equal to or 

greater than 150 μg/L selenium) rather than blended drainage 

in the western San Joaquin Valley, and that is combined with 

Table 23. Summary of forecasts of selenium concentrations for a composite freshwater endmember at the head of the estuary and 

at Carquinez Strait (at 17.5 practical salinity units) under projected selenium load scenarios. 

Scenario

Water-column selenium concentrations (μg/L)

Past San Luis Drain extension San Joaquin River

Prior to 

refinery 

cleanup

Half capacity 

at 50 μg/L

Full capacity 

at 62.5 μg/L

Full capacity 

at 150 μg/L

Full capacity 

at 300 μg/L

Targeted

Load

Restoration 

0.5 μg/L

Wet year/high flow

Load

(lbs per six months)

– 6,800 18,700 44,880 89,760 3,590 3,060

Endmember concentration

(μg/L)

0.22 0.28 0.51 1.02 1.88 0.12 0.11

Carquinez Strait concentration

(μg/L)

0.11 0.14 0.26 0.51 0.94 0.06 0.05

Wet year/low flow

Load

(lbs per six months)

– 6,800 18,700 44,880 89,760 3,400 1,020

Endmember concentration 

(μg/L)

0.39 1.21 2.99 6.97 13.8 0.57 0.23

Carquinez Strait concentration 

(μg/L)

0.20 0.60 1.49 3.49 6.9 0.28 0.12

Critically dry year/low flow

Load

(lbs per six months)

– 6,800 18,700 44,880 89,760 3,400 381

Endmember Concentration

(μg/L)

0.53 2.07 5.07 11.9 23.5 0.86 0.24

Carquinez Strait concentration

(μg/L)

0.27 1.03 2.54 5.93 11.8 0.43 0.12
 75

full flow in a San Luis Drain extension, then extreme concentrations are projected to occur in the Bay-Delta. Under a load

of 44,880 lbs selenium per six months, forecasted selenium 

concentrations of > 6.97 μg/L at Carquinez Strait are projected 

during the low flow season of both wet and critically dry 

years. 

A selenium concentration of 1 μg/L is threefold higher 

than presently found in the Bay-Delta in a normal rainfall year 

(Cutter 1989; Cutter and San Diego-McGlone, 1990; and San 

Francisco Bay Board, 1992a, b , also see table 18) and represents the current Canadian guideline for protection of aquatic 

life (Environment Canada/Health Canada, 1995; Outridge and 

others, 1999). This selenium concentration cannot be achieved 

near Carquinez Strait in the low flow season by any scenario 

that includes an extension of the San Luis Drain, except a load 

of 6,800 lbs per six months (fig. 21). In the high flow season 

of a wet year, concentrations forecasted at the Carquinez Strait 

are 0.14 to 0.94 μg/L. 

An important component of a monthly analysis, not 

evident in a six month analysis, for the illustrated San Luis 

Drain extension scenario (a constant 62.5 μg/L selenium 

concentrations) is the very elevated selenium concentrations that 

result each year in the fall (fig. 19). The strong dependence of 

selenium contamination on climate and water demand, which, 

together, determine discharge to the estuary, is also evident. 

Concentrations in excess of 2 μg/L would extend through much 

of Suisun Bay and San Pablo Bay for greater than six month 

of the year in this drain forecast (fig.19). It is possible that 

the dilution assumptions employed here might understate the 

geographic extent of selenium distributions in projections for 

October. Sophisticated physical models are being developed for 

the Bay-Delta and could be helpful in describing such important 

details (for example, Monsen, 2000; Monsen and others, 2002). 

Forecasts of Speciation and Transformation 

Speciation of selenium in the Bay-Delta is controlled 

by physicochemical processes and speciation in the sources 

of discharge (see previous discussion; Cutter and Bruland, 

1984; Cutter, 1989; Luoma and others 1992). Speciation 

will change as sources change in importance. Prior to 1998, 

refinery discharges of selenite were a principal influence on 

speciation and bioavailability. Refinery discharges declined 

in July 1998. A lower proportion of the total selenium was 

selenite in the late 1990s than in the 1980s (Cutter and Cutter, 

2004). It is likely that the proportion of selenate discharged to 

the Bay-Delta would increase if a San Luis Drain extension is 

built or if/when San Joaquin River inflows to the Bay-Delta 

increase. Biotransformation to Se(-II) and/or sediment accumulation and recycling of Se(-II) in the Bay-Delta are highly 

likely under increased San Joaquin River selenium load if the 

transformation conditions prevalent at present in the Bay-Delta 

are operable on the San Joaquin River discharge. This influx 

of Se(-II) into the Bay-Delta could be accentuated if marshes 

are restored in areas subjected to inflows from the San Joaquin 

River or a San Luis Drain extension. 

0

0

10

5

15

Selected discharge scenarios (per six months)

6,8003,500 18,700 44,880 89,760

20

25

20,000 40,000 80,000

High flow (wet yr)

Low flow (wet yr)

Low flow (dry yr)

60,000

Selenium discharge, in lbs

Selenium concentration,in micrograms per liter

SLD SLD

SJR — San Joaquin River

SLD — San Luis Drain extension

SLD SLD

SJR

Figure 21. Forecasts of seasonal composite freshwater endmember 

concentrations under five discharge scenarios (San Luis Drain 

extension at 6,800, 18,700, 44,880, and 89,760 lbs selenium per six 

months; San Joaquin River at 3,500 lbs selenium per six months) 

for the high flow season of a wet year and the low flow seasons of 

wet and dry years.

0

0

20,000

10,000

30,000

40,000

50,000

1 2 3 4 5

Total river flow, in millions of acre feet (MAF) per six months

0

20,000

10,000

30,000

40,000

50,000

10

Selenium

concentrations

(μg/L)

46,000 lbs

20,000 lbs

7,700 lbs

Dry year 1.3 MAF

Wet year 2.3 MAF

20,000 lbs

7,700 lbs

0.3

1.0

2.0

3.0

8.0 5.0 4.0

Selenium load from all sources, in lbs

a

b

Figure 22. (a) Calculation of eight composite freshwater 

endmember selenium concentrations as derived from different 

combinations of total input load and total river inflow (as 

composited mass of water that reaches the estuary in a six-month 

period); and (b) examples of resulting wet and dry year selenium 

concentrations for three selenium load scenarios.
76 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

As discussed previously, speciation is a critical consideration in estimating ecological effects of selenium. Speciation 

drives the transformation reactions that determine particulate 

selenium concentrations and forms. Bioaccumulation from 

particulates is the primary route by which selenium enters the 

food web, so the reactions that determine particulate concentrations are critical to eventual trophic transfer. 

Ultimately, forecasts of selenium speciation should be 

derived from biogeochemical kinetic speciation models. As 

discussed previously, thermodynamic equilibrium approaches 

are not suitable for selenium systems because of the dynamic 

nature of biological reactions that control transformation and 

transport processes within water, particulate matter, and organisms. A model of internal regenerative cycling of selenium in 

the Pacific Ocean focused on uptake, particulate transport, and 

the kinetics of selenium species inter-conversions (Cutter and 

Bruland, 1984). A general modeling framework for selenium 

outlined a strategy for considering the kinetics and transfer of 

the different forms of selenium (Bowie and others, 1996). This 

type of model is not yet ready for application to the Bay-Delta, 

although the completion of its development should be a high 

priority. In the absence of a model, speciation is included in 

the approach used here based on mixes of species that have 

been observed in nature under circumstances possible for the 

Bay-Delta. How each mix of species would affect transformations of dissolved selenium to particulate selenium (speciation 

is implicit in the choice of transformation reactions) is then 

forecast.

Transformation is quantitatively expressed by the distribution of selenium between particulate and dissolved forms, 

the Kd (see previous discussion). The effect of speciation 

and transformation is incorporated by using Kd's observed in 

previous studies (table 11) to project a ratio of total selenium 

typical of a given speciation regime. For each combination of 

Kd and speciation (the speciation/transformation regime), the 

form of particulate selenium observed under those circumstances is incorporated to enable a projection of overall 

bioavailability. 

Defining speciation, transformation, and 

bioavailability (speciation/transformation regime)

Three sets of speciation/transformation regimes are 

presented below in which a specific distribution of selenium 

among particulate forms is assumed. These speciation and 

biochemical behavior patterns are used throughout progressive 

forecasts presented here of selenium concentrations in particulates, bivalves, and predators. 

High Bioavailability (C1)

Speciation: high proportion of selenite plus organo-Se 

(≥60 percent) 

Kd: 1 × 104

Precedent: estuarine suspended material in the Bay-Delta

•

Particulate bioavailability: 60 percent high and 40 

percent moderate 

To bound a high bioavailability condition, Se(IV) and a 

portion of the Se(-II) are assumed to contribute to biotransformation to organo-Se. Preliminary studies in the late 1990s 

showed that as much as 60 percent of dissolved selenium was 

Se(IV) plus Se(-II) in Suisun Bay. Selenite has declined since 

refineries reduced their discharges, but organo-Se has become 

a larger proportion of dissolved selenium (Cutter and Cutter, 

2004). In Suisun Bay, this speciation regime is accompanied 

by a particle/dissolved distribution (Kd) of ≥104. For example, 

distribution coefficients for estuarine suspended material in 

most of the Bay-Delta were 8.2 × 10 3 to 2.1 × 104, between 

September 1986 and October 1996. Biotransformation may 

explain these high Kd's. Some species of diatoms, the most 

common phytoplankton in the North Bay, have Kd's higher 

than 104 in laboratory experiments (Reinfelder and Fisher, 

1991) (table 11). For bioavailability calculations, the form of 

the particulate selenium under these conditions is assumed to 

be 60 percent biotransformed and 40 percent oxidized material 

of moderate bioavailability. Biologically, this speciation/transformation regime is most relevant to water column-feeding 

species of consumer organisms. 

Moderate Bioavailability (C2) 

Speciation: low proportion of biotransformable Se(IV) 

or bioavailable Se(-II) (<30 percent) 

Kd: 3 × 103

Precedent: typical of shallow-water estuarine sediments or marine waters

Particulate bioavailability: 60 percent moderate and 

40 percent high 

If sources of selenium change, it is possible that the 

proportion of selenium as Se(IV) + Se(-II) in the Bay-Delta 

will decline to <60 percent. Even if the proportion of Se(IV) 

and Se(-II) remains high, it is possible that the bioavailability 

of Se(-II) is less than that of Se(IV). To account for either of 

these possibilities, 40 percent of total selenium is assumed 

to contribute to biotransformation at the rate of Se(IV). A 

speciation regime of 40 percent biotransformable selenium 

and 60 percent less reactive selenium is similar to that often 

observed in undisturbed marine waters, and so it is a scenario 

with some precedent. Shallow-water estuarine sediments also 

show a distribution coefficient of 3 × 103 to 1 × 104 (Velinsky 

and Cutter, 1991; Cutter and Cutter, 2004; Doblin and others, 

2006) (table 11). This speciation and Kd combination is 

assumed to result in particulate selenium that is 60 percent in a 

form of moderate bioavailability [detrital Se(-II) or particulate 

Se(IV) + (VI)]; and 40 percent in a form of high bioavailability (biotransformed organo-Se). Biologically, this speciation/transformation regime applies to biota that predominantly 

ingest sediments with concentrations diluted by non-transformed load. 

•
 77

Low Bioavailability (C3)

Speciation: predominantly Se(VI) 

Kd: 1 × 103

Precedent: Systems such as an area of a wetland near a 

discharge site of selenate-dominated irrigation drainage 

waters

Particulate bioavailability: 50 percent low, 40 percent 

moderate, and 10 percent high 

This condition assumes that most of the selenium 

entering the Bay-Delta remains as Se(VI). Selenate is transformed, but the Kd's of selenate-dominated waters are typically lower than where a higher proportion of the species are 

organo-Se. Circumstances exist, such as near the irrigation 

discharges at Benton Lake, Montana, where Kd's are about 

103 (Zhang and Moore, 1996). This value also is at the lowest 

end of the range of distribution coefficients characterizing 

Bay-Delta sediments and is probably the most optimistic 

scenario that can be hoped for, in terms of generating particulate selenium and ultimately biological effects. For forecasting 

bioavailability, this material is assumed to be 50 percent 

slurry-generated Se(0) of relatively low bioavailability, 40 

percent oxidized material of moderate bioavailability, and 10 

percent organo-Se of high bioavailability. This speciation/

transformation regime would apply most readily to deposit 

feeding benthos, especially those feeding within sediments. 

In general, it is recognized in the approach presented 

here that the Kd-concept has limitations and that there are 

uncertainties about future speciation should a San Luis Drain 

extension begin discharging selenium loads to the Bay-Delta. 

Nevertheless, the three speciation/transformation regimes 

described above are likely to fully bound the possibilities. 

Using these regimes, at the least, ranges of particulate selenium concentrations and particulate forms can be forecast.

Comparison of forecasted particulate 

concentrations to observed Bay-Delta conditions

It is instructive to visually compare forecasts using the 

three Kd's presented above to existing data for the Bay-Delta. 

In figure 23, concentrations observed in the Bay-Delta for 

suspended particulate selenium concentrations are plotted 

against observed dissolved concentrations (Cutter, 1989; 

Cutter and San Diego-McGlone, 1990; Cutter and Cutter, 

2004; Doblin and others, 2006). Lines describing predicted 

particulate concentrations using Kd's of 1 × 103 and 1 × 104

are superimposed on the plots. A Kd of 1 × 103 is too low to 

describe any of the existing suspended sediment data making 

it a low probability condition. The October 1996 data (the 

highest concentrations observed in any survey) exceed a Kd

1 × 104 and the September 1986 data fall between the two 

values. In figure 24, similar data are presented in a different 

way. Particulate concentrations are predicted from dissolved 

concentrations that occurred landward to seaward in the 

• Bay-Delta in October 1996. The three different Kd's presented 

above describe three different trend lines for particulate 

concentrations through the estuary. The observed October 

1996 particulate data is superimposed on these predictions. 

The superimposed data illustrate that a Kd of 1 × 104 is the 

best choice for this data set. A Kd between 3 × 103 and 1 × 

104 would best fit the September 1986 data, if it were plotted 

similarly. The three Kd's used for these predictions (fig. 24) 

were, of course, developed based on empirical observations. 

So, it is not surprising that direct comparison to data from the 

Bay-Delta are consistent with the choices.

Forecasts of Particulate Selenium 

Concentrations (all values are dry weight 

concentrations)

Sediment guidelines 

As discussed previously, the principal risk of sediment 

to fish and birds is through the aquatic food chain. Sediment 

guidelines are based on sediment concentrations as predictors 

of adverse effects through the food chain. Proposed sediment guidelines for selenium (μg/g in particulate material or 

sediment, dry weight) provide a context to evaluate forecasted 

particulate selenium concentrations. Skorupa (1998b) provided 

a compilation of background and biotic thresholds and effects 

levels for sediment. Canton and Van Derveer (1997) and Van 

Derveer and Canton (1997) recommended sediment criteria 

based on data from streams in Colorado and a relatively 

insensitive community analysis (Hamilton and Lemly, 1999). 

Luoma and others (1992) studied bioavailability of particulates 

in an estuarine environment, including modeling sediment 

ingestion and selenium tissue burdens in the clam M. balthica. 

The guidelines given below are based on few studies that 

include bioaccumulation as part of a comprehensive analysis. 

Most guidelines do not specify in detail whether the tested 

material was bed, fine, or suspended sediment or whether the 

collection method attempted to include living material (for 

example, diatoms) as an indicator of the degree of recycled 

material that is available as food for lower food web organisms. Assessing spatial variability and careful matching of 

invertebrate and sediment samples also are of importance 

in interpreting effects. Thus, concentrations in sediment 

provide one line of evidence of how selenium might affect 

foodwebs and ultimately predators. As discussed previously, 

low certainty results if a hazard evaluation is based on one 

line of evidence. The approach presented here, the Bay-Delta 

selenium model, attempts to rectify that situation and provide 

a systematic approach that links all relevant processes to forecast ecological effects from selenium on aquatic food webs. 

As such, the approach could provide a framework for developing new protective selenium foodweb guidelines, including 

sediment or particulate matter guidelines. The site specific 

guideline included below, addresses to some degree that interconnectedness.
78 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

site-specific for Bay-Delta: 1.5 μg/g. As discussed 

previously, site-specific protective guidelines depend 

on both bioavailabity of particulates and the specifics 

of food webs (for the Bay-Delta, the species of clam). 

Luoma and others (1992) showed that particulate concentrations in the range of 1.5 μg/g could result in the 

deposit-feeding bivalve concentrations (9 to 10 μg/g) 

that have a high certainty of producing toxicity in fish 

and birds. 

sedimentary level of concern: 2 μg/g. Van Derveer 

and Canton (1997) proposed a preliminary sedimentary 

selenium toxicity threshold (10th percentile for effects) 

of approximately 2.5 μg/g. Engberg and others (1998) 

suggest levels of 2 to 4 μg/g are of concern for adverse 

effects in freshwater environments. 

observed effect concentration: 4.0 μg/g. Adverse 

effects were always observed at selenium concentrations >4 μg/g (Canton and Van Derveer (1997). Concentrations in excess of this value have a high certainty 

of producing toxicologic and reproductive effects 

(Engberg and others, 1998). 

These guidelines may not be, individually, realistic 

indications of ecological risk, but are used in this report as 

reference points to provide context. 

Forecasts of particulate selenium 

concentrations 

Tables F3 to F5 in appendix F show detailed selenium particulate concentrations both at the head of the 

estuary (composite freshwater endmember concentration) 

and Carquinez Strait for four San Luis Drain extension load 

scenarios and two San Joaquin River scenarios under three 

different climate regimes (also see tables 19 through 21 for 

composite freshwater endmember concentrations). Speciation/

transformation regimes typical of suspended sediments (C1), 

shallow-water sediments (C2), and inefficient transformation 

(C3) are used in each set of calculations. Table 24 summarizes 

particulate selenium concentrations at the head of the estuary 

for these load scenarios. Forecasts are compared to data reflective of conditions prior to refinery cleanup.

Forecasts using a San Luis Drain extension discharging 

6,800, 18,700, or 44,880 lbs selenium per six months during 

the low flow season in a critically dry year show that (table 24):

all releases to the Bay-Delta under the three assumed 

speciation/transformation regimes (C1, C2, and C3) 

result in particulate concentrations >2.0 μg/g at the 

head of the estuary. 

only under the lowest discharge assumption (6,800 lbs 

per six months) combined with the least likely speciation/transformation regime (C3), would a particulate 

selenium value (2.07 μg/g) be observed below 4.0 μg/g. 

In all other cases the certainty of effects would be high. 

•

•

•

•

•

Compiled guidelines for sediment are: 

low risk: 0.4 to 1 μg/g. A concentration of 0.5 μg/g 

was used as an alert level for possible sediment 

contamination in the San Joquin Valley (Drainage 

Program, 1990b). A no effect boundary for birds in a 

specialized environment (nesting at shallow terminal 

evaporation ponds) was reported at 0.4 μg/g and the 

minimum total response boundary (100 percent lethality boundary) was reported at1 μg/g (Skorupa, 1998b).

•

0

0

2

1

3 Kd

 = 10,000

October 1996

September 1996

Kd

 = 1,000

7

8

0.05 0.10 0.15 0.20 0.25 0.30 0.35

Dissolved selenium, in micrograms per liter

Particulate selenium concentration,

in micrograms per gram dry weight

1

0

2

3

4

Salinity, in practical salinity units

0 10 20 30

Observed

Kd = 1 x 104

Kd = 3 x 103

Kd = 1 x 103

Particulate selenium concentration,

 in micrograms per gram dry weight

Figure 23. Observed suspended particulate selenium 

concentrations as a function of observed total dissolved selenium 

concentrations during September 1986 and October 1996, with 

predicted particulate concentrations (using Kd's of 1,000 and 

10,000) superimposed on the plot.

Figure 24. Observed (October 1996) and predicted particulate 

selenium concentrations as occurring landward (zero practical 

salinity units) to seaward (35 practical salinity units) in the BayDelta projected from dissolved concentrations (see figure 23) and 

three different Kd's (1,000; 3,000; and 10,000).
 79

if the speciation/transformation regime of suspended 

material was that observed in all existing studies of the 

Bay-Delta (C2), projected loads of selenium result in 

particulate selenium concentrations in upper Suisun 

Bay of 6.2 to 35.6 μg/g. The certainty of effects would 

be high to very high. 

Under all but the most optimistic speciation/transformation conditions, load scenarios with management of drainage 

quantity and quality (6,800 to 18,700 lbs per six months) yield 

particulate selenium concentrations in the upper estuary that 

exceed 4.0 μg/g. Selenium concentrations in particulates of 

approximately 12 to 119 μg/g are possible if management is 

not a priority (44,880 lbs per six months). 

 Forecasts for a San Luis Drain extension during the low 

flow season of a wet year yield particulate selenium concentrations that are approximately 60 percent of those projected for a 

critically dry year (table 24) if: 

a load of 6,800 lbs is discharged in six months. Under 

this approach, the projected range of selenium particulate concentrations is 3.6 to 12 μg/g under the most 

likely selenium speciation/transformation regimes (C1 

and C2). 

the drain is managed at full flow capacity, with selenium concentrations like those in the Grassland Bypass 

Channel Project (18,700 lbs per six months). The 

forecasted range of particulate concentrations is 9.0 

to 30 μg/g under C1 and C2 speciation/transformation 

regimes. The latter concentration is more than seven 

times higher than the level at which toxicologic and 

reproductive effects are likely.

Under a C3 speciation/transformation regime, only loads 

in the range of the lowest load scenario (6,800 lbs per six 

months) would result in particulate selenium concentrations 

of <1.5 μg/g. If monthly forecasts are considered, values in 

the late fall months would be considerably higher than these 

six-month averages [compare waterborne selenium data trends 

presented on a monthly basis (figs. 19 and 20; appendix F, 

tables F1 and F2)].

Discharges of 6,800, 18,700, or 44,880 lbs per six months

released from a San Luis Drain extension into the Bay-Delta 

during the high flow season of a wet year results in exceedances of 4 μg/g only if a speciation/transformation regimes 

typical of suspended sediment (C1) characterize transformations (table 24). However, it should be recognized that the 

projected concentrations are averages over the six-month high 

flow period. Flows are especially variable during this period, 

so the actual period of lower concentrations will probably be 

shorter than six months. This is also the time period when 

particulates from the San Luis Drain extension are most likely 

to add to the selenium load in the estuary.

 Forecasts for a targeted load (3,500 lbs selenium per six 

months) using the San Joaquin River for conveyance show that 

(table 24):

during the low flow season, forecasted particulate selenium concentrations is in excess of 4.0 μg/g if specia-

•

•

•

•

tion/transformation regimes are typical of suspended 

sediment (C1), but not if a shallow-water sedimenttype transformation prevailed (C2).

during the high flow season of a wet year, forecasted 

particulate selenium concentrations remain below 1.5 

μg/g for all three speciation/transformation regimes 

considered. 

The forecast for a restoration scenario in the San Joaquin 

River shows that (table 24):

during the high flow season of a wet year, particulate 

selenium concentrations under all three speciation/

transformation regimes are similar to those that would 

occur during the targeted load scenario (below 1.5 

μg/g). 

during the low flow season in a critically dry year or a 

wet year, particulate selenium concentrations are less 

than those that would occur during a targeted load 

scenario and remain below 2.5 μg/g under all three speciation/transformation regimes. 

All San Luis Drain discharge scenarios predict particulate 

selenium concentrations greater than those forecast for prior 

to refinery cleanup (table 24). Particulate selenium concentrations lower than those modeled prior to refinery cleanup are 

predicted to occur: 

in the restoration scenario for the San Joaquin River in 

all modeled water year types and seasons; and 

in the San Joaquin River targeted load scenario during 

the high flow season of a wet year.

Cumulative summary

Progressive forecasts for the head of the estuary show 

selenium loads, waterborne selenium concentrations, and 

particulate selenium concentrations (table 25). Three alternative speciation/transformation regimes are illustrated 

[suspended sediment (C1); shallow-water sediment (C2); 

and inefficient transformation (C3)] for each endmember 

concentration. Load scenarios are 18,700 lbs released during 

six months through a San Luis Drain extension or of approximately 3,500 lbs released during six months through the 

San Joaquin River (see tables 19 through 21 for composite 

loads). The forecasts for prior to refinery cleanup are given for 

comparison. The forecasts highlight the importance of speciation/transformation regimes in determining particulate concentrations. Clearly, benefit would come from knowing these 

dissolved to particulate transformations with more certainty 

for the Bay-Delta. 

For a San Luis Drain load scenario of 18,700 lbs per six 

months (table 25), it is notable that exceedance of the USEPA 

waterborne criterion of 5 μg/L at the head of the estuary 

(composite freshwater endmember concentration) in the low 

flow season of a critically dry year is always accompanied by 

•

•

•

•

•
80 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

exceedance of a sediment guideline (4 μg/g) in which effects 

are a certainty, no matter what the selenium transformation. 

Also under this load scenario, the USFWS recommended 

waterborne criterion of 2.0 μg/L is exceeded for the low flow 

season of a wet year. For this same climate regime, at an inefficient selenium transformation (C3) and a composite freshwater endmember selenium concentration of 2.0 μg/L, particulate selenium concentrations would exceed a guideline with 

a high certainty of producing effects based on site-specific 

factors (1.5 μg/g, see previous discussion). At typical estuarine 

suspended and shallow-water sediment transformations (C2 

and C3), forecasted particulate selenium concentrations are 

> 4 μg/g. Even during high inflows in a wet year, a 4.0 μg/g 

guideline is exceeded if a Kd typical of October 1996 (Kd of 1 

× 104) occurs. 

For the San Joaquin River targeted load scenario of 

3,500 lbs per six months (table 25), composite freshwater 

endmember selenium concentrations remain below 1 μg/L. 

However, particulate selenium concentrations only remain 

below 1.5 μg/g for an inefficient speciation/transformation 

regime (C3) or during the high flow season of a wet year. 

During low flow seasons of both wet and dry years, particulate 

selenium concentrations exceed 1.5 μg/g, and in the case of 

a speciation/transformation regime for a productive estuarine 

system (C1), could exceed 4 μg/g. 

In summary, selenium loads, river inflows, speciation, 

and dissolved/particulate transformation rates are critical to 

determining particulate selenium concentrations and thus 

important determinants of the ecological effects of a discharge 

conveyed directly to the Bay-Delta. Most feasible San Luis 

Drain extension discharges during low flow periods result 

in concentrations of particulate selenium that have a high 

certainty of producing toxicologic and reproductive effects 

(see previous descriptions). This is especially true if the 

speciation/transformation regime conditions currently prevalent at present in the Bay-Delta (C2 and C3) are operable on 

proposed discharges from an extension of the San Luis Drain. 

Only during wet years and high flows is a 1.5 μg/g selenium 

particulate material guideline not exceeded, and then only 

when transformations are inefficient. Note also that this guideline was exceeded during conditions prior to refinery cleanup 

All forecast particulate selenium concentrations exceed those 

forecast for conditions prior to refinery cleanup, except under 

the targeted load San Joaquin River scenario during the high 

Table 24. Forecasts of selenium concentrations in particulate matter at the head of the estuary under projected selenium load 

scenarios, identified speciation/transformation regimes, and different climatic conditions. 

[C1 = Kd of 1×104, typical of suspended sediment; C2 = Kd of 3 × 103, typical of shallow-water bed sediment; C3 = Kd of 1 × 103, typical of inefficient 

transformation]

Scenario

Selenium concentrations in particulate material (μg/g dry weight)

Past San Luis Drain extension San Joaquin River

Prior to 

refinery 

cleanup

Half capacity 

at 50 μg/L

Full capacity 

at 62.5 μg/L

Full capacity 

at 150 μg/L

Full capacity 

at 300 μg/L

Targeted

Load

Restoration 

0.5 μg/L

Wet year/high flow

Load (lbs per six months) – 6,800 18,700 44,880 89,760 3,500 3,060

 C1 (1×104

) 2.2 2.8 5.1 10.2 18.8 1.2 1.1

 C2 (3×103

) 0.66 0.84 1.53 3.06 5.6 0.36 0.33

 C3 (1×103

) 0.22 0.28 0.51 1.02 1.88 0.12 0.11

Wet year/low flow

Load (lbs per six months) – 6,800 18,700 44,880 89,760 3,400 1,020

 C1 (1× 104) 3.9 12.1 29.9 69.7 138 5.7 2.3

 C2 (3×103

) 1.2 3.63 8.97 20.9 41.4 1.71 0.39

 C3 (1×103) 0.39 1.21 2.99 6.97 13.8 0.57 0.23

Critically dry year/low flow

Load (lbs per six months) – 6,800 18,700 44,880 89,760 3,400 381

 C1 (1×104

) 5.3 20.7 50.7 118.7 235 8.6 2.4

 C2 (3×103) 1.6 6.21 15.2 35.6 70.6 2.58 0.72

 C3 (1×103) 0.53 2.07 5.07 11.9 23.5 0.86 0.24
 81

will not be reactive in the Bay-Delta ecosystem. This 

minimal reactivity would require that (1) dissimilatory 

reduction to sedimentary Se(0) not occur in sediments or 

wetlands; and (2) selenate uptake by primary producers 

not take place. Biotransformation of selenium is, indeed, 

minimized in at least some flowing water (lotic or river/

stream) systems, compared to wetlands. However, there is 

no precedent in nature for a complete absence of selenium 

biotransformation to particulate concentrations. At least 

a Kd of 0.5 × 103 is usually seen, especially if residence 

times are sufficient. Thus, the argument of minimal reactivity is extremely unlikely as inflows recede seasonally, 

during low inflow years, and in wetlands and shallowwater environments of the system. 

Direct San Luis Drain discharge of suspended particulate selenium from an extension of the San Luis Drain.

Input of suspended particulate material containing elevated 

concentrations of selenium is likely from a San Luis Drain 

extension directly into the Bay-Delta. The San Luis Drain 

during its operation from 1981 to 1985 acted as a partial 

treatment facility by removing selenium from agricultural 

drainage and sequestering it in sediment and biotic material that had settled in the bottom of the drain (Presser and 

Piper, 1998). Sediments that are highly contaminated with 

selenium have accumulated in the San Luis Drain to date 

and are likely to continue to accumulate during its renewed 

use by the Grassland subarea to convey drainage to the 

San Joaquin River (USBR and others, 1998 and ongoing) 

(appendix E, tables E1 and E2). Selenium concentrations 

in San Luis Drain sediment have exceeded the hazardous 

selenium waste criterion for solids (100 μg/g, wet weight) 

at times in the past and almost all concentrations are 

above a sediment guideline (4 μg/g) in which effects are 

a certainty (see previous discussion). Re-suspension and 

at least some transport of those sediments during elevated 

flows seems a reasonable prediction should the San Luis 

Drain be extended to the Bay-Delta. For example, the San 

Luis Drain was briefly re-opened in early 1995 to relieve 

flooding in the western San Joaquin Valley and it acted 

as a conduit for discharges into Mud Slough and the San 

Joaquin River (Presser and Piper, 1998). Transport and 

dilution of such particles probably cannot be estimated 

with any reasonable certainty. However, the discharged 

particulate selenium would probably originate as primarily 

Se(0) and oxidation also would occur with longer residence times in suspension or in the water column. Source 

material also may include algal mats that could contain 

organo-Se [bioavailable Se(-II)]. The following conditions 

and calculations for direct discharge of suspended particulate selenium from a San Luis Drain extension are instructive, but speculative. They illustrate how even small inputs 

of existing contaminated San Luis Drain sediment could 

affect the Bay-Delta.

If a San Luis Drain extension inflow is 5 percent of 

river inflow to the Bay-Delta and suspended material

2.

a.

flow period of a wet year. The restoration scenario for the 

San Joaquin River results in forecasted particulate selenium 

concentrations lower than those forecasted for conditions in 

the Bay-Delta prior to refinery cleanup

Other possible scenarios

No reaction of Se(VI). If discharges of agricultural drainage increase, it is possible that the predominant dissolved 

form in that discharge will be Se(VI). On a purely geochemical basis, it might be asserted that dissolved Se(VI) 

1.

Table 25. Cumulative summary of forecasts of selenium 

concentrations in a composite freshwater endmember and 

particulate matter at the head of the estuary under projected 

selenium load scenarios, identified speciation/transformation 

regimes, and different climatic conditions.

Climatic

conditions

Composite 

fresh-water 

endmember 

selenium (μg/L)

Particulate selenium (μg/g dry weight)

C3 

(Kd=1×103

)

C2 

(Kd=3×103)

C1 

(Kd=1×104)

San Luis Drain extension load of 18,700 lbs per six months 

(full capacity at 62.5 μg/L selenium)

Wet Year/ 

High Flow

0.46 0.5 1.5 5.1

Wet Year/ 

Low Flow

3.0 3.0 9.0 30.0

Critically 

Dry Year/ 

Low Flow

5.1 5.1 15.2 50.7

San Joaquin River targeted load of 3,590 lbs per six months for a high 

flow season (1.2 μg/L selenium); 3,400 lbs per six months for a low flow 

season (2.5 μg/L selenium)

Wet Year/ 

High Flow 

0.12 0.12 0.36 1.2

Wet Year/ 

Low Flow 

0.57 0.57 1.71 5.7

Critically 

Dry Year/ 

Low Flow

0.86 0.86 2.58 8.6

Conditions prior to refinery cleanup

WetYear/

High Flow

0.22 0.22 0.66 2.2

Wet Year/

Low Flow

0.39 0.39 1.2 3.9

Critically 

Dry Year/ 

Low Flow

0.53 0.53 1.6 5.3
82 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

concentrations (amounts) are similar in both the 

Sacramento River and the San Luis Drain (based on 

relative inflows in a wet year at low flow). 

If an average particulate selenium concentration in 

the San Luis Drain particles is 100 μg/g and particulate selenium in the Sacramento inflows is 0.2 μg/g.

Then 5 percent of the particles in the Bay-Delta at 

the confluence of the two will be San Luis Drain 

particles and the selenium concentrations in the 

particle mixture will be: 

[(0.05 × 100 μg/g) + (0.95 × 0.2 μg/g)] = 5.19 μg/g 

from direct particulate input. 

During a critically dry year, particulate selenium 

concentrations would be twice this value. 

Particulate selenium transformed from the dissolved 

selenium inputs from a San Luis Drain extension 

would add to these concentrations; therefore this 

estimate is conservative in this respect. 

Local hotspots. Selenium concentration forecasts discussed above represents broad scale average concentrations that would result from mixing. This approach does 

not allow determining the spatial details of distributions. 

More sophisticated hydrodynamic models would be necessary to provide such detail (for example, Cheng and others, 

1993; Monsen, 2000; Monsen and others, 2002). However, 

hotspots of particulate selenium contamination could 

develop in an ecosystem subjected to direct San Luis Drain 

extension discharges. Most notably, wetlands close to the 

discharge of a San Luis Drain extension would be likely to 

accumulate high concentrations of selenium.

Forecasts of Bioaccumulation in Consumer 

Organisms (all values are dry weight 

concentrations)

Calculating bioaccumulation in a generic bivalve 

(modeling)

A range of biological values are used in the DYMBAM

model to calculate selenium concentrations in bivalves of the 

Bay-Delta (table 26). The model is for a generic bivalve (physiological constants are averages over a small range from several 

bivalve species, Reinfelder and others, 1997; Schlekat and 

others, 2000, 2002, 2004). Calculations specific to P. amurensis

and C. fluminea also could be made. Some data for these species 

recently are available (table 26). The common parameters for a 

generic bivalve used in the model are as follows:

Ingestion rate (or feeding rate) of 0.25 gram food/gram 

tissue per day (estimate for many bivalves based on review 

of literature in Luoma and others, 1992). 

b.

c.

d.

e.

3.

1.

Efflux rates (or rate constant of loss) of 0.02 per day (average of 0.01– 0.03 per day). 

Assimilation efficiencies (AE) of about 20 percent (low 

bioavailability) to 80 percent (high bioavailability) as a 

function of particle type (see below). 

Combining the above factors and a range of particle 

transformations that affect bioavailability, bivalve bioaccumulation is cast here in terms of assimilation efficiencies (AE in 

percent): 

Inefficient transformation: Particulate forms are 50 articulate forms are 50 

percent Se(0) of relatively low bioavailability, 40 percent oxidized material of moderate bioavailability, and 

10 percent organo-Se of high bioavailability. The AE 

derived from this mixture is 35 percent: 

AE1 (0.23 × 50%) + (0.4 × 40%) + 

 (0.79 ×10%) = 35%

Shallow-water estuarine sediments: Particulate forms 

are 60 percent of moderate bioavailability [detrital 

Se(-II) or particulate Se(IV) + (VI)]; and 40 percent in 

a form of high bioavailability (biotransformed organoSe). The AE derived from this mixture is 56 percent: 

AE2 (0.40 × 60%) + (0.79 × 40%) = 56%

Estuarine suspended material: Particulate forms 

include 60 percent biotransformed selenium of high 

bioavailability and 40 percent oxidized material of 

moderate bioavailability. The AE derived from this 

material is 63 percent: 

AE3 (0.79 × 60%) + (0.40 × 40%) = 63%

Estuarine suspended material—purely biogenic: 

A fourth AE (79 percent) also is included to take into 

account the possibility that all suspended particulate 

selenium in the estuary would derive from biogenic 

transformation to Se(-II). 

AE4 (0.79 × 100 %) = 79%

To complete the range of considered AE’s, a fifth AE 

is derived for all particulate material being of a form 

of low bioavailability, Se(0). The AE derived is 23 

percent: 

For range (0.23 × 100%) = 23%

Comparing model predictions to observed BayDelta conditions prior to refinery cleanup

Generic bivalve physiological parameters (table 26) and 

the DYMBAM model are used to forecast bioaccumulation 

of selenium in consumers organisms (prey) for a range of 

concentrations using two extremes of assimilation efficiency, 

80 percent (all biotransformed) and 20 percent (all elemental 

selenium) (table 27). The purpose of these calculations is to 

verify that use of the DYMBAM model bracketed reasonable 

predictions of selenium bioaccumulation in bivalves. The 

2.

3.

•

•

•

•

•
 83

range of particulate selenium concentrations used in the calculations spanned the concentrations of selenium determined in 

surveys of the brackish Bay-Delta (0.5 to 3.0 μg/g) and at the 

head of the Bay-Delta (0.5 to 8.0 μg/g). Three observations are 

of interest from forecasted bivalve concentrations during BayDelta conditions prior to refinery cleanup:

The forecasted concentrations of bioaccumulated 

selenium in bivalves span the exact range of selenium 

concentrations found in bivalves in this system (figs. 

13 through 15). Thus, the independently derived physiological constants, when used with environmental 

values collected through field studies, bound bioaccumulation with reasonable accuracy (results similar to 

those reported by Luoma and others, 1992; and Wang 

and others, 1996). 

A fourfold difference in bioaccumulation in bivalves 

would be expected if the particulate form of selenium 

changed. At the same concentration of particulate 

selenium, bivalves would bioaccumulate four-times 

more selenium from the biotransformed particulate 

selenium than from elemental selenium. Although this 

bioaccumulation is significant, the effect is relatively 

small compared to the effects of changing the mass of 

selenium in the load. 

The field validation results verify that the DYMBAM 

model will be useful in forecasting the range of consumer organism bioaccumulation under different input 

scenarios for selenium. 

•

•

•

Bivalves as food for predators

The most sensitive response of ecosystems to selenium 

occurs in higher trophic level predators (such as birds and fish) 

(Ohlendorf, 1989; Hamilton and others, 1990, 2005a, b, c, d; 

Lemly, 1996b, c; Skorupa, 1998a). Effects on predators (see 

reviews in Lemly, 1998b; Skorupa, 1998a; Hamilton, 2003 and 

2004; Ohlendorf, 2003) have been defined based on:

selenium concentrations in their food 

effects on predators themselves expressed as selenium 

residues in tissue.

Bivalves (clams) are an important food source for the 

predators of interest in the present evaluation. Therefore, one 

type of guideline for bivalve tissues should be based on their 

use as a food source for fish and birds. The guidelines for 

food webs show the narrow difference between concentrations 

considered safe and those considered harmful. Marginal risk 

levels, which are between levels considered safe (no effect) 

and those considered harmful (substantive risk) are intended to 

provide protection for the environment in that they are based on 

data for sensitive endpoints and species. Guidelines for predators based on selenium in food are (also see tables 13 and 15):

3 – 7 μg/g in food = Level of concern range. Selenium 

concentrations in predator food (invertebrate tissues) 

within this range are a concern for development and 

survival, especially for sensitive lifeforms of sensitive 

species (tables 13 and 15). Reviews and studies by 

Lemly (1993b, 1997b, and 2002) and Hamilton (2004) 

document a 2 to 5 μg/g selenium in diet in the field as a 

hazard. Ohlendorf (2003) reported a hatchability effect 

•

•

•

Table 26. Laboratory-derived physiological constants for selenium bioaccumulation by several species of 

bivalve and composite values for a generic bivalve.

[Data from Luoma and others, 1992; Reinfelder and others, 1997.]

Species Ingestion rate

(grams food/ grams 

tissue/day)

Assimilation 

efficiency (AE) 

(%)

Rate constant of 

loss (ke) (per day)

Assimilation 

efficiency/rate of 

loss (AE/ ke)

Oyster (Crassostrea virginia) – 70 ± 6 0.07 ± 0.0008 10

Clam (M. balthica) 0.25 80 ±7 0.03 ± 0.001 26.7

Clam (Mercenaria mercenaria) – 92 ± 2 0.01 ± 0.004 92.0

Mussel (M. edulis) 0.27 74 ± 8 0.02 ± 0.007 37.0

Generic bivalve 

(from diatom)

0.2 79 0.02 39.5

Generic bivalve 

(from sorbed selenium)

0.2 40 0.02 20

Generic bivalve 

(from elemental selenium)

0.2 23 0.02 11.5
84 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

level of 10 percent in mallards at 4.87 μg/g selenium 

(confidence interval 3.56 to 5.74 μg/g) in diet based on 

a compilation of laboratory studies. Mortality (a less 

sensitive endpoint) in juvenile bluegill occurred when 

they were fed a diet of 5.2 μg/g during simulated winter-stress conditions in the laboratory (38 percent effect 

level) (Lemly, 1993b). 

10 μg/g in food = Effects on predators a certainty.

Selenium concentrations in predator food above 10 μg/g 

have been conclusively implicated in adverse effects 

on reproduction in predators (Saiki, 1986; Hodson and 

Hilton, 1983; Johns and others, 1988; Heinz and others, 

1989; Coyle and others, 1993; Lemly, 1985, 1993a, c, 

1997b; Hamilton and others, 1990, 2000b; Heinz, 1996; 

Adams and others, 1998; Linville and others, 2002; 

Hamilton, 2003 and 2004) (also see tables 13 and 15). 

For example, Heinz and others (1989) produced a 43 

percent reduction in healthy ducklings in laboratory 

feeding studies with mallards using a diet of 8 μg/g 

(seleno-methionine). Although these studies suggest 

effects begin at lower concentrations, 10 μg/g is considered here as a value of least uncertainty. When invertebrate tissues exceed 10 μg/g the expectation is strong 

that adverse effects are occurring in birds and fish.

•

15– 20 μg/g in food = Observed conditions that coincide with extinction of some fish species and failure 

to produce healthy young birds. This is the range 

of annual maximum concentrations of selenium in P. 

amurensis observed between 1995 and 1996 near Carquinez Strait in Suisun Bay (figs. 13 through 15). This 

range of selenium concentrations in diets of fish are 

linked to reproductive and survival effects (Skorupa, 

1998a; Lemly, 2002; Hamilton, 2003 and 2004) (tables 

13 and 15). Mallards fed a diet (seleno-methionine) 

of 16 μg/g failed to produce any healthy young birds 

(Heinz and others, 1989). Levels of 30 to 35 μg/g 

(seleno-methionine) caused total reproductive failure 

(catastrophic impairment) in adult bluegill (Woock and 

others, 1987; Coyle and others, 1993). 

40 μg/g in food = Extinction of numerous fish species. In field studies, all but the most tolerant populations of fish species were eliminated when selenium 

concentrations in invertebrates reach 40 to 100 

μg/g (Lemly, 1985, 1993a, 1997c, 2002; Saiki, 1986; 

Saiki and Lowe, 1987; Presser and Ohlendorf, 1987; 

Skorupa, 1998a). Heinz and Fitzgerald (1993) found 

a 95 percent mortality rate when adult male mallards were fed a 40 μg/g diet (2 percent moisture) and 

subjected to winter stress, whereas Albers and others 

(1996) and Hoffman and others (1991) reported less 

mortality at approximately the same or a somewhat 

less concentrated diet in the absence of winter temperatures. Thus, values >40 μg/g might be defined as 

invertebrate tissue selenium concentrations where risks 

of extinction of multiple fish species are high. 

100 μg/g in food = Widespread invertebrate toxicity. 

Although large-scale invertebrate toxicity is probably 

not the most sensitive response to selenium, it could be 

an additional outcome of extreme selenium contamination. Rarely are invertebrates found in ecosystems 

where selenium concentrations in invertebrates are > 

150 μg/g (Lemly, 1993a, 1997c; Saiki and Lowe, 1987). 

For the sake of discussion, 100 μg/g is assumed as the 

level of outright, broad scale invertebrate toxicity.

As previously noted for sediment selenium guidelines, 

these guidelines for predators based on selenium in food may 

not be, individually, realistic indications of ecological risk, but 

are used in this report as reference points for context. Again, 

the intent in the approach presented here, is to consider several 

lines of evidence to reduce uncertainty.

Forecasts of generic bivalve selenium 

concentrations (contamination of prey)

Details of load scenarios and calculation of generic 

bivalve selenium concentrations are shown for both the head 

of the estuary and Carquinez Strait in appendix F, tables F6 to 

F9. Table 28 summarizes projected concentrations in particu-

•

•

•

Table 27. Modeled selenium concentrations in a generic bivalve 

when exposed to different concentrations of particulate organoselenium or particulate elemental selenium. 

[Data from Luoma and others, 1992 and Reinfelder and others, 1997. 

Measured particulate selenium concentrations range from 0.5 to 3 μg/g dry 

weight in brackish water of the Bay-Delta and 0.5 to 8 μg/g dry weight at 

the head of the estuary (Cutter, 1989; Cutter and Cutter, 2004).]

Particulate 

selenium 

concentration 

(μg/g dry wt) 

Absorption

efficiency (AE) 

(%)

Rate constant 

of loss (ke) 

(per day)

Tissue selenium 

concentration 

at steady state 

(μg/g dry wt) 

Exposure: particulate organo-selenium

0.5 0.8 0.02 4.0

1.0 0.8 0.02 8.0

1.5 0.8 0.02 12.0

2.0 0.8 0.02 16.0

3.0 0.8 0.02 24.0

Exposure: particulate elemental selenium

0.5 0.2 0.02 1.0

1.0 0.2 0.02 2.0

2.0 0.2 0.02 4.0

3.0 0.2 0.02 6.0

4.0 0.2 0.02 8.0

5.0 0.2 0.02 10.0

8.0 0.2 0.02 16.0
 85

late material and generic bivalve tissue for four combinations 

of speciation/transformation regimes and generic bivalve 

assimilation efficienties (C1/AE4, C1/AE3, C2/AE2, C3/

AE1). Forecasts are for three load scenarios (6,800; 18,700; 

and 44,880 lbs selenium per six months) using a San Luis 

Drain extension and for a San Joaquin River discharge of a 

targeted load of 3,500 lbs selenium per six months under three 

different climate regimes. Also included for comparison are 

forecasted concentrations during Bay-Delta conditions prior to 

refinery cleanup 

Contamination of prey would be sufficient to cause widespread extinction of fish species (>40 μg/g selenium in food) 

during the low flow season of any year, but especially in critically dry years (table 28), if selenium transformations occur at 

a Kd of 3 × 103 or higher (C1 and C2) and: 

a proposed San Luis Drain extension discharges at 

300 ft3/s, even if management succeeds in limiting 

concentrations to 62.5 μg/L (44,880 to 18,700 lbs per 

six months). Some of these scenarios also could cause 

widespread elimination of invertebrates in addition to 

predicted effects on predators (>100 μg/g in food). 

a proposed San Luis Drain extension discharges at 150 

ft3/s (half capacity) with a drainage concentration of 50 

μg/L (6,800 lbs per six months); and transformations 

and assimilations are for suspended sediment (C1/AE3 

or C1/AE4).

In low flow seasons with a discharge of 18,700 lbs per 

six months through a San Luis Drain extension, an inefficient 

C3/AE1 speciation/transformation regime results in forecasted 

selenium concentrations in bivalves of 8.7 to 15 μg/g. In low 

flow seasons with a discharge of 6,800 lbs per six months 

through a San Luis Drain extension, a C2/AE2 speciation/

transformation regime results in forecasted selenium concentrations in bivalves of 17 to 28 μg/g. In low flow seasons 

with a discharge of 3,500 lbs per six months through the San 

Joaquin River, a C2/AE2 shallow-water regime results in forecasted bivalve concentrations of 7.8 to 12 μg/g. 

Lower selenium concentrations (<10 μg/g) in bivalves are 

forecasted under certain conditions (table 28):

3.5 to 6.1 μg/g: in the low flow season of both wet 

and critically dry years, a proposed San Luis Drain 

extension discharges 50 μg/L drainage at half capacity 

(6,800 lbs per six months); and selenium transformation and assimilations are inefficient (C3/AE1). 

1.7 to 2.5 μg/g: in the low flow season of both wet and 

dry years, the San Joaquin River discharges 3,500 lbs 

per six months; and selenium transformation is the 

lowest found in any of the receiving waters previously 

studied; and assimilation is inefficient (C3/AE1). 

3.9 to 0.4 μg/g: in the high flow season of wet years, a 

drain extension discharges of 6,800 lbs per six months 

or the San Joaquin River discharges 3,500 lbs per six 

•

•

•

•

•

months; and transformations are that of shallow-water 

sediment or are inefficient (C2/AE2 and C3/AE1).

6.3 to 8 μg/g: in the high flow season of wet years, the 

San Joaquin River discharges 3,500 lbs per six months; 

and transformations and assimilations are efficient 

(C1/AE3 or C1/AE4). 

In general, San Luis Drain discharges that would meet 

demands for drainage pose risks to fish and bird reproduction 

and the risk of fish extinction from contamination of their 

invertebrate food (table 28). If biogeochemical conditions 

such as those that exist today in the Bay-Delta predominate 

during projected discharges, low flow periods would be a time 

of extreme risk for fish and bird species, especially those that 

include bivalves among their prey. Some low flow conditions include forecasts where extreme risks might be somewhat reduced. Most of those conditions are of low likelihood 

(transformations that result in a Kd of 103) in that such low 

Kd's are not typical of the Bay-Delta. Similarly, a targeted load 

scenario for the San Joaquin River results in prey containing 

<10 μg/g only if transformation and assimilation are inefficient (C3/AE1) during low flow seasons. At other combinations of transformations and assimilations (C2/AE2, C1/AE3 

or C1/AE4) during low flow seasons, concentrations in prey 

approach (8.7 μg/g) or exceed 10 μg/g (12 to 38 μg/g). 

Selenium loads from 6,800 to 18,700 lbs per six months, 

if released during the highest flows, would result in selenium concentrations in bivalves that have a high certainty of 

producing adverse effects (10 μg/g) only if the most efficient 

speciation/transformation regime (C1) were observed (that 

is, if the particulate selenium turns out to be as reactive as 

observed during longer residence times than usually occurs 

at high inflows). Thus, releases during high flows carry less 

risk for fish extinctions. However, it is important that releases 

during high flows be studied carefully before it is concluded 

that they lower risks. The fate of selenium that enters the 

Bay-Delta estuary during high inflows is not fully known. 

For example, it is not known how much is retained and reacts 

during subsequent low flow periods or how much is transported to the South Bay during high flows and subsequently 

retained (Conomos and others, 1979, 1985; Nichols and 

others, 1986; Peterson and others, 1989). Also during high 

inflows, highly contaminated particulate material from either 

the San Joaquin River or the San Luis Drain is most likely to 

add to the selenium load in the estuary (although, at present, 

suspended particulates are not typically highly contaminated 

during high inflows).

For comparison, forecasted selenium concentrations in 

bivalves during conditions in the Bay-Delta prior to refinery 

cleanup are (a) above the 40 μg/g extinction guideline during 

the low flow season of a critically dry year at a combination of 

inefficient transformation and high assimilation efficiency (C3/

AE4); and (b) above the 10 μg/g guideline where effects are 

a certainty at a combination of moderate transformation and 

assimilation efficiency for shallow-water sediments (C2/AE2). 

During the low flow season of a wet year, 10 μg/g is exceeded 

•
86 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

at two combinations of efficient transformation and assimilation efficiency (C1/AE3 and C1/AE4). Even during high flows 

in wet years, this high reactivity produces prey with selenium 

concentrations > 10 μg/g. 

Effects on predators based on selenium 

concentrations in food

Two scenarios, one for a San Luis Drain extension load of 

18,700 lbs selenium per six months and one for a San Joaquin 

River targeted load of approximately 3,500 lbs per six months, 

are taken forward to progressively link uptake by bivalves and 

effects on predators (table 29). Forecasts are shown for three 

climate regimes and for three combinations of transformations 

and assimilation efficiencies previously illustrated (C1/AE3, 

C2/AE2, and C3/AE1). This cumulative summary shows 

waterborne, particulate, and bivalve selenium concentrations 

at the head of the estuary (composite freshwater endmember 

concentration). Forecasted invertebrate selenium bioaccumulation is compared to guidelines for effects on fish and birds 

from contaminated food. In the case presented here, clams are 

assumed to constitute that food. 

Forecasts for a San Luis Drain extension scenario of 

18,700 lbs selenium per six months show that (table 29): 

Selenium concentrations at the head of the estuary 

are projected to reach the USEPA criterion of 5 μg/L, 

on average, during the low flow season of a critically 

dry year. At the level of this criterion, effects on fish 

•

Table 28. Summary of forecasts of selenium concentrations in a generic bivalve at the head of the 

estuary under projected selenium load scenarios, identified speciation/transformation regimes, bivalve 

assimilation efficiencies (AE’s), and different climatic conditions. 

[C1 = Kd of 1×104, typical of suspended sediment; C2 = Kd of 3 × 103, typical of shallow-water bed sediment; C3 = Kd of 1 

× 103, typical of inefficient transformation. AE4 = 0.8; AE3 = 0.63; AE2 = 0.55; and AE1 = 0.35.]

Scenario

Particulate selenium/bivalve selenium (μg/g dry weight)

Past San Luis Drain extension San Joaquin R.

Prior to refinery 

cleanup

Half capacity at 

50 μg/L

Full capacity 

at 62.5 μg/L

Full capacity 

at 150 μg/L Targeted load

Wet year during high flow season

 Load 

(lbs per six 

months)

– 6,800 18,700 44,880 3,500

 C1 and AE4 2.2/22 2.8/19 5.1/34 10/68 1.2/8.0

 C1 and AE3 2.2/17 2.8/15 5.1/27 10/54 1.2/6.3

 C2 and AE2 0.66/4.5 0.84/3.9 1.5/7.0 3.1/14 0.36/1.7

 C3 and AE1 0.22/0.96 0.28/0.8 0.5/1.5 1.0/3.0 0.12/0.4

Wet year during low flow season

 Load

(lbs per six 

months)

– 6,800 18,700 44,880 3,400

 C1 and AE4 3.9/39 12/81 30/199 70/465 5.7/38

 C1 and AE3 3.9/31 12/64 30/157 70/366 5.7/30

 C2 and AE2 1.2/8.0 3.6/17 9.0/41 21/96 1.7/7.8

 C3 and AE1 0.39/1.7 1.2/3.5 3.0/8.7 7.0/20 0.57/1.7

Critically dry year during low flow season

 Load

(lbs per six 

months)

– 6,800 18,700 44,880 3,400

 C1 and AE4 5.3/53 21/138 51/338 119/793 8.6/57

 C1 and AE3 5.3/42 21/109 51/266 119/625 8.6/45

 C2 and AE2 1.6/11 6.2/28 15/70 36/163 2.6/12

 C3 and AE1 0.53/2.3 2.1/6.1 5.1/15 12/35 0.9/2.5
 87

(predator) populations from selenium contaminated 

food (15 to 266 μg/g) would be expected, no matter 

what the efficiency of the transformation or assimilation for selenium in the food web (concentrations posing a serious risk would be reached under all feasible 

biogeochemical conditions).

Selenium concentrations at the head of the estuary are 

projected to fall between the USEPA criterion and the 

USFWS recommended criterion of 2 μg/L in the low 

flow season of a wet year. Bioaccumulation would 

not produce 10 μg/g in food under these conditions if 

selenium is inefficiently transformed and assimilated. 

However, at a typical estuarine Kd, bioaccumulation in 

bivalves would result in exceedance of both the 10 μg/

g dietary guideline where effects are a certainty and a 

40 μg/g extinction guideline, thus threatening an array 

of fish and birds in the estuary. So, in the most likely 

circumstances (those with precedent in the estuary) 

significant risk exists. 

Even during high inflows (high flow season in a wet 

year), effects on predators are expected if a Kd typical 

of October 1996 (C2) occurs. So risk is reduced, but 

risk of harm (to fish and birds) is not eliminated during 

this period.

In summary, under a loading scenario of 18,700 lbs selenium per six months, San Luis Drain discharges usually result 

in forecasted selenium concentrations in water, particulate 

matter, and prey (bivalve) that exceed guidelines with a high 

certainty of producing adverse effects during the six months or 

more of each year when river inflows are reduced (table 29). 

This condition is the most likely if a transformation prevalent 

at present in the Bay-Delta is operable in the future. Biogeochemical transformation rates and assimilation efficiencies are 

critical determinants of the degree of contamination in food of 

predators in the Bay-Delta and these factors need to be better 

understood. 

The projection for the San Joaquin River targeted scenario 

(about 3,500 lbs selenium per six months) shows that (table 29): 

Under the most likely biogeochemical conditions 

(speciation/transformation regime C2) risks to predators are greatly reduced compared to San Luis Drain 

discharge scenarios. Invertebrate concentrations of 

selenium would exceed the 10 μg/g dietary guideline 

where effects are a high certainty in critically dry 

years. In the low season of a wet year, concentrations in clams still reach 7.8 μg/g, a level with a high 

certainty of affecting sensitive species. Risk at this or 

at inefficient transformation (C3) would be reduced in 

intensity compared to prior to refinery cleanup, based 

on contamination of bivalve prey. 

If Kd's are like those often observed for suspended 

material in the Bay-Delta, contamination of food 

would be sufficient to indicate a high risk of toxicity 

•

•

•

•

(>10 μg/g ) and fish extinctions (>40 μg/g) during the 

low flow season of both wet and critically dry years. 

Under these same conditions in a high flow season of 

a wet year, selenium concentrations in clams would 

reach 6.3 μg/g. 

These forecasts show that the risk of conditions that are 

ecologically inconsistent with restoration cannot be eliminated, even under this most carefully managed condition. 

Forecast of Selenium Concentrations in 

Tissues of Predators (all values are dry weight 

concentrations)

Choice of predators

Forecasts of selenium concentrations in tissue that would 

result from different selenium loads scenarios are developed 

for white sturgeon, surf scoter, and scaup (greater and lesser). 

Three reasons for this choice of species are:

These are the species for which the most data is available for the Bay-Delta (the Selenium Verification 

Study: White and others, 1987, 1988, 1989; Urquhart 

and Regalado, 1991), and these data remain the best 

available data on predators. 

These are the upper trophic level species that bioaccumulate the most selenium, and thus seem to receive the 

highest internal exposure. Changes in selenium exposures in the Bay-Delta food web should have the greatest 

effect on concentrations of selenium in these species. 

The fish and birds with the greatest selenium bioaccumulation in the Bay-Delta are also likely to be the most 

at risk for adverse effects. Observations from other 

systems show that fish with the highest bioaccumulated 

concentrations of selenium are the first to disappear 

from contaminated reservoirs (Lemly, 1995, 1996a). 

Relation of selenium concentrations in bivalves 

to selenium concentrations in predators

As discussed previously, pharmacokinetic models are 

the optimal approach for forecasting how changes in selenium concentration or form might affect bioaccumulation by 

predators. Unfortunately, such models are not available for 

predators relevant to the Bay-Delta. An alternative approach is 

to statistically link predator tissue concentration to bioaccumulation by prey (food)(table 12; figs. 16 and 17). Urquhart and 

Regalado (1991) determined selenium in white sturgeon, surf 

scoter, greater scaup, and lesser scaup at a number of times 

and locations when they or others also determined selenium 

in bivalves (tables 30 and 31). The bivalve C. fluminea was 

collected from 1987 to 1990 in Suisun Bay (White and others 

1987, 1988, 1989; Urquhart and Regalado, 1991). Johns and 

•

•

•
88 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

correlation remains strong. The 1990 concentrations in C. 

fluminea are not as strongly correlated with the predators as in 

other years , but P. amurensis was the predominant benthos in 

1990 in both San Pablo Bay and Suisun Bay. 

Regression equations developed from data in tables 

30 and 31 are used to forecast selenium concentrations in 

predators under different load scenarios and climate regimes 

employed previously. In table 30, the average bivalve selenium 

concentration was matched to the average tissue selenium 

concentration for white sturgeon, surf scoter, greater scaup, 

and lesser scaup. Table 31 represents a further regression of 

the data. In this regression, the average for all bivalves for 

each year of data for North Bay or Humboldt Bay is regressed 

for a specific predator. It is recognized that the uncertainty in 

this calculation is substantial because of a linear extrapolation 

from a small set of available data. Nevertheless, the calculation adds an important and highly relevant perspective to the 

forecasts presented earlier. Once these selenium concentrations are forecasted they can be compared to known adverse 

effects guidelines for selenium concentrations in tissues of 

others (1988) also collected C. fluminea from Suisun Bay in 

1986. The bivalve Mya arenaria was collected from Humboldt 

Bay and from San Pablo Bay in 1988 (Urquhart and Regalado, 

1991). P. amurensis invaded North Bay initially in 1986, and 

by the late 1980s was established as the dominant bivalve in the 

ecosystem. No data for selenium concentrations in P. amurensis

were collected until 1995; but, average selenium concentrations from 1995 through 1996 in this species might be used to 

estimate concentrations in 1990 (Linville and others, 2002). 

The bivalves discussed above are assumed here as a 

major food source for surf scoter, greater scaup, lesser scaup, 

and white sturgeon during the period 1986 to 1990. Figure 

25 shows relations between bivalve selenium concentrations 

and selenium in the livers and flesh of these predators. Each 

data point represents data from a common year and common 

location (table 30). Average selenium concentrations in the 

liver and flesh of white sturgeon, surf scoter, greater scaup, 

and lesser scaup are significantly and strongly correlated 

with average selenium concentrations in bivalves. If data for 

P. amurensis are used to match the predator data in 1990, the 

Table 29. Cumulative summary of forecasts of selenium concentrations in a composite freshwater endmember, particulate material, 

and a generic bivalve at the head of the estuary under projected selenium load scenarios, identified speciation/transformation 

regimes, bivalve assimilation efficiencies (AE’s), and different climatic conditions.

[C1 = Kd of 1×104, typical of suspended sediment; C2 = Kd of 3 × 103, typical of shallow-water bed sediment; and C3 = Kd of 1 × 103, typical of inefficient 

transformation. AE1 = 0.35; AE2 = 0.55; and AE3 = 0.63.]

Climatic conditions

Composite freshwater 

endmember selenium 

(μg/L)

Particulate selenium/bivalve selenium (μg/g dry 

weight) C3 and AE1

Particulate selenium/bivalve selenium (μg/g dry 

weight) C2 and AE2

Particulate selenium/bivalve selenium (μg/g dry 

weight) C1 and AE3

San Luis Drain extension load of 18,700 lbs per six months (full capacity, 62.5 μg/L selenium)

Wet year during high flow 

season

0.5 0.5/1.5 1.5/7 5.1/27

Wet year during low flow 

season

3.0 3.0/9 9.0/41 30/157

Critically dry year during 

low flow season

5.1 5.1/15 15.2/70 51/266

San Joaquin R. targeted load (3,590 lbs per six months for a high flow season, 1.2 μg/L selenium; 3,400 lbs per six months for a low flow season, 

2.5 μg/L selenium)

Wet year during high flow 

season

0.12 0.12/0.4 0.36/1.7 1.2/6.3

Wet year during low flow 

season

0.57 0.57/1.7 1.7/7.8 5.7/30

Critically dry year during 

low flow season

0.86 0.86/2.5 2.6/12 8.6/45

Conditions prior to refinery cleanup

Wet year during high flow 

season

0.22 0.22/0.96 0.66/4.5 2.2/17

Wet year during low flow 

season

0.39 0.39/1.7 1.2/8.0 3.9/31

Critically dry year during 

low flow season

0.53 0.53/2.3 1.6/11 5.3/42
 89

birds and fish (see previous discussion and tables 14 and 15). 

This line of evidence is a second demonstration, in addition to 

concentrations in food, of how selenium might affect predators 

in the system. 

Forecasts of selenium concentrations in 

predators

A range of hepatic (liver) concentrations of selenium in 

white sturgeon, surf scoter, greater scaup, and lesser scaup 

result from regression with bioaccumulated selenium in 

bivalves (table 32) . Two possible selenium load scenarios 

(18,700 lbs per six months for a San Luis Drain extension 

discharge and approximately 3,500 lbs selenium per six 

months for a targeted San Joaquin River discharge) are illustrated. The forecasts are for the low flow season of a critically 

dry year, which is the most relevant time period for Bay-Delta 

migratory predators (see discussion below). The forecasts 

include consideration of three possible combinations of 

speciation/transformation regimes and generic bivalve assimilation efficiencies (C1/AE3, C2/AE2, and C3/AE1). A range 

of concentrations in liver tissue (10 to 18 μg/g) associated with 

adverse effects on reproduction in birds and fish (tables 14 and 

15) can be applied to forecasted concentrations. As previously 

noted for sediment and dietary selenium guidelines, these 

guidelines for predators based on tissue may not be, individually, realistic indications of ecological risk, but are used in this 

report as reference points to provide context. 

White sturgeon, surf scoter, greater scaup, and lesser 

scaup are all in the estuary during the fall and early winter, 

when selenium concentrations rise to their highest concentrations in bivalves. White sturgeon generally migrate to freshwater in March to breed; the migratory waterfowl move north 

for the same purpose shortly thereafter. A lag occurs in the 

decline of selenium concentrations in bivalves in response to 

higher river inflows, so in most years that have been studied, 

elevated selenium concentrations in bivalves extend into 

February or March. A further lag is expected in the response 

of predators to changing selenium concentrations in their 

food. Thus, the burdens of selenium these migratory predators would carry as they leave the Bay-Delta would probably 

be reasonably close to those forecasted in table 32. The low 

flow condition forecasts may depict the high-end of risk to 

these animals, but that is an ecologically reasonable expectation of exposure. 

Selenium concentrations in tissues of predators are well 

above adverse effects guidelines (even when full latitude is 

given for uncertainties about linkages between tissue concentrations and effects) when a load of 18,700 lbs selenium per 

six months is released from a San Luis Drain extension during 

the low flow season of a critically dry year. There is no condition when a San Luis Drain extension carrying such loads 

would not greatly threaten these species. The San Joaquin 

River targeted load of approximately 3,500 lbs per six 

months also threatens these species if partitioning of selenium 

follows the suspended sediment or shallow-water sediment 

partitioning observed in the past. If partitioning to particulate selenium follows a Kd typical of estuarine shallow-water 

sediment, bivalve bioaccumulation is forecasted as similar 

to that which probably existed prior to refinery cleanup The 

resultant forecast of risk is thus similar to that forecasted to 

exist prior to cleanup This forecast is another line of evidence 

that the targeted load of 3,500 lbs selenium per six months, 

if conveyed to the Bay-Delta by the San Joaquin River, would 

0

0

100

200

300

4 8 12

Selenium in scoter liver,

in micrograms per gram dry weight

0

0

5

10

15

20

4 8 12

Selenium in sturgeon flesh,

in micrograms per gram dry weight

0

0

10

20

30

40

4 8 12

P. amurensis

P. amurensis

P. amurensis

Selenium in bivalves, in micrograms per gram dry weight

Selenium in sturgeon liver,

in micrograms per gram dry weight

a

b

c

Figure 25. Observed selenium concentrations in (a) surf scoter 

liver, (b) white sturgeon flesh, and (c) white sturgeon liver as a 

function of bivalve selenium concentrations. (Data from California 

Department of Fish and Game Selenium Verification Study, White 

and others, 1987; 1988; 1989; Urquhart and Regalado, 1991).
90 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

have the ecological effect of replacing the selenium load scheduled for removal through treatment by oil refiners by 1998.

Ecological Risk

Cumulative Effects on the Bay-Delta

Some uncertainty characterizes transformations and 

other aspects of the analysis given above. However, enough is 

known about the biogeochemistry and biotransfer of selenium 

that, using multiple lines of evidence, relevant conditions and 

outcomes can be bracketed for the Bay-Delta. It is useful to 

consider four levels of certainty when developing a statement 

of risk for selenium:

The greatest certainty occurs if waterborne, particulate, 

bioaccumulation, and predator lines of evidence are 

accompanied by direct observations of toxicity, teratogenesis, or reproductive impairment.

A strong level of certainty is possible if data are available from all links in the chain of processes, but no 

observations of effects are available. 

Moderate certainty results if more than one line of 

evidence from a chain of evidence is available.

•

•

•

Table 30. Regression and curve-fit data (correlation coefficient, slope, and y-intercept) for two species of bivalve 

and three bivalve predators. 

[Data sources: White and others, 1987, 1988, 1989; Urquhart and Regalado, 1991; Johns and others, 1988; Linville and others, 2002.]

Average selenium (μg/g dry weight)

Bivalves Surf scoter 

(flesh)

Surf scoter 

(liver)

Greater or lesser 

scaup (flesh)

Greater or lesser 

scaup (liver)

White sturgeon 

(flesh)

White sturgeon 

(liver)

Bivalves = Corbicula fluminea

4.8 12.5 92.8 7.1 25.8 7.81 9.20

2.77 12.5 92.8 7.1 25.8 7.81 9.20

2.2 4.0 15.5 3.9 9.7 – – 

5.13 21.3 137 12.0 29.1 9.84 – 

2.01 3.0 12.5 6.57 13.57 – – 

5.73 37.8 228 23.93 65.12 7.47 – 

6.87 51.8 263 – – 12.38 14.19

7.90 35.8 174 – – 16.81 35.50

Correlation R2

 = 0.77 R2 = 0.74 R2 = 0.59 R2 = 0.64 R2 = 0.66 R2 = 0.62

Slope 7.12 36.06 3.42 9.63 1.68 4.33

Intercept – 10.98 – 41.57 -2.80 -8.14 1.04 – 7.15

Bivalves = Potamocorbula amurensis 

4.8 – 92.8 – – – 9.2

2.77 – 92.8 – – – 9.2

2.20 – 15.5 – – – – 

5.13 – 137 – – – – 

2.01 – 12.5 – – – – 

6.87 – – – – – 14.19

11.63 – 228 – – – 35.5

11.63 – 263 – – – – 

11.63 – 174 – – – – 

Correlation – R2 = 0.86 – – – R2 = 0.91

Slope – 19.28 – – – 3.15

Intercept – – 2.35 – – – – 3.50
 91

Table 31. Data employed in regression of bivalve selenium concentrations and bivalve predator selenium concentrations.

[Means from different years are aggregated. Bivalves are from different species (Corbicula fluminea; Mya arenaria; Macoma balthica; and 

Potamocorbula amurensis) and different studies (White and others, 1987, 1988, 1989; Urquhart and Regalado, 1991; Johns and others, 1988; 

Linville and others, 2002).]

Average selenium (μg/g dry weight)

Date Bivalves Surf scoter 

(flesh)

Surf scoter 

(liver)

Greater or lesser 

scaup (flesh)

Greater or lesser 

scaup (liver)

White sturgeon 

(flesh)

White sturgeon 

(liver)

North Bay (Suisun Bay and San Pablo Bay)

1986 4.8 12.5 92.8 7.1 25.8 7.81 9.20

1987 5.13 21.3 137 12.0 29.1 9.84 – 

1988 5.73 37.8 228 23.9 65.1 7.47 – 

1989 6.9 51.8 264 – – 12.4 14.2

1990 7.9 35.8 174 – – 16.8 35.5

1995– 96 11.6 35.8 174 – – 16.8 35.5

Humboldt Bay

1986 2.2 4.0 15.5 3.9 9.7 – – 

1988 2.0 3.0 12.5 6.57 13.6 – – 

Table 32. Measured selenium concentrations in clams (C. fluminea, 1988 to 1990; P. amurensis, 1995 to 1996), scoter, scaup, and 

sturgeon (1988 to 1990); and a summary of forecasts of selenium concentrations in a generic bivalve, scoter, scaup, and sturgeon 

at the head of the estuary under two projected selenium load scenarios, identified speciation/transformation regimes, and bivalve 

assimilation efficiencies (AE’s) for the low flow season of a critically dry year.

[Forecasted predator liver concentrations are predicted by extrapolation from regressions between bivalve and predator concentrations using data from 1986 to 

1990 (tables 30 and 31). C1 = Kd of 1×104, typical of suspended sediment; C2 = Kd of 3 × 103, typical of shallow-water bed sediment; and C3 = Kd of 1 × 103, 

typical of inefficient transformation. AE1 = 0.35; AE2 = 0.55; and AE3 = 0.63]

Critically dry year, low flow season

Scenario

or date

Bivalve selenium 

(μg/g dry weight)

Surf scoter liver selenium

 (μg/g dry weight)

Greater or lesser scaup liver 

selenium (μg/g dry weight)

White sturgeon liver selenium 

(μg/g dry weight) 

San Luis Drain extension load of 18,700 lbs per six months

Inefficient transformation: 

C3 and AE1

15 248 136 45

Shallow sediment: 

C2 and AE2

70 1,293 664 221

Suspended sediment: 

C1 and AE3

266 5,017 2,546 848

San Joaquin River targeted load of 3,400 lbs per six months

Inefficient transformation: 

C3 and AE1

2.5 10 16 5

Shallow sediment: 

C2 and AE2

11.8 187 105 35

Suspended sediment: 

C1 and AE3

45 818 424 141

Measured in North Bay (average)

1988– 90 8 

(Corbicula fluminea)

164 64 30

1995– 96 12 

(Potamocorbula 

amurensis)

– – – 
92 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

Low certainty results if a risk evaluation is based on 

one line of evidence. 

The scenarios, model, and forecasts demonstrate that 

many of the most likely combinations of load, hydrology, 

climate, transformation, and bioavailability pose a significant ecological risk to the Bay-Delta. In general, San Luis 

Drain discharges that would meet demands for drainage pose 

risks to fish and bird reproduction and the risk of fish extinction as a result of contamination of their invertebrate food. If 

biogeochemical conditions like those currently in the BayDelta predominate during projected selenium discharges, 

low flow periods would be the time of greatest risk for fish 

and bird species, especially those that include filter-feeding 

bivalves among their prey. Where selenium undergoes reactions typical of low flow or longer residence times, highly 

problematic bioaccumulation is forecast to result. There are 

some conceivable scenarios of increased selenium discharge 

to the Bay-Delta where the potential of risk is reduced, such 

as in a targeted load scenario for the San Joaquin River, but 

only if particulate transformation and assimilation are inefficient during low flow seasons. Those conditions are of low 

likelihood in that such inefficient particulate and suspended 

matter reactions are not typical of the Bay-Delta. Discharge 

of selenium from the San Joaquin Valley would be predominantly selenate, rather than the selenite released by refineries prior to 1998. Transformation of selenate to particulate 

selenium is observed throughout nature where residence times 

are extended. The efficiency of this transformation and the 

resulting particulate selenium concentrations are key to forecasting selenium bioaccumulation and effects. 

Dry year and wet year, low flow season

Critically dry years and low flow seasons will determine 

the ecological effects of selenium. Surf scoter, greater and 

lesser scaup, and white sturgeon arrive 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 highly 

vulnerable. So, low flow forecasts are probably the most 

relevant to describe their exposures. 

A cumulative summary for the low flow season of a critically dry year (table 33 and fig. 26) shows forecasted selenium 

concentrations for each media (water, sediment, invertebrate, 

predator) employed in the Bay-Delta selenium model, along 

with concern levels (see previous discussion; tables 13, 14, 

and 15). The forecasts are for the head of the estuary for a 

range of selenium loads (6,800; 18,700; or 44,880 lbs released 

per six months) discharged from a proposed San Luis Drain 

extension. The assumed conditions are a particulate speciation/

transformation regime indicative of shallow-water sediment 

(C2, 3 × 103) and a moderate generic bivalve assimilation 

efficiency (AE2, 0.56) to reflect bioaccumulation potential. 

In general, forecasted waterborne, particulate, dietary, and 

predator tissue selenium concentrations exceed illustrated 

guidelines in every forecast considered, where the input is 

• from a proposed San Luis Drain extension (table 33 and fig. 

26). In these critically dry year/low flow season forecasts, a 

40 μg/g dietary extinction guideline also is exceeded in all 

forecasted bivalve (food) concentrations except that bivalve 

concentration forecasted at the lowest load considered (6,800 

lbs per six months). However, that concentration in prey (28 

μg/g) results in concentrations in liver tissue of white sturgeon 

and greater and lesser scaup that exceed the adverse effects 

tissue guideline range (10– 18 μg/g) in liver.

If a San Luis Drain extension discharges selenium during 

low flow seasons, a high hazard seems likely, with loss of fish 

and bird species. If an out-of-valley resolution to the drainage 

problem results in carefully managed discharges of selenium 

to the Bay-Delta through the San Joaquin River (for example 

at 3,500 lbs per six months), the risks are less than for those 

forecasted for a discharge through a San Luis Drain extension. However, for the low flow season of a dry year, selenium 

concentrations in prey and predators are forecasted that are 

similar to selenium concentrations observed (and forecasted) 

during conditions in the Bay-Delta prior to refinery cleanup. 

During this time, forecasted selenium concentrations for both 

prey (food) and predator tissue exceed concentration with 

a high certainty of producing adverse effects. Thus, selenium from the San Joaquin Valley replaces, in terms of food 

web exposure and effects, the selenium removed in refinery 

cleanup Selenium contamination documented from 1986 to 

1996 was sufficient to threaten reproduction in key species 

within the Bay-Delta estuary ecosystems and to trigger human 

health advisories. 

Illustrated low-flow season scenarios where risks to 

benthic predators is somewhat reduced are found in five forecasts, but only if:

during both wet and critically dry years, a proposed 

San Luis Drain discharge is 150 ft3/s (half the capacity), the drainage is treated to attain a selenium 

concentration of 50 μg/L (6,800 lbs per six months), 

and selenium transformation and assimilation in the 

Bay-Delta is inefficient (C3/AE1); or 

during a wet year, the San Joaquin River discharges 

3,500 lbs per six months and selenium transformation 

and assimilation are inefficient (C3/AE1) or indicative 

of shallow-water sediments (C2/AE2); or 

during a dry year, the San Joaquin River discharges 

3,500 lbs per six months and selenium transformation 

and assimilation are the least inefficient found in any 

of the receiving waters studied previously (C3/AE1).

The necessary inefficient transformation is unprecedented 

in the Bay-Delta during low flows, so these seem unlikely 

scenarios. 

Wet year, low and high flow seasons

High flow conditions afford some protection under 

certain forecast conditions. Under these conditions, poten-

•

•

•
 93

San Luis Drain

3 Scenarios

Dry year/low flow season

Pumped south

S I E R R A N E V A D A

C O A S T

Sacramento R. San Joaquin R. R A N G E S

Delta

San Francisco Bay

C E N T R A L V A L L E Y

6.2

15

36

12*5.12.1

163 70 28

519 221 87

10–18

Guidelines

(μg/g dry wt)

12–15

2–5

0.1–1.5

1–5

1,557 664 261 Birds

(Scaup liver)

(Sturgeon liver)

Oil refineries

Partitioning coefficient (3 x 103)

Assimilation efficiency (0.55)

AE AE AE

AE

Kd

Kd

Kd

Kd Selenium concentrations in the food web

(μg/g dry weight)

Fish

Clams

Particulates

Water

* Concentrations (μgSe/L) 

 in the North Bay near 

 the site of input 

 (i.e., head of estuary) 

 with instantaneous 

 mixing

(μg/L)

6,800

18,700

44,880

141

* Critically dry year

 average (1986–1998)

Selenium inputs

(lbs selenium per six months)

3–5 3,433*

680

Figure 26. Schematic representation of forecasts of selenium concentrations in water, suspended material, a generic bivalve, 

and predators at the head of the estuary under three projected selenium load scenarios (lbs per six months) for a San Luis 

Drain extension directly to the Bay-Delta for a critically dry year during the low flow season. [Other assumptions: (1) refinery 

input, 680 lbs per six months; (2) speciation/transformation regime, Kd of 3,000; (3) bivalve assimilation efficiency, AE of 0.55.]

Table 33. Risk guidelines and cumulative summary of forecasts of selenium concentrations in water, particulate material, a 

generic bivalve, scaup, and sturgeon at the head of the estuary historically and under projected selenium load scenarios, 

identified speciation/transformation regimes, and bivalve assimilation efficiencies (AE’s) for the low flow season of a critically 

dry year. 

[Forecasted predator liver concentrations are predicted by extrapolation from regressions between bivalve and predator concentrations using data from 

1986 to 1990 (tables 30 and 31). C2 = Kd of 3 × 103, typical of shallow-water bed sediment. AE2 = 0.55]

Critically dry year, low flow season

Selenium

Load (lbs per 

six months)

Composite freshwater 

endmember

(μg/L)

Particulate

(μg/g dry weight)

C2 = Kd of 3×103

Bivalve

(μg/g dry weight) 

AE2 = 0.55

White sturgeon liver 

(μg/g dry weight)

Greater and lesser 

scaup liver

(μg/g dry weight)

San Luis Drain extension 

6,800 2.1 6.2 28 87 261

18,700 5.1 15 70 221 664

44,880 12 36 163 519 1,557

San Joaquin River, targeted load

3,500 0.86 2.6 11.8 35 105

Conditions prior to refinery cleanup

– 0.53 1.6 11 30 65

Guidelines (concern)a

– 1−5 0.4– 1.5 2– 5 12– 15 10– 18

a

Guidelines may not be, individually, realistic indicators of risk, but are used here as reference points for context (see discussion in text and tables 

13, 14, and 15).
94 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

tial of risk can be reduced in wet years during high flows at 

selenium loads of 6,800 lbs or 18,700 lbs discharged through 

a San Luis Drain extension or 3,500 lbs discharged through 

the San Joaquin River per six months where transformations 

are those of shallow-water sediment or are inefficient (C2/AE2 

and C3/AE1). During wet years and low flows, selenium 

concentrations in prey remain at <10 μg/g only at the inefficient transformation (C3). During the San Joaquin River 

selenium load scenario, higher transformation and assimilations (C1/AE3 or AE4) also result in prey of <10 μg/g, but not 

at San Luis Drain loads of 6,800 lbs or greater per six months. 

If concentrations in the San Joaquin River are regulated under a concentration management plan, increased San 

Joaquin River inflows will result in increased selenium loads 

to the Bay-Delta. Under this scenario, the low flow season of a 

wet year might be more vulnerable than a dry year depending 

on the regulated concentration for the San Joaquin River (fig. 

18). Higher concentrations result because the higher selenium 

load during the low flow season of a wet year may not be 

offset as much by increased flows as those that occur seasonally. Hence, meeting a triple goal of releasing a specific load 

during a limited period of naturally high flows and keeping 

concentrations below a certain objective to protect against 

bioaccumulation may not always be attainable. 

As some forecasts show, some releases during high flows 

may carry less direct risk for fish extinctions. However, it is 

important that releases during high flows be studied carefully before it is concluded that they lower risks. The fate of 

selenium that enters the Bay-Delta estuary during high inflows 

is not fully known. For example, it is not known how much 

is retained and reacts during subsequent low flow periods or 

how much is transported to the South Bay during high flows 

and subsequently retained (Conomos and others, 1979, 1985; 

Nichols and others, 1986; Peterson and others, 1989). Also 

during high inflows, highly contaminated particulate material 

from the San Joaquin River and/or a San Luis Drain extension 

is most likely to add to the selenium load in the estuary. 

Implications for Water Quality Criteria for the 

Protection of Aquatic Life

In many forecasts, the considered load scenario results 

in selenium concentrations in prey and predators that equal 

or exceed selenium concentrations forecasted and measured 

in the Bay-Delta prior to refinery cleanup In some forecasts, 

selenium concentrations in the Bay-Delta remained below the 

2 μg/L water quality criterion recommended for the protection of aquatic life (USFWS and NMFS, 1997 and amended 

2000), but those predators using the specific bioaccumulation 

pathway from sediment and benthic/suspended biomass to 

bivalves were, nevertheless, affected. Forecasts described here 

suggest that even at waterborne selenium concentrations at the 

head of the estuary of 1 μg/L, all risk of adverse effects cannot 

be eliminated. 

Conclusions

Extent and Sustainability of Agricultural 

Discharge from the San Joaquin Valley 

Taking a broad view, two lines of evidence are used here 

to show the general magnitude of the accumulated selenium 

reservoir in the western San Joaquin Valley. Calculations at the 

lower range of projections show that a long-term reduction in 

selenium discharge would not be expected for 63 to 304 years, 

if selenium is disposed of at a rate of about 42,500 lbs per year. 

Drainage of wastewaters outside of the San Joaquin Valley 

may slow the degradation of San Joaquin Valley resources, but 

drainage alone cannot alleviate the salt and selenium build-up 

in the San Joaquin Valley, at least within a century, even if no 

further inputs of selenium from the Coast Ranges occur. The 

amounts of ground water, salt, and selenium that have accumulated in the internal reservoir of the San Joaquin Valley may 

make it impractical to limit management to an annual imbalance (where input is greater than output) because of comprehensive effects to soils, aquifers and wildlife habitats. 

However, forecasts of annual San Joaquin Valley agricultural discharges provide a basis for determining the upper 

and lower limits of selenium discharge from the western San 

Joaquin Valley (tables 6 to 9; 17). Secondarily, the projections 

provide the basis for determining the magnitude of selenium 

load reductions that may become necessary to achieve a 

specific targeted selenium load for environmental or restoration targets or objectives. 

Agricultural inputs or discharges in the analysis presented 

here are divided into three groups depending on management 

scenarios to narrow the range of possibilities: 

Supply-driven management. A range of 3,000 to 8,000 

lbs selenium per year is assumed to address an environmental protection priority through a targeted load that cannot be exceeded. The basis for this scenario stems from:

WY 1997 to 2001 load limits for the Grassland 

subarea are from 5,661 to 6,660 lbs selenium per 

year for discharge through the San Joaquin River. 

Grassland subarea loads modeled for the river as part 

of TMDL regulation to meet the 5 μg/L concentration objective in the San Joaquin River are approximately 1,400 to 6,500 lbs per year. The State enacted 

Grassland subarea drainage prohibition is 8,000 lbs 

per year (tables 5 and 8; appendix C). 

The Westlands subarea load estimated as part of 

evidentiary hearings is 8,160 lbs selenium per year 

(assuming 200,000 affected acres; drainage generation 

of 0.3 acre-ft per acre per year; and a selenium concentration of 50 μg/L) (table 7). Thus, a load of 8,000 lbs 

selenium per year may be a lower limit of discharge 

through a proposed San Luis Drain extension.

1.

a.

b.
 95

Demand-driven load with management of land and/or 

drainage quality. A range of 15,000 to 45,000 lbs selenium per year is assumed to address agricultural needs, to 

some degree, for draining saline or waterlogged soils. In 

this scenario, the quality and quantity of drainage are controlled by managing volume per acre and/or quality of the 

drainage. A range of loads (19,584 to 42,704 lbs selenium 

per year) is projected using a selenium concentration of 50 

μg/L selenium (controlled concentration) and the amount of 

problem water or subsurface drainage with implementation 

of a management plan (demand driven volume) (table 6). 

Demand-driven load with minimum management. A 

range of 45,000 to 128,000 lbs per year is possible if the 

demand for restoring saline soils drives drainage and neither quantity nor quality objectives can be (or are chosen 

to be) met. For this scenario, a range of loads (42,704 to 

128,112 lbs selenium per year) is projected using a selenium concentration of 150 μg/L (non-controlled concentration) and the amount of problem water defined by the 

Drainage Program for year 2000 without implementation 

of a management plan (demand driven volume) (table 6). 

Graphical tools such as presented in appendix B (figs. 

B2 to B3) could help model additional probable scenarios of 

drainage for each subarea. 

Water Management Implications

Implications for water management found through use 

of a range of selenium load scenarios and the comprehensive 

approach illustrated in the Bay-Delta selenium model are:

The most significant effects of irrigation drainage 

disposal into the Bay-Delta will occur during low flow 

seasons and especially during low river flow conditions 

in dry or critically dry years. Dry or critically dry years 

have occurred in 31 of the past 92 years; as noted earlier, critical dry years comprised 15 of those years. Any 

analysis of selenium effects must take the influences of 

variable river inflows into account. 

Selenium effects in the Bay-Delta also could increase 

if water diversions increase or if San Joaquin River 

inflows increase with concomitant real-time discharge 

of selenium that increases selenium loading (the 

selenium issue and the water management issues are 

tightly linked). 

Construction of an extension of the San Luis Drain 

would increase selenium exposures of Bay-Delta 

organisms under any scenario partly because the entire 

load is unequivocally conveyed directly to the BayDelta. The greatest risks occur if discharge is continuous through high and low flow periods. Discharges 

from a San Luis Drain extension are especially problematic if they are constant through low inflow periods, 

when the dilution capacity of the estuary subsides dra2.

3.

•

•

•

matically because of diversions of freshwater inflows. 

Freshwater diversions, the resultant volume of inflow, 

and the degree of treatment of the waste are critical in 

determining the extent of the effect of a San Luis Drain 

extension.

Treatment also may be important in determining source 

loads effects. 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 selenium in the 

influent, but result in enhanced selenium food chain 

concentrations if speciation in the effluent changes to 

increase the efficiency of uptake. 

 Low flow conditions are considered here as the critical 

time (the ecological bottleneck) that will determine the effects 

of selenium on the ecological health of the Bay-Delta. Biological damage once per year can limit populations of species 

with a generation time of more than a year; biological damage 

incurred once per year can be carried over into the remainder 

of the year. Exposures to selenium are probably near their 

maxima when migratory species leave the estuary, enhancing 

risk of biological damage. Animals that will be most vulnerable to selenium effects probably include those that feed on 

benthos such as bivalves and those that are active (preparing 

for reproduction or for which early life stages develop) in the 

estuary in September through March. 

If water quality criteria are to be used in managing 

selenium inputs, the composite freshwater selenium input 

concentration might be managed as if it were a point source 

discharge. The calculation is a simple way to take into account 

hydraulic and inflow conditions that interact to determine 

the composite endmember selenium concentration that is the 

starting point for determining the exposure that Bay-Delta 

organisms will experience. 

Indicators of Ecological Risk and Monitoring 

Needs

Various protective guidelines and criteria are employed 

in this report as reference points. These may not be, individually, realistic indications of ecological risk. For example, in 

the Bay-Delta neither the USEPA criterion of 5 μg/L selenium 

nor the recommended USFWS criterion level of 2 μg/L alone, 

would be sufficient to protect the estuary if selenium transformations to particulate concentrations are efficient. The most 

effective interpretation and determination of risk includes use 

of monitoring data and development of guidelines for all critical media. Used in-combination, such data and criteria might 

be the most useful way to manage selenium in an ecosystem. 

Hence, the need for systematic long-term monitoring that 

includes all food web components is crucial to protection of 

ecosystems receiving selenium discharges. The linked components (water, particulate material, food, and predator tissue) 

and processes (speciation, transformation to particulate forms, 

bioaccumulation, and trophic transfer to predators) addressed 

•
96 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension 

here provide the necessary framework for a feasible approach 

for site-specific monitoring and analysis.

 Monitoring, as conceptualized below, would sample 

critical environmental components at a frequency relevant to 

each process to determine the impacts of management changes, 

trends in selenium contamination, and changes in reactions that 

determine fate and effects of selenium. A linked or combined 

approach would include all considerations that cause systems to 

respond differently to selenium contamination. 

In any site-specific analysis of selenium 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 selenium (i.e., 

agricultural drainage from the San Joaquin Valley via 

either a dedicated conveyance or the San Joaquin River). 

The vulnerability of downstream water bodies should be 

considered when evaluating of 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 selenium 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 selenium effects must take the influences 

of variable river inflows into account. Selenium impacts in 

the Bay-Delta could increase if water diversions increase 

or if San Joaquin River inflows increase with concomitant 

increases in selenium loading (i.e. the selenium 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 low-river 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. 

A mass balance or budget of selenium through the estuary is crucial because internal (oil refinery) and external 

(agricultural drainage) sources of selenium are changing 

as a result of management. At a minimum, a mechanism 

for tracking selenium 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 ongoing 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 con1.

2.

3.

4.

5.

taining high concentrations and loads of selenium. If the 

precipitation-dependence of agricultural selenium 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 selenium and suspended selenium; 

selenium speciation in water and sediment; assimilation 

capacities of indicator food chain organisms; and selenium 

concentrations in tissues of prey and predator species. 

Determination of transformation efficiency and processes 

that determine Kd's (distribution or partitioning coefficients) of selenium 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 selenium 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 selenium bioaccumulation in 

food webs are a part of this process. 

Determination of food web inter-relations would help 

identify the most vulnerable species. Specific protocols 

that include life cycles of vulnerable predators including 

migratory and mobile species would then document selenium 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 selenium, 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 selenium and 

consider 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:

identification of vulnerable food webs;

6.

7.

8.

9.

a.
 97

identification of sites most at risk from impacts of 

agricultural drainage;

analysis of effects on predators that includes food 

web components;

identification of elevated risk periods for effects 

based on hydrodynamics; and

calculation of protective loads/concentrations based 

on bioaccumulation in prey.

In view of the analysis of the existing selenium reservoir 

in the San Joaquin Valley, consideration of the degradation 

of groundwater aquifers needs to be a factor in manage-

ment 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. Monitor-

ing and assessment of storage also will show if treating 

discharge on an annual basis will suffice to manage the 

current regional imbalance of water, salt, and selenium. 

Treatment also may 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 selenium in the influent, but 

result in enhanced selenium food chain concentrations if 

speciation in the effluent changes to increase the efficiency 

of uptake. 

Concluding Perspective

Demonstrated and validated here is a methodology 

that uses existing knowledge of each considered factor in a 

sequence of linked processes that control the ecological effects 

of selenium. These linked processes are then incorporated 

into an internally consistent evaluation using multiple lines 

of evidence. Any future analysis of effects from selenium 

discharged to the Bay-Delta through a proposed San Luis 

Drain extension needs to be at least as complete and could 

profitably build from the framework presented here.

This new tool, the Bay-Delta selenium model (fig. 2), 

is employed to generate site-specific forecasts of selenium 

concentrations and effects based on loads, prey, and preda-

tors. It is concluded here that protective criteria be biologically 

based and consider (1) vulnerable food webs and elevated 

risk periods; (2) speciation and contaminant concentrations 

in sources such as particulate material that most influence 

bioavailability; (3) bioaccumulation or biodynamic models 

that help integrate exposure; and (4) multiple media concentra-

tions (water, particulate material, and tissue of prey and preda-

tors) that, in-combination, determine risk or hazard. In the 

Bay-Delta, bivalves appear to be the most sensitive indicator 

of selenium contamination.

b.

c.

d.

e.

10.

11.
98 
 99

Appendices A to F
100 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Appendix A. Export Drain Planning History and Geologic Inventory

Contents

Envisioned Drainage Discharges and Salt Loads ..........................................................................................................................................101

Geologic Inventory and Reservoir of Selenium in the San Joaquin Valley................................................................................................107

Characteristics and Timing of Selenium Source Water Release as Drainage..........................................................................................110

Figures

Figure A1. Map of San Luis Unit of the Central Valley Project.....................................................................................................................102

Figure A2. Ultimate Waterflow Conditions as known in 1978 of the San Luis Unit showing the (1) complexity of surface and 

ground water interactions; and (2) quantities of water influx and efflux [note prediction of 144,200 acre-ft (AF) 

for disposal in a valley drain] as known........................................................................................................................................104

Figure A3. Expected salt loads and drainage volume from the San Luis Unit to the San Luis Drain 

during the period 1995 to 2095 (USBR, 1983) ................................................................................................................................104

Figure A4. Conceptual water budget for the western San Joaquin Valley................................................................................................105

Figure A5. A representation of salt balance in the western San Joaquin Valley showing salt inflow (approximately 40 railroad 

cars per day) and outflow (approximately 17 railroad cars per day discharged from the Grassland subarea through 

the San Joaquin River).......................................................................................................................................................................106

Figure A6. Schematic diagram of selenium sources of the Coast Ranges and the accumulated reservoir of selenium 

within the western San Joaquin Valley.........................................................................................................................................107

Figure A7. Generalized selenium oxidation rate as a function of oxygen flux ..........................................................................................111

Figure A8. Generalized selenium load and selenium concentration as a function of water flux...........................................................112

Figure A9. Selenium load for Drainage Problem Area/Grassland Bypass Project Area, San Joaquin River 

at Crows Landing, and Vernalis for water years 1986–1998......................................................................................................112

Figure A10. CIMIS (California Irrigation Management Information System) station #124 precipitation for WYs 1986–1998............113

Figure A11. Monthly selenium load targets for San Luis Drain discharge to Mud Slough for WYs 1997 and 1998 ............................113

Tables

Table A1. Historical prediction of drainage from the San Luis Unit (San Luis Service Area and 

the Delta-Mendota Service Area)...................................................................................................................................................103

Table A2. Predicted selenium reservoir in the San Joaquin Valley based on alluvial fill (an average soil selenium 

concentration applied to different affected acreages, soil densities, and soil depths)........................................................108

Table A3. Selenium loads generated in upper Panoche Creek watershed during storms of WY 1998 and in lower 

Grassland area watershed during WY 1997..................................................................................................................................109

Table A4. Selenium concentrations in suspended sediment (silt and clay fraction; sand fraction) associated with 

storms of February, 1998...................................................................................................................................................................110

Table A5. Predicted selenium reservoir in the San Joaquin Valley based on Panoche Creek storm runoff (deposition 

and recharge).....................................................................................................................................................................................111
Appendix A. Export Drain Planning History and Geologic Inventory 101

Envisioned Drainage Discharges and Salt Loads

Planning

The San Luis Unit (fig. A1) in the western San Joaquin 

Valley encompasses over 700,000 acres in the Westlands, 

Panoche, Broadview, Pacheco, and San Luis Water Districts of 

the Grassland and Westlands subareas (USBR, 1981). Agricultural development and irrigation has continued on these lands 

despite salinized soils, with an attendant increase in areas that 

require drainage. Limiting factors include soil, topography, 

and drainage.

 Starting in 1954, land in the San Luis Unit was classified as to suitability for crop production and management cost 

(USBR, 1978; Ogden, 1988). Land was rated based on presence 

of alkali (salt), hardpan (impeded drainage), and roughness 

(uneven land surface). A large segment of Class 3 land (that is, 

land known to require difficult and costly management) was 

identified adjacent to the valley trough. By 1962, 12 percent of 

the San Luis Unit was comprised of Class 4 land (that is, land 

known to have a reduced payment capacity for irrigation and/or 

drainage improvements based on agricultural return). Class 4

land mainly was identified in areas directly affected by erosion 

from the Coast Ranges to the west (USBR, 1978). Agriculture 

continues to expand into Class 4 land, even though this expansion is controversial. These areas require the most capital for 

drainage removal, but have the least ability to pay for drainage 

improvements. As recently as 1997, the USBR petitioned to 

expand the place of use of Central Valley Project water supplies 

into areas of the San Luis Unit that never before have received 

federal water supplies (State Board, 1997). 

Historic estimates of drainage needs (that is, envisioned 

rates of flow or volume of drainage necessary to lower 

the water table) provide an interesting context for modern 

estimates. Of general note is that, even though amounts of 

drainage for conveyance out of the San Joaquin Valley have 

increased since planning began in 1955, the design capacity 

of the main component of a drainage facility has remained 

relatively unchanged through time (300 ft3/s). Estimates do 

vary, however, for the rate of flow for the north and south ends 

of the drain (100 ft3/s in the south and 450 ft3/s in the north).

 Consideration and assessment of hydrologic balance in 

a subarea also gives insight into expected drainage requirements. In a 1988 analysis (CH2M HILL, 1988), the Northern 

and Grassland subareas were considered in hydrologic 

equilibrium, which implies little future change in the extent 

of land that need drainage. A distinction was made in the 

analysis between managing the accumulated hydrologic 

imbalance (area of drainage affected land) and managing the 

annual imbalance (rate of water table rise). Short-term objectives would work toward hydrologic balance by stemming the 

rate of deterioration, while reclaiming existing problem lands

would require releasing from storage a large accumulation of 

water, salt, and selenium. Achieving hydrologic balance also 

would not achieve salt balance. Salts would continue to accumulate in the soils and aquifers of the San Joaquin Valley.

In addition to estimates of flow and volume, planning 

documentation gave estimates of water quality (based on total 

dissolved solids or specific conductance) to enable calculation of expected loads of salt (tons per year). The amount of 

salt projected for discharge from the San Joaquin Valley, as a 

whole, helps determine the magnitude of salt build-up. Differences in the amounts of salt discharged per subarea helps 

distinguish differences due to geology and hydrology in the 

affected areas. Selenium analyses on which to base calculation of selenium loads were not available until the mid-1980s 

(Presser and Ohlendorf, 1987). 

Export of both salt and nitrate (7,604 tons of nitrate [NO3

+ NO2 (N)] calculated for a worst case scenario for 2020) 

were considered problematic for receiving waters (USBR, 

1978; Interagency Drainage Program, 1979a, b). Salt would 

aggravate problems of salinity intrusion into the Delta thereby 

interfering with beneficial uses of Delta waters. Nitrates 

would disturb the balance of nutrient levels in the estuary, 

thereby causing eutrophication and elevated turbidity. Limited 

data on toxicity and constituents of concern (such as, nitrate, 

phosphate, pesticides, dissolved oxygen, boron, arsenic, heavy 

metals) in drainwater are listed in historical reports (Department of Water Resources, 1965a; Interagency Drainage 

Program, 1979a, b; Brown and Caldwell, 1986; USBR, 1984b 

through h), but are not considered further here.

 Compiled here are examples of the many sets of data for 

drainage volume and drained acreage that existed throughout 

the planning history for a drain to export agricultural drainage 

from the San Joaquin Valley; however, the review presented 

here is by no means exhaustive. References are mainly 

documentation by or for Federal agencies and joint Federal 

and State efforts (such as Hydroscience, 1977; USBR, 1978; 

Interagency Drainage Program, 1979a; CH2M HILL, 1985; 

Drainage Program, 1990a; USBR, 1992; Drainage Implementation Program, 1998). A parallel set of reports that document 

early State planning efforts are not as extensively cited (see, 

for example, Department of Water Resources, 1965a, b, 1969, 

1974, 1978; State Board, 1979). Many documents contain 

similar estimates (or reference the same data) based on generalized data for future conditions. For example, studies in 1979 

and 1990 both state concern over 400,000 acres of affected 

farmland that needs drainage due to a high water table (Interagency Drainage Program, 1979a; Drainage Program, 1990a). 

Evaluations of alternative disposal areas, which show engineering aspects and the net revenue disposal benefit of different 

drainage conveyances, mainly address management aspects, 

not source loads estimates (see, for example, USBR, 1955, 

1962; Department of Water Resources, 1965a; Interagency 

Drainage Program, 1979b; Brown and Caldwell, 1986).

Specific Estimates

 From 1975 to 1977, both the Interagency Drainage 

Program and the USBR prepared estimates of discharge from 

the San Luis Unit (USBR, 1978). The 1970’s planners envisioned an agricultural drainage canal with a design capacity of 
102 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

0 30 km

N

0 30 mi

CALIFORNIA

Map area

Tulare

Lake Bed

S i e r r a N e v a d a

S a n J o a q u i n V a l l e y

C o a s t R a n g e s

Fresno

San Luis Drain (closed)

San Luis Unit

Delta Mendota Canal

Kesterson National Wildlife Refuge

California Aqueduct

Kings River

Panoche Cr

San Luis Drain

(reopened)

San Luis Drain

(proposed)

San

Joaquin River

Merced R.

Tuolumne R. Stanislaus R.

Delta

Sacramento

San Francisco

Sacramento River

San Francisco Bay

P

A

C

I

F

I

C

O

C

E

A

N

Cantua Cr

Kern

subarea

Tulare subarea

Westlands

subarea

Grassland subarea

Northern

subarea

San Luis Reservoir

San Pablo

Bay

Figure A1. Map of San Luis Unit of the Central Valley Project, California.
Appendix A. Export Drain Planning History and Geologic Inventory 103

300 ft3/s and a length of 197 miles. Estimates of quantity were 

calculated through the year 2080 (approximately 100 years 

into the future) and of quality through the year 2030 (table 

A1). Maximum quantities of drainage originally were not 

anticipated for at least another 100 years in the original plan, 

but revised estimates showed the ultimate (maximum) quantity

of drainage would be available by 2030 (table A1). A hydrologic schematic of Ultimate Waterflow Conditions developed 

for the San Luis Unit shows a drain discharge of 144,200 acreft per year from 300,000 acres underlain by subsurface drains 

(fig. A2). The historic numerical model simulations were 

based on salinity measurements. The model predicted that 

the discharge of the poorest quality of drainage would occur 

during early years of irrigation and drainage. Annual discharge 

of salt from the San Luis Unit would increase from 43,710 

tons per year to a maximum of 1.5 million tons per year after 

40 years of discharge (USBR, 1978). As equilibrium conditions between soil and water were approached, concentrations 

of dissolved minerals in the drainage water were expected to 

decrease. The model also predicted salt concentrations (mg/L 

total dissolved solids, TDS) would decrease by 50 percent 

after 40 years of drainage.

In 1979, a final report was prepared by the Interagency 

Drainage Program recommending completion of a valleywide 

drain to service five areas (North, Delta-Mendota, San Luis, 

Tulare Lake, and Kern County) and to discharge into the BayDelta at Chipps Island. The report also included a first stage 

environmental impact report (Interagency Drainage Program, 

1979a, b). Estimates of expected annual quantities of drainage 

ranged from 57,000 acre-ft in 1985 to 668,000 acre-ft in 2085, 

when drained acres were expected to reach over one million 

acres. Loads of salt requiring disposal were estimated to range 

from 3.1 to 3.9 million tons per year for a valleywide drain. 

 In 1983, the USBR estimated drainage quantity and 

quality (concentration of salt, seven major elements, and 

twelve minor elements, but selenium was absent) for expected 

discharge from the San Luis Unit during the period 1995 to 

2095 (USBR, 1983) (fig. A3). Water-quality projections were 

based on concentration averages in the San Luis Drain for the 

period September 1982 to January 1983 (USBR, 1983), before 

the discovery of deformities at Kesterson National Wildlife 

Refuge. Estimates of drainage volume ranged from 84,525 

acre-ft in 1995 to 274,270 acre-ft in 2095 for the combined 

discharge from the San Luis Service Area (equivalent to 

Westlands Water District; 48,885 to 192,105 acre-ft) and 

the Delta-Mendota Service Area (encompassing Grassland 

subarea and other northern water districts; 35,660 to 82,158 

acre-ft). A steady rise in discharge was predicted from 1995 to 

about year 2035 when the rate of increase slows, but continues 

rising through the projected year 2095 (fig. A3). The worstcase scenario was to occur in year 2020 when 1.8 million tons 

per year of salt was to be discharged in 201,025 acre-ft of 

drainage. 

 In 1988, salt and water inflows and outflows to the San 

Joaquin Valley were conceptualized (CH2M HILL, 1988) (fig. 

A4). Calculations specific to five subareas determined the 

annual groundwater and salt accumulation. Results of these 

studies showed volumes of water and tons of salt recharged or 

discharged by specific processes (such as evapotranspiration), 

sources (such as canal imports), or reservoirs (such as confined 

aquifers). The annual salt accumulation determined for 1988 

in the semi-confined aquifer of the valley for all five subareas 

was 3.3 million tons per year. The annual accumulation per 

subarea ranged from 1,000 tons per year to 1.5 million tons 

per year, due to differing hydrology, geology, and drainage 

options (see later discussion). An analysis for the Westlands 

subarea showed 44 percent of the salt was from dissolution of 

salts internal to the San Joaquin Valley; 49 percent imported 

from outside sources including irrigation water; and 7 percent 

from other sources such as seepage. The predicted conditions in the Westlands subarea showed the largest proportion 

of internal salt to imported salt for the five subareas. Westlands subarea is the most impacted by Coast Range sources 

of selenium because of its location on the Panoche Creek 

alluvial fan (see later discussion; Presser and others, 1990; 

Presser, 1994b). For the Westlands subarea, importation of 

higher quality water would have a diminished effect compared 

to other subareas because of this large reservoir of salt. The 

Northern and Grassland subareas showed high proportions of 

Table A1. Historical prediction of drainage from the San Luis Unit 

(San Luis Service Area and the Delta-Mendota Service Area). 

[Both sets of data and estimates (Interagency Drainage Program (1975) and 

USBR (1977) are included within USBR (1978). Model annual loads of salt 

were verified by sampling and analyses of drainage waters (USBR, 1978). 

The ultimate or maximum condition is defined by the Interagency Drainage 

Program as drainage of 300,000 acres.]

Future 

year

Interagency Drainage 

Program drainage 

estimate

(acre-ft/year)

USBR drainage 

estimate 

(acre-ft/year)

USBR modeled 

load

(tons salt/year)

1980 20,000 3,100 43,710

1985 – 8,700 159,210

1990 47,000 19,000 317,300

2000 64,000 33,100 521,400

2010 71,000 107,400 1,385,460

2020 78,000 152,300 1,538,230

2030 88,000 154,100 1,094,110

2040 98,000 – –

2050 107,000 – –

2060 114,000 – –

2070 122,000 – –

2080 129,000 – –

Ultimate 150,000 – –
104 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

imported salt to internal salt and relatively low salt accumulations because of the availability of the San Joaquin River for 

salt discharge.

A 1989 analysis for the Drainage Program estimated 

that salt was accumulating at a rate of about 100,000 tons per 

year in the Grassland subarea (Drainage Program, 1989). On 

a recent detailed basis, calculations for the lower San Joaquin 

River basin, that includes the Grassland subarea and recycling 

to and from the San Joaquin River, show a doubling of salt 

within the basin every five years despite drainage to the San 

Joaquin River (net gain of 207,000 tons per year of a mean salt 

inflow of 917,000 tons per year) (Grober, 1996). 

Re-evaluation in 1998 of salt importation data (neglecting 

salt reservoir calculations as done in 1988) showed an 

excess of salt inflow over outflow in all subareas (Drainage 

Implementation Program, 1998) (fig. A5; one railroad car is 

equivalent to 100 tons salt). The total annual imported salt 

was 1.5 million tons per year. This value does not include the 

calculated 620,000 tons per year discharged out of the valley 

through the San Joaquin River (Drainage Implementation 

Program, 1998). No data were given for internal salt or the 

status of subarea salt reservoirs. 

Figure A2. Ultimate Waterflow Conditions as known in 1978 of the San Luis Unit showing the 1) 

complexity of surface and ground water interactions; and 2) quantities of water influx and efflux [note 

prediction of 144,200 acre-ft (AF) for disposal in a valley drain] (adapted from USBR, 1978 Plate 2).

Figure A3. Expected salt loads and drainage volume from the 

San Luis Unit to the San Luis Drain during the period 1995 to 2095 

(USBR, 1983).

12,000 AF

32,000 AF

97,100 AF

20,000 AF

West-Side Materials

Corcoran Clay

East Side-Materials

219,500 acres

91,000 acres

Tile-drained acres

300,000 acres

to valley drain

 144,200 AF

30,000 AF

190,000 AF 40,000 AF

48,000 AF

(seepage through wells)

168,000 AF

(pumpage)

57,000 AF

(pumpage)

30,000 AF

35,000 AF

(seepage

through wells)

86,300 AF

(pumpage)

65,000 AF

(pumpage)

56,700 AF

(pumpage)

11,000 AF

65,000 AF

5,400 AF

17,000 AF

(seepage through wells)

21,000 AF

107,700 AF

16,000 AF

30,000 AF

(pumpage)

32,000 AF

Ultimate waterflow conditions

47,200 AF

(to drain)

(Coast Ranges streams)

(losses)

(streams)

(losses) (losses)

120,000 AF

(seepage)

(losses)

(streams)

100

0

200

300

0.5

0

1.0

1.5

2

1995 2015 2025 2045 2065 2085

Salt

Delta-Mendota Canal

San Luis Unit Study

Delta-Mendota Canal and 

San Luis Unit Study

Drainage, in thousands of acre-feet

Salt, in million tons
Appendix A. Export Drain Planning History and Geologic Inventory 105

 Coincidentally, the input of 1.5 million tons per year of 

salt calculated as part of this 1998 re-evaluation also is the 

annual tonnage that was quoted in 1978 by the San Luis Task 

Force. The task force reviewed the management, organization, 

and operation of the San Luis Unit to determine the extent to 

which the San Luis Unit conformed to the purpose and intent 

of Public Law 86-488. The task force noted that planning 

documents looked 40 years into the future (1950 to 1990):

At about the 1990 level of agricultural development 

in the San Joaquin River Basin, slightly more than 

1.5 million tons of new salt will be added annually 

to the valley from applied irrigation water (page 161).

Implemented Management

 Current implemented agricultural wastewater management plans for five subareas are:

Northern (26,000 drained acres) and Grassland (51,000 

drained acres) subareas discharge agricultural drainage 

to the San Joaquin River. A State permit has been in 

place since 1997 to regulate drainage from the Grassland subarea to the San Joaquin River through use of a 

portion of the San Luis Drain as a conveyance facility 

(Central Valley Board, 1998a). The reuse of a 28-mile 

section of the San Luis Drain has been renamed the 

Grassland Bypass Channel Project (USBR and San 

Luis Delta-Mendota Water Authority, 1995 and 2001; 

USBR and others, 1998 and ongoing). 

•

Westlands subarea (5,000 drained acres, alleviating 

salinization in 42,000 acres) has a no discharge policy, 

that is, storage of drainage in the underlying groundwater aquifer and use of agricultural water supplies and 

the aquifer for dilution. Some consider this a recycling 

program (Drainage Program, 1989), although it has 

temporal storage, displacement, and distribution components to it. Degradation of groundwater aquifers is 

expected to occur. Ground water with dissolved solids 

of greater than 2,500 mg/L is considered unsuitable for 

irrigation (Drainage Program, 1990a) 

Tulare (42,000 drained acres) and Kern (11,000 

drained acres) subareas are internally drained basins 

that discharge to privately owned evaporation ponds. 

Discovery of bird deformities in 1987 through 1989 

caused the State to call for closure of some ponds and 

operation of the remaining ponds under permits (State 

Board, 1996a). State permits have regulated evaporation pond discharges since 1993 with various areas of 

mitigation wetlands required (Central Valley Board, 

1993, 1997, and 1998c). Many evaporation ponds 

have closed or are in the process of closure; remaining 

ponds have been modified to lessen bird use. Documentation in 1999 showed that the number of individual basins and pond operators decreased by about 

60 percent, but surface area of ponds only decreased 

from 6,715 to 4,895 acres (Drainage Implementation 

Program, 1999d).

•

•

CONFINED

PUMPING

UNCONFINED

PUMPING

Figure A4. Conceptual water budget for the western San Joaquin 

Valley (adapted from USBR, 1989; and CH2M HILL, 1988).
106 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Figure A5. A representation of salt balance in the western San Joaquin Valley showing salt inflow (approximately 40 railroad 

cars per day) and outflow (approximately 17 railroad cars per day discharged from the Grassland subarea through the San 

Joaquin River) (printed with permission, Drainage Implementation Program, 1998).
Appendix A. Export Drain Planning History and Geologic Inventory 107

Geologic Inventory and Reservoir of Selenium in 

the San Joaquin Valley

Selenium Geologic Inventory and Mass Balance

Sediments enriched in salts (and by inference, selenium) have been accumulating for 1.0 to 1.2 million years 

on the alluvial fans of the San Joaquin Valley (Bull, 1964; 

Deverel and Gallanthine, 1989; Gilliom and others, 1989; 

Andrei Sarna-Wojcicki, U.S. Geological Survey, Menlo Park, 

Calif., personal commun., July 23, 1998). Salt and other trace 

elements originate from marine sedimentary rocks of the California Coast Range (Presser and Ohlendorf, 1987; Presser and 

others,1990; Presser, 1994b). Figure A6 visually illustrates 

some of the characteristics of the geologic sources of selenium in the Coast Ranges; the processes or erosion and runoff 

occurring in the valley; irrigation and drainage systems; and 

potential reservoirs (selenium inventory components) in soils 

and aquifers (Presser and Ohlendorf, 1987; Presser and others, 

1990; Presser, 1994a; Presser and Piper, 1998). A summary of 

selenium concentration and load data, which provide the basis 

of this conceptual model of selenium sources, transport, and 

mobility, also is given in figure A6. 

The San Joaquin Valley has a net negative annual water 

budget (evaporation exceeds precipitation). Prior to development of a water management system, a permanent shallow 

groundwater table only occurred in groundwater discharge 

zones near the valley trough. The present shallow ground water 

and attendant subsurface drainage flows are mainly the result of 

water management including massive irrigation. Micro-management seemingly has enabled agricultural production to continue 

at a high rate without excessive abandonment of lands. 

Estimates of geologic and hydrologic reservoirs of 

selenium within the alluvial fans and in the valley provide 

perspective on the amount of selenium potentially available for 

discharge through a drainage conveyance. Such estimates are 

necessary to understand the minimum bounds on how much 

selenium would be discharged over the course of time, should 

an out-of-valley conveyance system be built. Relating the size 

of selenium reservoirs to an estimate of the time necessary to

discharge accumulated selenium in a drainage conveyance also 

provides planning context. 

Prediction of Long-Term Selenium Reservoirs

Data collected from the Panoche Creek alluvial fan area 

allows preliminary calculations of the reservoir of selenium 

COAST

RANGES

SAN JOAQUIN VALLEY RESERVOIR

(water, soil, biota) 

SAN FRANCISCO BAY-DELTA

 SELENIUM AVAILABLE FOR DISCHARGE

1) Source scenario: 7 feet of soil/160,000–444,000 acres

 Load: 3–11 million lbs Se

 Assumed removal rate: 42,785 lbs Se/yr

 Years to remove: 63–180 yrs

2) Source scenario: 0.5 million yrs, 1 storm/100 yrs

 Load: 13–188 million lbs Se

 Assumed removal rate: 42,785 lbs Se/yr

 Years to remove: 304–4,394 yrs

CURRENT SAN JOAQUIN R. OUTLET

NOTE: All ppm = μg/g dry weight

 All ppb = μg/L

Drains

43–430 ppb

Sediment: 1–2 ppm

 Runoff: 2–60 ppb

Aggradation

Erosion

Panoche Cr. alluvial fan

0.68 ppm (max 4.5 ppm) Sumps 140–4,200 ppb

Wells 96–7,300 ppb

SEEPS

<2 – 3,500 ppb 

Tulare Formation

1.4 ppm (max 2.6 ppm)

Kreyenhagen Formation

11 ppm

Moreno Formation

 (max 45 ppm)

9.1 ppm (max 35 ppm)

Panoche Formation

10 ppm 

12 ppm (max 34 ppm, core samples)

Regulation

WY 1997-98 load limit: 6,600 lbs Se

Prohibition: 8,000 lbs Se

USEPA criterion for the

protection of aquatic life: 5 ppb Se

San Joaquin River

Proposed

San Luis Drain extension

Figure A6. Schematic diagram of selenium sources of the Coast Ranges and the accumulated reservoir of selenium 

within the western San Joaquin Valley.
108 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

within the alluvial fans of the San Joaquin Valley; that is, 

the selenium potentially available for discharge through a 

drainage conveyance over the long-term. Two methodologies are presented here for estimating selenium reservoirs and 

consequently determining the time necessary to discharge the 

accumulated selenium from the alluvial fans of the valley. The 

methodologies are based on:

concentrations of selenium in soils of the western 

San Joaquin Valley and estimates of either Panoche 

Creek alluvial fan area acreage or problem acreage, 

but neglecting the amount of selenium in groundwater 

reservoirs; or

suspended and dissolved selenium loads brought down 

in runoff from the Coast Ranges in the Panoche Creek 

alluvial fan area.

Methodology Based on Alluvial Fill—Soils Scenario

General surveys of selenium concentrations in soils 

across the western United States show an average of 0.34 μg/g 

(all soil concentrations are in dry weight), although sampling 

was limited (Shacklette and Boerngen, 1984). The average is 

0.26 μg/g across the conterminous United States. Surveys of 

selenium concentrations in soils of the western San Joaquin 

Valley were conducted in 1982 and 1985 (Tidball and others, 

1986; 1989). The interfan area below Monocline Ridge and 

between Panoche Creek in the north and Cantua Creek in the 

south showed the highest selenium concentrations (maximum 

•

•

ungridded value 4.5 μg/g). The geometric mean for the 

Panoche Creek alluvial fan was 0.68 μg/g selenium (721 sites, 

1.6 kilometer interval, 66 to 72 inch depth). Tidball and others 

(1986, 1989) also found a geometric mean of 0.14 μg/g for 

the San Joaquin Valley western slope (297 sites, 10 kilometer 

intervals, 0 to 12 inch depth). 

An average soil concentration of 0.68 μg/g selenium 

was employed here along with several estimates of affected 

acreage, soil densities, and soil depths to estimate the amount 

of selenium in the soil reservoir of the Panoche Creek alluvial 

fan area (table A2). Predicted selenium deposition under the 

various modeled conditions range from 2.7 to 356 million lbs 

selenium. If a removal rate of 42,785 lbs per year is hypothesized (see main text and later discussion, appendix B), it 

would take 63 to 8,321 years to discharge the calculated soil 

reservoir of selenium (table A2) (fig. A6). This estimate does 

not factor in loading that would occur over the course of that 

time due to further weathering and runoff from the Coast 

Ranges, nor the amount of selenium in groundwater reservoirs

Methodology Based on Panoche Creek Runoff—Runoff 

Scenario

Runoff was transported in WY 1995 in the existing 

section of the San Luis Drain when extreme flooding in the 

Coast Ranges caused the drain to be used as a runoff collector 

system. A selenium load estimated at 1,750 lbs was eventually discharged via the drain to the San Joaquin River (Central 

Table A2. Predicted selenium reservoir in the San Joaquin Valley based on alluvial fill (an average soil selenium 

concentration applied to different affected acreages, soil densities, and soil depths).

[Selenium concentration in soil is dry weight. Applied problem acreage is from Drainage Program (1990s); applied alluvial farm acreage is from Bull (1964). For assumed removal rate, see main text table 5 or generalization of 42,704 lbs selenium per year based on 

314,000 acre-ft of drainage at a selenium concentration of 50 μg/L. A kesterson (kst) is 17,400 lbs selenium (see previous discussion 

and Presser and Piper, 1998).]

Applied 

acreage

(acres)

Depth

(meters)a

Density

(g/cm3)

a

Soilb 

(μg/g 

selenium)

Reservoir

(million lbs 

selenium)

ksts Assumed removal 

rate (million lbs 

selenium/year)

Years of 

loading to 

Bay/Delta

Problem acreage scenarioc

444,000 2 (6.6 ft) 2.0 0.68 10.8 621 0.043 252

444,000 2 1.46 0.68 7.7 442 0.043 180

444,000 15 (50 ft) 1.46 0.68 59 3,391 0.043 1,379

444,000 91 (300 ft) 1.46 0.68 356 20,460 0.043 8,321

Panoche Creek alluvial fan acreage scenarioa

160,000 2 1.46 0.68 2.7 155 0.043 63

160,000 15 1.46 0.68 20.3 11,667 0.043 474

160,000 91 1.46 0.68 123 7,069 0.043 2,875

a

Bull, (1964).

bTidball and others, (1986 and 1989).

c

Drainage Program, (1990a).
Appendix A. Export Drain Planning History and Geologic Inventory 109

Valley Board, 1996a,b; Presser and Piper, 1998). This amount 

represents 22 percent of the annual 8000-pound selenium 

prohibition for discharge to the San Joaquin River enacted by 

the State in 1996. The runoff load for the one major storm of 

WY 1997 was estimated at 137 lbs selenium based on monitoring downstream channels (USBR and others, 1998 and 

ongoing; appendix B, table B8). This amount represents 1.9 

percent of the annual load discharged to the San Joaquin River 

in WY 1997. In 1998, 487 lbs selenium was estimated transported by Coast Ranges runoff, representing 5 percent of the 

total load discharged though the Grassland Bypass Channel 

Project (USBR and others, 1998 and ongoing). These latter 

data represent approximations of anecdotal events and should 

only be used to assess an order-of-magnitude for runoff loads 

during a series of short duration storms (total precipitation 

of 0.6 inches) in WY 1997. Comparison then can be made to 

the amount discharged in an extremely wet year in WY 1995 

(total precipitation greater than 11.5 inches). 

No complete sets of data (flow, selenium concentration 

in water and sediment, and amounts of sediment) are available for Panoche Creek alluvial fan area, the area of greatest 

selenium source influx, prior to 1997. Reconnaissance in 1987 

to 1988 (Presser and others, 1990) showed dissolved selenium 

concentrations of 44 to 57 μg/L in runoff samples. Suspended 

sediment selenium concentrations were relatively low (1.2 to 

2.9 μg/g selenium), but the volume of sediment relatively high 

(10 percent or 91,500 mg/L).

The rate of sediment and selenium source influx has 

been under study at Panoche Creek since September 1997 

(U.S. Geological Survey, 1999; Kratzer and others, 2003). A 

recently installed gaging station provided flow data and hydrographs for WY 1998 storms. Storms of WY 1998 were the 

result of an El Niño year of precipitation and therefore represent an extremely wet year (see below, occurrence interval of 

large magnitude storms). Sediment and water samples were 

taken during flood events to determine dissolved, total, and 

suspended selenium loads (U.S. Geological Survey, 1999; 

Kratzer and others, 2003). Flow data are integrated here with 

these selenium concentration data to calculate dissolved and 

total selenium loads, with suspended selenium loads calculated by difference (table A3). The calculated selenium load 

was 5,995 lbs selenium for runoff discharged from Panoche 

Creek during two storms (table A3). Estimation here of two 

intervening storms showed a total of 2,050 lbs. The total is 

8,045 lbs for runoff loads of selenium for WY 1998, with 16 

percent of the load as the dissolved fraction and 84 percent as 

Table A3. Selenium loads generated in upper Panoche Creek watershed during storms of WY 1998 and in lower Grassland area 

watershed during WY 1997. 

[Storm runoff for WY 1998 was measured at Panoche Creek at highway I-5 by USGS; sampling during these storms was on a limited basis because of the 

large magnitude of some events (USGS, 1999; Kratzer and others, 2003). The integrated area under the hydrograph for WY 1998 is used here with total 

and dissolved selenium concentration data to calculate selenium load; suspended load is calculated by difference. Upper watershed loads measured for WY 

1998 may represent maximum infrequent loading through Panoche Creek, rather that being representative of annual historic loading (see text for detailed 

discussion). The selenium loads for WY 1998 form the basis for predicting the magnitude of geologic and hydrologic selenium reservoirs in the western San 

Joaquin Valley (see Table A4, one large magnitude storm per 10, 50 or 100 years). Loads for WY 1997, given for comparison, were measured as amount 

discharged as overflow to a wetland slough in the Grassland subarea (USBR and others, 1998 and ongoing).]

Storm dates Duration

(hours)

Initial 

flow (ft3

/s)

Maximum 

flow (ft3/s)

Ending flow 

(ft3/s)

Dissolved 

selenium (lbs)

Suspended 

selenium (lbs)

Total 

selenium(lbs)

WY 1998

February 3−4 34.8 310 8,000 750 640 3,850 4,490

February 6–7 28.0 1,800 2,800 200 179 699 878

February 8 (approximated) – – 6,500a – 50 – 1,800

February 19–20 (approximated) – – 1,600a – 30 – 250

February 21–22 28.5 2 1,400 220 76 236 312

February 23–24 21.8 510 2,100 180 67 248 315

SUBTOTAL (measured storms) – – – – 962 (16%) 5,033 (84%) 5,995

TOTAL (all storms) – – – – – – 8,045

WY 1997

January and February, 1997b – – – – – – 137

TOTAL WY 1997 – – – – – – 137

a

Flow is approximated from gage height measurements, making load values generated from these flows also approximate; selenium concentrations are 

assigned for these two storms. 

bSee table B9.
110 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

the suspended fraction. Although the concentration of selenium in suspended sediment is relatively low (0.6 to 1.5 μg/g 

dry weight) (table A4), the large volume of material leads 

to a high load in the particulate material as compared to the 

dissolved load (also see Presser and others, 1990). Calculations cannot be made at this time to estimate the load of 

selenium discharged from the watershed to receiving waters to 

compare to input loads because of the lack of adequate downstream monitoring stations (Presser and Piper, 1998). So influx 

and efflux cannot be directly compared. However, 8,045 lbs 

per year source selenium influx measured in the extremely wet 

year of 1998 is comparable to the State limitation on discharge 

from the San Joaquin Valley through the San Joaquin River, 

that is, an efflux of 8,000 lbs per year (Central Valley Board, 

1996c). In general though, under average rainfall amounts, the 

annual load from these natural sources is calculated to be a 

small percentage of the selenium load potentially discharged 

from the San Joaquin Valley (USBR and others, 1998 and 

ongoing). Only when source loads from the Coast Ranges are 

considered in sum (see discussion below) or during a year in 

which a large magnitude storm occurs, are the influx amounts 

significant compared to efflux amounts currently regulated. 

Selenium discharge data for Panoche Creek for WY 

1998 were extrapolated here to give estimates of the amount 

of selenium deposition that has occurred over a time period 

of either 0.5 million years or 1.1 million years to give a range 

of accumulation. Deposition over these two time periods was 

calculated for a) one large magnitude storm in 10 years; b) one 

large magnitude storm in 50 years; or c) one large magnitude storm in 100 years. Table A5 shows amounts of total, 

dissolved, and suspended selenium deposited under those 

conditions. The range of dissolved selenium deposition over 

0.5 million years is 13 to 86 million lbs selenium; and over 

the course of 1.1 million years, 28 to 188 million lbs selenium. The range of suspended selenium deposition over the 

course of 0.5 million years is 67 to 449 million lbs selenium; 

and over the course of 1.1 million years, 147 to 989 million 

lbs selenium. The range of total selenium deposition over the 

course of 0.5 million years is 80 to 535 million lbs; and over 

the course of 1.1 million years, 175 to 1,177 million lbs selenium. If the selenium removal rate is hypothesized as 42,785 

lbs per year (0.043 million lbs per year) (see later discussion, 

appendix B), then it would take 1,870 to 27,510 years to 

discharge this reservoir of selenium in the Panoche Creek alluvial fan based on total selenium deposition from runoff (table 

A5) (fig. A6). Ranges based on dissolved selenium deposition 

from runoff are 304 to 4,394 years; and based on suspended 

selenium deposition from runoff are 1,566 to 23,116 years. 

These estimates do not factor in the loading that would occur 

over the course of that time due to further weathering and 

runoff from the Coast Ranges. The estimate does attempt to 

include selenium in the groundwater reservoir. 

Characteristics and Timing of Selenium Source 

Water Release as Drainage

Mobility of Selenium: Source Flow, 

Concentration, and Load

The behavior and speciation of selenium, and hence its 

solubility and mobility, are determined by a combination of 

processes including inorganic (for example, weathering of 

the Coast Ranges) and organic (for example, oxidation by 

bacteria) reactions. Oxidative reactions are partly responsible 

for selenium mobility from source geologic formations of the 

Coast Ranges and the adjacent derived alluvial fans of the San 

Joaquin Valley (Presser and others, 1990; Gilliom and others, 

1989; Presser, 1994b) (fig. A7). Selenium is oxidized to 

selenate, a form readily soluble in water. Selenate is mobile in 

aqueous systems as a function of oxygen flux or availability of 

oxygen and/or water in weathered rocks and soils. As oxygen 

saturation is reached, the rate of reaction may approach a 

constant value and selenium remains in its highest oxidation 

state (+6, SeO4

=) (fig. A7). Source agricultural drainage waters 

are selenate-dominated, a fact of major significance in deterTable A4. Selenium concentrations in suspended 

sediment (silt and clay fraction; sand fraction) 

associated with storms of February, 1998. 

[Selenium analysis by hydride generation, with a detection limit 

of 0.1 μg/g. Storms are those illustrated in table A3 for February 

3−4 and 6−7, 1998. Time is expressed as military time.] 

Suspended sediment selenium (μg/g dry weight)

Date and time

Silt and clay 

fraction 

(<0.062 mm)

Sand fraction 

(< 2 mm)

2/3/98 3:00 1.2 –

2/3/98 7:00 1.5 0.9

2/3/98 10:30 1.4 0.9

2/3/98 12:00 1.4 1.1

2/3/98 14:00 1.5 1.0

2/3/98 16:00 1.4 0.8

2/3/98 19:00 1.3 0.6

2/4/98 0:00 1.2 0.8

2/4/98 7:00 1.1 0.8

2/6/98 11:40 1.5 0.8

2/6/98 12:40 1.5 1.0

2/6/98 13:40 1.3 1.1

2/6/98 15:30 1.4 1.0

2/6/98 18:30 1.4 0.9

2/6/98 22:30 1.4 0.8

2/7/98 3:30 1.4 1.0

2/7/98 9:30 1.4 0.8
Appendix A. Export Drain Planning History and Geologic Inventory 111

Table A5. Predicted selenium reservoir in the San Joaquin Valley based on Panoche Creek storm runoff (deposition and recharge) (see 

Table 3A for data used for extrapolation). 

[For assumed removal rate, see main text table 5 or generalization of 42,704 lbs per year selenium based on 314,000 acre-ft of drainage at a selenium concentration of 50 μg/L. A kesterson (kst) is 17,400 lbs selenium (see previous discussion)]

Runoff scenario

(deposition and 

recharge)

Total selenium

 [dissolved plus

suspended]

(million lbs)

Dissolved 

selenium

[assumed as 

16% of total] 

(million lbs)

Suspended

selenium

[assumed as 

84% of total] 

(million lbs) 

ksts

(range)

Assumed

removal rate

(million lbs 

selenium/

year)

Years of 

loading to

Bay-Delta

[range based on 

total selenium]

Minimum years 

of loading to

Bay-Delta [based 

on dissolved 

selenium]

0.5 million years

1 large magnitude 

storm year/10 

years

345−535 55−86 290−449 3,161−30,747 0.043 8,064−12,504 1,285

0.5 million years

1 large magnitude 

storm year/50 

years

140−387 22−62 118−325 1,264−22,241 0.043 3,272−9,045 514

0.5 million years

1 large magnitude 

storm year/100 

years

80−188 13−30 67−158 747−10,804 0.043 1,870−4,394 304

1.1 million years

1 large magnitude 

storm year/10 

years

759−1,177 121−188 638−989 6,954−67,644 0.043 17,740−27,510 2,828

1.1 million years

1 large magnitude 

storm year/50 

years

240−499 38−80 201−420 2,184−28,678 0.043 5,609−11,663 888

1.1 million years

1 large magnitude 

storm year/100 

years

175−415 28−66 147−348 1,609−23,850 0.043 4,090−9,700 654

mining the mobility of selenium in surface-water and groundwater systems and, hence, the extent and impact of selenium in 

drainage water discharges (such as subsurface drainage) from 

those systems. 

The effect of a large reservoir of selenium on recent 

subsurface drainage flow (potentially discharged source 

waters) is illustrated in figure A8. Figure A8 is generalized 

from data collected (USBR and others, 1998 and ongoing) 

during frequent sampling of drainage source water (current 

agricultural discharges to the San Joaquin River in WYs 1997 

and 1998 from the Grassland subarea) (appendix D, figs. D15 

and D16). Flow or discharge increases with increased water 

flux (applied irrigation or precipitation). The concentration 

of selenium in the discharged source agricultural wastewater 

increases as water flux increases. Only at elevated water 

fluxes seen during extremely wet years (the maximum rainfall 

occurring in a February over a 50-year record) does a dilution 

effect occur, lowering the concentration. The higher concentrations of selenium discharged under high flow conditions are 

Rate of selenium oxidation

Oxygen flux

Asymptote

Figure A7. Generalized selenium oxidation rate as a 

function of oxygen flux.
112 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

an indication of the magnitude of the selenium reservoir and 

the conditions under which displacement of variable-quality 

shallow ground water may occur. Selenium load in source water 

also increases as a result of increased water flux (fig. A8). The 

combined effect of increasing concentration and increasing flow 

as water flux increases assures an increase in selenium load 

discharged as more irrigation water is applied or more precipitation falls. 

Control and Timing 

During 1986 to 1998, the highest annual loads from 

agricultural drainage in the San Joaquin Valley (fig. A9) were 

discharged in years of normal or above average precipitation 

(Central Valley Board, 1996b, c; 1998d, e, f, g, h; 2000b, c; 

Department of Water Resources, 1986 to 1998) (fig. A10) (also 

see later discussion). Regulatory load targets also are highest 

during February, March, April, and May, reflecting agricultural practices (fig. A11) (USBR, 1995; Central Valley Board, 

1996c, 1998a). It is possible that dilution afforded during 

wetter years by the increased volume of water in rivers could

decrease salt and selenium concentrations at compliance 

points in the San Joaquin River or in the Bay-Delta, especially 

seaward from the inflows of the Sacramento River. The extent 

of dilution depends upon uncontaminated water inputs relative to San Joaquin River loads. However, selenium and salt 

concentrations do not necessarily decrease in wet years in agricultural drainage water itself, or in agricultural drainage canals 

where discharge is predominantly selenium-laden water (fig. 

A7). An out-of-valley agricultural drainage discharge to the 

Bay-Delta also may be subjected to these natural or seasonal 

effects (see later discussions on modeled discharge to the San 

Joaquin River). The effect could be larger loads discharged to 

receiving waters during wet seasons than might otherwise be 

expected through management. 

Control of release of agricultural discharge to take advantage of the high-volume river flows was suggested in 1955, 

when the San Luis Drain was planned, and throughout many 

of the later planning reports (such as Interagency Drainage 

Program, 1979a, b). In 1997, the State Board Draft Environmental Impact Report (DEIR) for Implementation of the 1995 

Bay-Delta Water Quality Control Plan concluded that scheduling the release of subsurface agricultural drainage from the 

western San Joaquin Valley is crucial to meeting the Bay-Delta 

water-quality standards, including salinity (State Board, 1997). 

Further documentation in the DEIR of future drainage systems 

conceptualized the temporary control of potential drainage 

discharges stored in the soil profile using a system of valves, 

weirs, and sumps. A similar management technique using 

DO-SIR valves is in practice in the Grassland subarea to enable 

storage of subsurface drainage [Grassland Area Farmers, 1997; 

USBR and others, 1998 and ongoing]. Grassland area farmers 

in discussions with regulators have pointed out the effect of 

this type of storage technique by calculating the amount of 

0

15,000

10,000

Drainage Problem Area/

Grassland Bypass Project Area

Crows Landing

Vernalis

5,000

20,000

8,000 lbs

86 88 90 92 94 96 87 89 91

Water year

93 95 97 98a 98b

Selenium, in lbs

6,000 lbs

Selenium concentration

Water flux

Load

Concentration

Fall Summer El Niño

Selenium load

Figure A8. Generalized selenium load and selenium 

concentration as a function of water flux.

Figure A9. Selenium load for Drainage Problem 

Area/Grassland Bypass Project Area, San Joaquin 

River at Crows Landing, and Vernalis for WYs 

1986–1998.
Appendix A. Export Drain Planning History and Geologic Inventory 113

selenium they have not discharged to the San Joaquin River 

on an annual basis (for example, WY 1997, 3,680 lbs selenium not discharged or stored compared to 7,097 lbs selenium 

discharged) (USBR and others, 1999). These types of drainage 

management activities emphasize the importance of considering changes in selenium reservoirs (storage) and of documenting a selenium inventory or mass balance, as opposed to 

focusing on short-term averages of discharges that represent 

annual leaching to sustain a year-to-year farming effort. 

6

0

12

18

Average 1986–94

7.13 inches

86 88 90 92 94 96 87 89 91

Water year

93 95 97 98

Precipitation, in inches

400

0

800

1200

O

348 348 389

533

866

799

666

599 599

533

350

1066

N J M D F A J A

Month

M J S

Selenium, in lbs

Figure A10. CIMIS (California Irrigation Management Information 

System) station #124 precipitation for WYs 1986–1998.

Figure A11. Monthly selenium load targets for San Luis Drain discharge to Mud Slough for WYs 1997 and 1998.
114 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Appendix B. San Joaquin Valley Agricultural Drainage Projections

Contents

Projected Selenium Loads from Historic Data and Evidentiary Testimony................................................................................................116

Projections from Drainage Program Management Options.........................................................................................................................124

Projections from Currently Available Data......................................................................................................................................................124

Estimates of Capacity of Drainage Conveyance (proposed San Luis Drain extension) ..........................................................................135

Total flux from Agricultural Drainage Discharge (lbs selenium per day) ...................................................................................................135

Figures

Figure B1. Annual selenium load projections at (a) 50, (b) 150 and (c) 300 μg/L selenium for drainage 

discharges from the Northern, Grassland, Westlands, Tulare, and Kern subareas..............................................................125

Figure B2. Projected drainage volume and annual selenium loads for variable selenium concentrations for (a) Northern 

subarea, (b) Grassland subarea, (c) Westlands subarea, (d) Tulare subarea, and (e) Kern subarea ...............................135

Figure B3. Projected drainage volume and annual selenium loads for select minimum and maximum selenium 

concentrations for (a) Northern subarea, (b) Grassland subarea, (c) Westlands subarea,

(d) Tulare subarea, and (e) Kern subarea.....................................................................................................................................136

Figure B4. Projected (a) minimum and (b) maximum selenium flux (lbs per day) for the Northern, Grassland, 

Westlands, Tulare, and Kern subareas .........................................................................................................................................136

Tables

Table B1. Westlands Water District historical data for acreage and selenium concentrations employed 

to project selenium loads ................................................................................................................................................................117

Table B2. Projections of annual selenium loads discharged to a San Luis Drain extension using (1) evidentiary 

estimates and selenium concentrations of 50, 150, and 300 μg/L for Westlands Water District drainage; 

and (2) 62.5 μg/L applied to 30,000 to 40,000 acre-feet of drainage for Grassland Area Farmers .......................................118

Table B3. Grassland subarea loads to the San Joaquin River for years 2000 and 2040 using San Joaquin Valley 

Drainage Program drainage volumes and selenium concentrations for Zones A, B, and C ...............................................118

Table B4. Annual acre-feet, selenium concentrations, and selenium loads from the Grassland Area 

Farmers Drainage Problem Area....................................................................................................................................................119

Table B5. Annual flow, selenium concentrations, and selenium loads from Mud and Salt Sloughs ...................................................120

Table B6. Annual flow, selenium concentrations, and selenium loads measured at the San Joaquin River 

near Crows Landing/Patterson.................................................................................................................................................................... 120

Table B7. Annual flow, selenium concentrations, and selenium loads measured at the San Joaquin River near Vernalis ............120

Table B8. Acreage, annual discharge, selenium concentrations and selenium loads for the Grassland Bypass 

Channel Project (reuse of a 28-mile portion of the San Luis Drain) for WYs 1997 and 1998 and selenium 

load target for regulatory purposes...............................................................................................................................................121

Table B9. Grassland Bypass Channel Project (reuse of a 28-mile portion of the San Luis Drain) WY 1997 drainage, 

selenium concentrations, selenium loads, and selenium load targets for regulatory purposes ........................................122
Appendix B. San Joaquin Valley Agricultural Drainage Projections 115

Table B10. Grassland Bypass Channel Project (reuse of a 28-mile portion of the San Luis Drain) WY 1998 drainage, 

selenium concentrations, selenium loads, and selenium load targets for regulatory purposes.....................................123

Table B11. Acreage used by the Drainage Program for planning purposes in 1985 −1990...................................................................125

Table B12. Acreage (irrigated, abandoned, and problem), problem water, and annualized cost (problem water 

reduction and management plan implementation) used by the Drainage Program..........................................................126

Table B13. Projected drainage using Drainage Program (1990a) tile-drained acreage for 1990, 2000, and 2040 .............................126

Table B14. Projected drainage using a drainage improvement factor of 0.40 acre-ft/acre/year and Drainage

Program (1990a) data....................................................................................................................................................................127

Table B15a. Projections of annual selenium loads per subarea using Drainage Program problem water estimates for 

2000 (without future alternative, 0.60 to 0.75 acre-ft/acre/year) and a 50 μg/L selenium concentration in drainage..128

Table B15b. Projections of annual selenium loads per subarea using Drainage Program problem water estimates for 

2000 (without future alternative, 0.60 to 0.75 acre-ft/acre/year) and a 150 μg/L selenium concentration in drainage 128

Table B15c. Projections of annual selenium loads per subarea using Drainage Program problem water estimates for 

2000 (without future alternative, 0.60 to 0.75 acre-ft/acre/year) and a 300 μg/L selenium concentration in drainage 128

Table B16a. Projections of annual selenium loads per subarea using Drainage Program subsurface drainage volumes

for 2000 (without future alternative, 0.60 to 0.75 acre-ft/acre/year) and selenium concentrations 

of 50, 150, and 300 μg/L .................................................................................................................................................................129

Table B16b. Projections of annual selenium loading per subarea using Drainage Program subsurface drainage volumes

for 2000 (with future alternative, 0.40 acre-ft/acre/year) and selenium concentrations 

of 50, 150, and 300 μg/L .................................................................................................................................................................129

Table B16c. Projections of annual selenium loading per subarea for 2000 using Drainage Program subsurface drainage 

volumes, with targeted future alternative (0.20 acre-ft/acre/year), and selenium concentrations of 50, 150, 

and 300 μg/L....................................................................................................................................................................................129

Table B17. Projections of annual selenium loads per subarea using Drainage Program drainage estimates (subsurface 

drainage, problem water, drainage without future, drainage with future, and drainage with a targeted future)

and selenium concentrations of 50, 150, and 300 μg/L............................................................................................................130

Table B18. Summary of projections of annual selenium loads per subarea with Drainage Program estimates of drainage 

volume and different assigned selenium concentrations (50, 150, 300 μg/L)......................................................................131

Table B19. Tulare subarea drainage and selenium concentrations in 1988 and 1989 for privately owned evaporation basins.....131

Table B20. Tulare subarea drainage and selenium concentrations from 1993 to 1997 for privately owned evaporation basins...132

Table B21. Kern subarea drainage and selenium concentrations in 1988, 1989, and 1993 through 1997 ...........................................133

Table B22. Selenium load scenarios using planned capacities of the San Luis Drain or valley-wide drain and 

assigned selenium concentrations of 50, 150, and 300 μg/L. ................................................................................................133

Table B23a. Projected selenium loads using Drainage Program (1990a) data for problem water and subsurface 

drainage and daily fluxes from the western San Joaquin Valley to a proposed San Luis Drain extension...................134

Table B23b. Projected low-range selenium loads and daily fluxes from the western San Joaquin Valley to a 

San Luis Drain extension..............................................................................................................................................................134

Table B23c. Projected high-range selenium loads and daily fluxes from the western San Joaquin Valley to a 

San Luis Drain extension..............................................................................................................................................................134
116 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Projected Selenium Loads from Historic Data 

and Evidentiary Testimony

Envisioned drainage volumes were presented in earlier 

discussions concerning water quality conditions in groundwater aquifers and sustainability of discharge from the San 

Joaquin Valley (appendix A). Presented here are selenium load 

projections for the Westlands, Grassland, Tulare, Kern, and 

Northern subareas based on documentation for planning and 

available measurements of drainage discharge.

Westlands Water District and Subarea

Projections from Historic Data 

Westlands subarea projections of selenium loads are 

based on 1) historic measurements of drainage discharged 

from Westlands Water District into the San Luis Drain from 

1981 until its closure in 1986; and 2) design estimates used 

in testimony by Westlands Water District. Using a historical 

range of 330 to 430 μg/L selenium for the initial hook-up of 

subsurface drains to the San Luis Drain, the projected load 

is 6,283 to 8,187 lbs selenium per year (table B1). These 

amounts are higher than those estimated by the USBR as 

having occurred over the 57-month period of San Luis Drain 

operation (January 1981-September 1985, average of 4,776 

lbs per year) (USBR, 1986).

A recent compilation from Westlands Water District 

indicated a discharge of 38,450 acre-ft from January 1981 

through May 1986 (Westlands Water District, 1998). An 

estimated 22,660 lbs of selenium was discharged to Kesterson 

Reservoir during this time (USBR, 1986). This estimated 

input of selenium includes 17,400 lbs that were distributed 

in the water, biota, and sediment of Kesterson Reservoir and 

5,280 lbs of selenium contained in 95,271 cubic yards of bed 

sediment still residing in the San Luis Drain. The cumulative 

17,400-lb amount is hereafter referred to as one kesterson 

(kst). The kst unit represents a measure of potential cumulative hazard to wildlife based on mass loading directly released 

into an ecosystem (Presser and Piper, 1998). This unit will be 

used later to provide historical and quantitative perspectives. 

Projections from Evidentiary Testimony

Evidence presented in 1996 referred to estimates 

prepared in 1965 for planned discharges from Westlands 

Water District. These estimates preceded use of management 

practices that place an emphasis on more efficient water use 

(Westlands Water District, 1996). Table B1 shows projected 

discharge to the San Luis Drain by 1980 in comparison to that 

estimated to actually have occurred from 1981 to 1985. The 

planning estimates were expressed as volumes of drainage or 

acreage to be drained. If a 330 to 430 μg/L selenium concentration range (see previous discussion) is used in conjunction 

with an estimate of 38,000 acre-ft of annual drainage, then the 

projected selenium load is 34,109 to 44,445 lbs per year from 

76,000 acres in Westlands Water District (Westlands Water 

District, 1996). Using these estimates, projections of generated drainage and selenium are: 0.50 acre-ft of drainage per 

acre per year; 0.449 to 1.02 lbs selenium per acre per year; or 

0.898 to 1.17 lbs selenium per acre-feet per year (table B1). 

Data for selenium concentrations in drainage presently 

are not available from Westlands Water District because, 

since closure of the San Luis Drain in 1986, drainage is being 

stored in the subsurface (Jones and Stokes Associates, Inc., 

1986a, b; Drainage Program, 1989, 1990a). This practice 

could potentially endanger the quality of San Joaquin Valley 

groundwater aquifers. The eventual loss of use of the ground 

water basin beneath the San Luis Unit has been predicted at 

various stages of planning processes as a justification for an 

out-of-valley drain. Trade-offs were to be among lands kept 

in production, water export from the Bay-Delta, groundwater 

quality, and San Joaquin River degradation (USBR, 1978). 

The Drainage Program (1990a) estimated the remaining life 

of the semi-confined aquifer beneath the Westlands subarea 

(576,000 acres) based on salinity (total dissolved solids) at a 

mean of 110 years. Minimum life remaining in some areas of 

the western San Joaquin Valley was as low as 25 years. 

Several evidentiary proceedings concerning the disposition of drainage from Westlands Water District and the 

San Luis Unit have resulted in judgments and testimony 

concerning the quantity of drainage (table B2) (Westlands 

Water District, 1996). Annual drainage discharge from the 

San Luis Unit of the Central Valley Project was estimated 

as part of the Barcellos judgment (1986) to be an amount 

of discharge not greater than 100,000 acre-ft and not less 

than 60,000 acre-ft (USBR, 1992). Using assigned selenium 

concentration of 50, 150, 300 μg/L (see discussion in main 

text), selenium loads would range from 8,160 to 81,600 lbs 

per year (table B2). 

Estimates of drainage from the Westlands Water District 

presented in testimony in 1996 were based on including 

42,000 acres in the northeastern corner of Westlands Water 

District. Subsurface drains have been installed there, but are 

not connected to the San Luis Drain. The evidence stated 

that an additional 29.5 miles of the San Luis Drain would be 

constructed to reach this area, if drainage was to be provided 

for all areas of Westlands Water District needing drainage. 

An estimate of the volume of drainage (1,900 to 2,300 acre-ft 

per year) to be discharged upon initial reconnection to the San 

Luis Drain from Westlands Water District is not well justified, 

but is presented here for comparison to those estimates given 

by Westlands Water District in 1980 (7,000 acre-ft per year). 

The evidence presented showed a total problem acreage of 

200,000 acres for Westlands Water District, with 60,000 acreft of drainage generated annually (Westlands Water District, 

1996). This estimate represents a 0.3 acre-ft per acre per 

year rate of generation of drainage. Using assigned selenium 

concentrations of 50, 150, and 300 μg/L, projected selenium 

loads are 8,160 to 48,960 lbs per year from the Westlands 

Water District, with an initial hook-up contributing 258 to 

1,877 lbs selenium (table B2). 
Appendix B. San Joaquin Valley Agricultural Drainage Projections 117

Grassland Subarea (WYs 1986–1996)

Projections from Historic Data

Provision of a drainage outlet was initially focused on 

Westlands Water District, but drainage specifications actually apply to a larger area designated as the San Luis Unit 

of the Central Valley Project (USBR, 1992) (fig. A1). Westlands Water District within the San Luis Unit is referred to 

as the San Luis Service Area (irrigation service from the San 

Luis Canal portion of the California Aqueduct). Parts of the 

Grassland area within the San Luis Unit are referred to as 

the Delta-Mendota Service Area (irrigation service from the 

Delta-Mendota Canal). In general, the Grassland problem area 

considered here has approximately 100,000 acres in production, with 50,000 acres requiring subsurface drainage. Designated zones within the Grassland subarea are mainly based 

on water quality: zone A, 72,000 acres; Zone B, 14,000 acres; 

and Zone C, 30,000 acres (table B3) (Drainage Program, 

1990a). Zone A is projected to generate drainage of poor 

enough quality to impair State beneficial uses for receiving 

waters and therefore is a focus of drainage analysis. The water 

and drainage districts of the Grassland subarea continue to 

consolidate into regional groups based on varying needs and 

legal ramifications, adding to already complex historical alignments (USBR, 1992; Environmental Defense Fund, 1994). 

The area generally generates blended subsurface drainage that 

is discharged out of the region through the San Joaquin River. 

Discharge of selenium from the State-designated Grassland Drainage Area to the San Joaquin River has been moniTable B1. Westlands Water District historical data for acreage and selenium concentrations employed to project selenium loads. 

Use of San Luis Drain by Westlands 

Water District to discharge selenium 

to Kesterson Reservoir

Westlands Water 

District planned 

drainage acreage/ total acreage (acres)

Problem 

acreage 

with onfarm drains 

(acres)

Problem 

drainage 

(acre-ft)

Selenium 

(μg/L)

Selenium load

(lbs/time interval)

Factors

(acre-ft/acre,

lbs selenium/

acre-ft, or lbs 

selenium per yr)

San Luis Drain discharge 

(measurement average 1983-1984) 

(State Board, 1985; Westlands Water 

District, 1998)

− − 38,450 

(total discharge 

for 65 months; 

Jan. 1981 to 

May 1986)

330−430 − −

Estimated Westlands Water District 

annual discharge to San Luis Drain 

from Jan. 1981−Sept. 1985 (selenium 

concentrations from use of drain in 

1983−1984) (State Board, 1985)

− 5,000 

(42,000a

)

 7,000 330−430 6,283−8,187/yr 0.17−1.4 acre-ft/ 

acre; 

0.898−1.17 lbs/

acre-ft

Projected Westlands Water District 

discharge to San Luis Drain by 1980 

(based on 1965 plans and selenium 

concentrations from use of drain in 

1983−84) (Westlands Water District, 

1996) 

300,000/600,000 

(approximately 

566,500 irrigated 

acres)

76,000 38,000/yr 330−430 34,109−44,445/yr 0.50 acre-ft/acre; 

0.898−1.17 lbs/

acre-ft; 

0.449−1.02 lbs/ 

acre/yr

1986 Environmental Impact Statement (EIS) estimated San Luis Drain 

discharge (USBR, 1986): total (Jan. 

1981−Sept. 1985) or annual (total 

averaged over 57 months) 

− − − − 22,660 

or 4,776/yr

−

1986 EIS estimated San Luis Drain 

selenium load to Kesterson Reservoir 

(1981– 85) (USBR, 1986)

− − − − 17,400b (1 kst) −

1986 EIS estimated San Luis Drain 

bed sediment accumulation (95,271 

cubic yards) (USBR, 1986)

− − − − 5,280 −

a

Westlands Water District contends that the drainage from 5,000 subsurface-drained acres actually represents drainage from 42,000 acres because of upslope 

contributions drained to this downslope area (State Board, 1985).

bThe 17,400-lb amount is referred to as one kesterson (kst). The use of this unit provides perspective on the quantity of selenium that was a hazard to wildlife 

when released directly to the wetland at Kesterson Reservoir (Presser and Piper, 1998). 
118 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

tored since 1986 (Central Valley Board, 1996b, c, 1998 d, e, f, 

g; h; 2000b, c; Henderson and others, 1995; USBR and others, 

1998 and ongoing). Drainage discharge was through Grassland 

area wetland channels to San Joaquin River during this period, 

with the drainage configuration changing in 1997 (see discussion below, discharge through the San Luis Drain and Mud 

Slough to the San Joaquin River). Selenium load summaries at 

four monitoring sites from WY 1986 to 1998 in this area are 

given in tables B4 through B7. 

Selenium is persistently discharged from the Grassland 

area to the San Joaquin River, but selenium loads depend on 

monitoring-site location within the Grassland area because 

of uptake and release of selenium throughout the watershed 

(tables B4 –B7). The upstream drainage source discharge 

represents managed components of flow and load. However, 

annual data are not available from individual farm-field sumps 

to help qualify source-area shallow groundwater conditions 

and determine long-term variability in selenium concentrations. Affected downstream sites reported here are the San 

Joaquin River at Crows Landing/Patterson (CL/PATT, about 

50 miles downstream from the farm agricultural discharge 

sumps), and the San Joaquin River at Vernalis (VERN, about 

Table B3. Grassland subarea loads to the San Joaquin River for years 2000 and 2040 using Drainage Program drainage volumes and 

selenium concentrations for Zones A, B, and C (Drainage Program, 1989; 1990a). 

Drainage Program 2000 Drainage Program 2040

Grassland 

subarea

Projection 

(drained 

acres)a

Projection 

(acre-ft of 

problem 

water) b

Projection 

(acre-ft 

discharged to 

San Joaquin 

River)b

Projected 

selenium 

(μg/L)b

Projected 

selenium 

load (lbs/

year)

Factor 

(lbs/

acre-ft)

Projection 

(acre-ft

discharged to 

San Joaquin 

River)b

Projected 

Selenium 

(μg/L)b

Projected 

selenium 

load (lbs/

year)

Factor 

(lbs/

acre-ft)

Zone A 72,000 54,000 10,700 150 4,366 0.408 21,000 75 4,284 0.204

Zone B 14,000 10,600 7,000 2 38 0.0054 17,600 2 96 0.0054

Zone C 30,000 22,000 22,000 2 120 0.0054 63,500 2 345 0.0054

Total 116,000 86,600 39,700 − 4,524 − 102,100 − 4,725 −

a

Drainage Program (1989), page 4-23 (assumption, drained acres will more than double by year 2000).

bDrainage Program (1990a) table 29 and page 139. 

Table B2. Projections of annual selenium loads discharged to a San Luis Drain extension using 1) evidentiary estimates and selenium 

concentrations of 50, 150, and 300 μg/L for Westlands Water District drainage; and 2) 62.5 μg/L applied to 30,000 to 40,000 acre-feet of 

drainage for Grassland Area Farmers. 

[This scenario includes resumption of discharge to the San Luis Drain by Westlands Water District and continuing discharge by Grassland Area Farmers to a 

28-mile portion of the San Luis Drain under the Grassland Bypass Channel Project Data sources: USBR, 1992; Westlands Water District, 1996).] 

Westlands subarea or 

San Luis Unit

Problem 

drainage 

(acre-ft)

Factor 

(acreft/acre)

Projected 

selenium 

(μg/L)

Projected 

selenium load 

(lbs/year)

Projected 

selenium 

(μg/L)

Projected 

selenium load 

(lbs/year)

Projected 

selenium 

(μg/L)

Projected 

selenium load 

(lbs/year)

Barcellos Judgment not < 60,000

not > 100,000

− 50 8,160−

13,600

150 24,480−

40,800

300 48,960−

81,600

Planning Alternatives 24,000 0.23 50 3,264 150 9,792 300 19,584

Initial hook-up of 7,600 

acreage of on-farm drains

1,900−

2,300

− 50 258−

313

150 775−

938

300 1,550−

1,877

Drainage of 200,000 

acres of problem acreage

60,000 0.30 50 8,160

(0.041 lbs 

/acre; 0.136 

lbs/acre-ft)

150 24,480 

(0.122 lbs/ 

acre; 0.408 

lbs/acre-ft)

300 48,960 

(0.245 lbs/ 

acre; 0.816 

lbs/acre-ft)

Grassland Area Farmers 30,000−

40,000a

− 62.5a 5,100−

6,800

 62.5a 5,100−

6,800

62.5a 5,100−

6,800

Total (Westlands and 

Grassland)

90,000−

100,000

− − 13,518−

15,273

− 30,355−

32,218

− 55,610−

57,637

a

Measured in WY 1997 (see appendix B, table B8).
Appendix B. San Joaquin Valley Agricultural Drainage Projections 119

130 miles downstream from the agricultural discharge). Data 

for WY 1986 to 1998 generally can be related to physical 

variables that affect drainage conditions (see, for example, 

appendix A, fig. A10, annual rainfall measured at station 

#124, Department of Water Resources database http://www.

ceresgroup.com/col/weather/cimis). Noted climatic changes 

during this time period are: drought from 1987 through 

1992; flooding in the Coast Ranges in 1995; and flooding in 

the Sierra Nevada and San Joaquin Valley in the winter of 

1997– 98 as a consequence of El Niño conditions. Specific 

variables affecting selenium load are discussed in appendix D. 

For management purposes, analysis of loads for WYs 

1986 to 1988 showed an annual average of 10,850 lbs selenium per year (Environmental Defense Fund, 1994). For WYs 

1986 to 1998, the range of managed source selenium loads 

is from 5,083 to 11,875 lbs per year (table B4). For the same 

time period, the range of annual loads for the State compliance 

point for the San Joaquin River at Crows Landing is 3,064 to 

15,884 lbs per year (table B6). The range of loads for the San 

Joaquin River at Vernalis, considered the entrance to the BayDelta, is 3,558 to 17,238 lbs per year (table B7). Higher loads 

in recent years (San Joaquin River at Crows Landing, 8,667 

lbs in WY 1997; and 15,501 lbs in WY 1998) are noteworthy 

because they occur after issuance of (1) State agricultural 

drainage control plans issued in 1985; (2) joint Federal-State 

agricultural drainage management plans issued in 1990; (3) a 

State limitation for annual drainage to the San Joaquin River 

of 8,000 lbs selenium adopted in 1996 (Central Valley Board, 

1996c and 1998a, h; USBR and others, 1998 and ongoing; and 

see also appendix A, fig. A9). 

 For WYs 1986 through 1998, the cumulative selenium 

load discharged to the San Joaquin River at Crows Landing/

Patterson was 114,879 lbs selenium (table B6). This equates 

to 6.6 kestersons (ksts) as a measure of potential cumulative 

hazard based on load (see later discussion) (Presser and Piper, 

1998). However, these data compilations may not represent 

all sources, reservoirs, and discharges of selenium for the 

San Joaquin River system. For example, unregulated sumps 

discharge agricultural drainage into the Delta-Mendota Canal 

and other potential sources of selenium are outside of regulated areas (Central Valley Board, 2000d and 2002; USBR, 

2002b).

As described earlier as context for future discharges, 

regulatory enactments of Daily or Total Maximum Monthly 

Load models call for discharges of 1,001 to 3,088 lbs selenium 

per year from the Grassland subarea by the year 2010 (also see 

appendix C). 

Grassland Bypass Channel Project (Reuse of the San Luis 

Drain, WY 1997 to present)

In 1990, the Drainage Program considered re-routing 

drainage from the Grassland subarea through reuse of a 

portion of the San Luis Drain to avoid wetland contamination 

(drainage through the San Luis Drain and Mud Slough to San 

Joaquin River). Table B3 shows estimates by the Drainage 

Program of potential drainage from the zones of the Grassland 

subarea. A selenium concentration of 2 μg/L was assumed 

in both drainage from wetlands (Zone B) and in discharges 

from drained areas (Zone C). The discharge from the 72,000-

acre Zone A was estimated at either 10,700 acre-ft containing 

a selenium concentration of 150 μg/L; or 21,000 acre-ft 

containing a selenium concentration of 75 μg/L. The projected 

selenium load from the entire Grassland subarea is 4,524 lbs 

and 4,725 lbs for year 2000 and 2040, respectively. These 

planning values are less than the loads measured historically 

(tables B4 to B7) and those more recently through the Grassland Bypass Channel Project (see below and table B8).

Consideration of a project to re-open part of the San 

Luis Drain for use by the Grassland subarea was of enough 

concern to elicit a U.S. Congressional hearing in 1993 (U.S. 

House of Representatives, 1993). Although, environmental 

concerns were voiced, the interim-use project was seen as a 

way to relieve the pressure of the long-standing agricultural 

drainage problem in the San Joaquin Valley. In September 

1996, the USBR initiated the Grassland Bypass Channel 

Project to reopen a 28-mile portion of the San Luis Drain on 

an interim five-year basis (USBR, 1995). Cooperative support 

for the project among agriculture, environmental groups, 

Table B4. Annual acre-feet, selenium concentrations, and 

selenium loads from the Grassland Area Farmers Drainage 

Problem Area.

[ Data sources: Central Valley Board, 1996b, c; 1998d, e,f, g,h; 2000b, c; 

USBR and others, 1998 and ongoing.]

WateryearDrainage

(acre-ft/

year)

Selenium

(μg/L)

Selenium 

load

(lbs/year)

Factor

(lbs selenium/ 

acre-ft)

1986 67,006 52.3 9,524 0.142

1987 74,902 53.8 10,959 0.146

1988 65,327 56.8 10,097 0.154

1989 54,186 59.2 8,718 0.161

1990 41,662 65.2 7,393 0.177

1991 29,290 73.5 5,858 0.200

1992 24,533 76.2 5,083 0.207

1993 41,197 79.0 8,856 0.215

1994 38,670 80.5 8,468 0.219

1995 57,574 75.8 11,875 0.206

1996 52,978 70.0 10,034 0.189

1997a 37,483 62.5 7,097 0.186

1998a 45,858 66.9 9,118 0.199

TOTAL – – 113,080 

(average 

8,698)

–

a

Measured at San Luis Drain discharge to Mud Slough (site B) after 

initiation of Grassland Bypass Channel Project.
120 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table B5. Annual flow, selenium concentrations, and selenium loads from Mud and Salt Sloughs. 

[Central Valley Board, 1996b, c; 1998d, e,f, g,h; 2000b, c; USBR and others, 1998 and ongoing.]

Wateryear

Flow 

(combined Mud and 

Salt Sloughs) (acreft/year average)

Selenium

(combined Mud 

and Salt Sloughs) 

(μg/L average)

Selenium load 

(combined Mud 

and Salt Sloughs) 

(lbs/year)

Mud Slough 

(μg/L monthly 

average range)

Salt Slough

(μg/L monthly 

average range)

1986 284,316 8.6 6,643 2.3−22 1.4−22

1987 233,843 12.0 7,641 1.7−26 5.2−26

1988 230,454 13.0 8,132 1.4−18 1.6−27

1989 211,393 14.1 8,099 0.7−5.0 2.7−33

1990 194,656 14.6 7,719 0.6−8.1 4.2−36

1991 102,162 14.0 3,899 0.7−38 0.9−30

1992 85,428 12.6 2,919 0.8−48 0.6−27

1993 167,955 15.0 6,871 1.0−5.0 0.5−42

1994 183,546 16.0 7,980 0.5−22 1.2−44

1995 263,769 14.9 10,694 0.7−4.2 0.8−38

1996 267,344 13.0 9,697 – –

1997 288,253 10.0 7,722 5.0−80 0.5−3.4

1998 378,506 14.0 10,446 6.9−67.3 0.6−4.0

TOTAL – – 98,462

(8,890 average)

– –

Table B6. Annual flow, selenium concentrations, and selenium loads 

measured at the San Joaquin River near Crows Landing/Patterson. 

[Data sources: Central Valley Board 1996b, c; 1998d, e,f, g,h; 2000b, c; USBR 

and others, 1998 and ongoing.]

Wateryear

Flow

(average 

million acreft/year)

Selenium

(average 

μg/L)

Selenium 

load

(lbs/year)

Selenium 

(monthly 

average μg/L 

range)

1986 2.67 1.6 11,305 <1–4

1987 0.66 4.9 8,857 3.6–12

1988 0.55 6.2 9,330 0.8–12

1989 0.44 6.3 7,473 3.4–17

1990 0.40 5.6 6,125 1.6–13

1991 0.29 4.5 3,548 0.9–11

1992 0.30 3.7 3,064 0.7–11

1993 0.89 3.5 8,379 0.4–8.0

1994 0.56 4.8 7,270 <0.4–13

1995 3.50 1.6 14,291 0.6–12

1996 1.44 3.0 10,686 –

1997 4.18a 1.0 8,667a 0.1–10

1998 5.13 – 15,501 0.4–4.1

TOTAL – – 114,496

(8,807

average/yr)

–

a

Data from the Grassland Bypass Channel Project shows 3.713million acreft and 9,054 lbs for WY 1997.

Table B7. Annual flow, selenium concentrations, and selenium 

loads measured at the San Joaquin River near Vernalis. 

[Data sources: Central Valley Board 1996b, c; 1998d, e,f, g,h; 2000b, c; 

USBR and others,1998 and ongoing.]

Wateryear

Flow

(average 

million acreft/year)

Selenium

(average 

μg/L)

Selenium 

load

(lbs/year)

Selenium 

(monthly 

average μg/L 

range)

1986 5.22 1.0 14,601 <0.1-1.4

1987 1.81 1.8 8,502 0.6-3.2

1988 1.17 2.7 8,427 0.8-4.0

1989 1.06 3.0 8,741 1.7-6.8

1990 0.92 3.0 7,472 0.8-9.6

1991 0.66 2.0 3,611 0.5-4.8

1992 0.70 1.9 3,558 0.4-4.4

1993 1.70 1.9 8,905 <0.4-6.1

1994 1.22 2.3 7,760 0.4-6.3

1995 6.30 1.0 17,238 0.5-3.5

1996 3.95 1.1 11,431 –

1997 6.77 0.6 11,190 –

1998 8.50 – 15,810 –

TOTAL – – 127,246 

(9,788

average/yr)

–
Appendix B. San Joaquin Valley Agricultural Drainage Projections 121

and government included a regional drainage analysis and 

an approach to controlling non-point source pollution that 

integrated tradable permits and incentives (Environmental 

Defense Fund, 1994). The collector drain now transports 

drainage more directly to the San Joaquin River, thereby 

removing it from wetland channels. The goals include (1) 

measuring and eventually reducing drainage loads through a 

regional program; (2) protecting riparian wildlife habitat by 

assuring wetlands of an adequate clean-water supply; and (3) 

monitoring the effects that result from re-routing of drainage. 

A regional drainage agency that includes local water and 

drainage districts is assigned responsibility for pollution. A 

Federal/State interagency committee monitors flow, water 

quality, sediment quality, biota, and toxicity in the San Luis 

Drain, Mud Slough, Salt Slough, and the San Joaquin River 

(USBR and others, 1996). Monetary penalties for exceedance 

of loads have been agreed upon and a long-term management 

strategy to achieve water-quality objectives is being developed (Grassland Area Farmers and San Luis Delta-Mendota 

Water Authority, 1998). 

Selenium load targets for the reuse of the San Luis 

Drain are defined by the commitment that the input loads to 

the San Joaquin River will not worsen over historical loads 

(USBR, 1995). Appendix A (fig. A11) shows the monthly 

load targets adopted for the first two years of the Grassland 

Bypass Channel Project. Compliance loads are measured at 

the discharge of the San Luis Drain into Mud Slough rather 

than at the San Joaquin River at Crows Landing, as previously regulated by the State (Central Valley Board, 1996c). In 

September 1998, a State waste discharge permit was issued 

for the Grassland Bypass Channel Project which contained 

negotiated load targets (Central Valley Board, 1998a). Tables 

B8 to B10 show annual and monthly load targets for 1997 

through 2001. The target is 6,660 lbs for each of the first two 

years of the project with a 5 percent reduction each year for 

the next three years. If the annual target amount is exceeded 

by 20 percent, consideration would be given to shutting down 

the San Luis Drain and terminating the Grassland Bypass 

Channel Project (USBR, 1995). During the first two years of 

the project, loads were above load targets. It is also notable 

that drain water discharged to the San Joaquin River through 

the San Luis Drain is more consistently concentrated than 

were historic discharges to the wetlands channels system. 

Wastewater in the San Luis Drain is not diluted by wetlands 

flows and loss of selenium to sediment and biota, as occurred 

during transit through wetland channels (in-transit loss), may 

be reduced (USBR, 1995; Presser and Piper, 1998). Adoption 

by the State of a water-quality objective of less than 2 μg/L 

selenium for the Grassland wetland channels as promulgated 

by USEPA (USEPA, 1992; Central Valley Board, 1996c, 

Table B8. Acreage, annual discharge, selenium concentrations, and selenium loads for the Grassland Bypass Channel Project (reuse 

of a 28-mile portion of the San Luis Drain) for WYs 1997 and 1998 and selenium load target for regulatory purposes.

Use of San Luis Drain by Grassland Area Farmers 

(Grassland subarea Zone A) for discharge of selenium 

to the San Joaquin River

Problem 

acreage 

(acres)

Problem water 

or drainage

(acre-ft)

Selenium

(μg/L)

Selenium 

load

(lbs/year)

Factor

(lbs selenium/

acre or acre-ft)

Factor

(acre-ft/

acre)

Central Valley Board limitation of selenium discharge 

to the San Joaquin River or tributaries from tile or 

open drainage systems (effective October 1, 1996; 

Central Valley Board, 1996a, d)

– – – 8,000 – –

WY 1997-2001 San Luis Drain/Grassland Bypass 

Channel Project negotiated annual load targets for 

discharge through the San Luis Drain to the San 

Joaquin River (USBR, 1995)

93,400 – – 5,661– 

6,660a

0.06-0.07/acre –

WY 1997 San Luis Drain/Grassland Bypass Channel 

Project measured load discharged through the drain 

to the San Joaquin River (USBR and others, 1998)

97,400 37,483 62.5 6,960 0.073/acre

0.189/acre-ft

0.38

January 26, 1997 estimated load from Coast Range 

runoff discharged through the San Luis Drain 

(Grassland Area Farmers, 1997)

– – – 137 – –

WY 1998 San Luis Drain/Grassland Bypass Channel 

Project measured load discharged through the San 

Luis Drain to the San Joaquin River (USBR and others, 1998 and ongoing) 

97,400 45,858 66.9 9,118 0.094/acre

0.199/acre-ft

0.47

February, 1998 estimated load from Coast Range runoff discharged through the San Luis Drain (Grassland Area Farmers, 1997)– – – 487 – –

a

Note: Negotiated annual load targets (6,600 lbs selenium) differs from a total of monthly load targets (7,096 lbs selenium). 
122 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

1998a) has essentially removed these channels as possible 

alternative flow paths for drainage water. This regulation also 

will make it difficult to reuse the wetland channels as alternative channels during flood runoff or in the event that Westlands 

Water District once again uses the San Luis Drain. 

 Tables B9 and B10 give detailed monthly data for 

the Grassland Bypass Channel Project including volumes, 

targets, loads, and concentrations (USBR and others, 1998 

and ongoing). The annual load of 7,104 for WY 1997 includes 

6,960 lbs selenium that was discharged from the San Luis 

Drain to the San Joaquin River and 137 lbs selenium that was 

discharged to wetland channels during a flood in January 

1997. A fee of $60,000 was paid by the Grassland Area 

Farmers for exceedances of monthly and annual selenium 

load targets by 437 lbs (6.6 percent) in the first year of the 

project. The annual load represents 0.073 lbs selenium per 

acre or 0.189 lbs selenium per acre-ft for the Grassland Area 

of 97,400 acres. The average selenium concentration for WY 

1997 was 62.5 μg/L and the total volume was 37,483 acre-ft. 

The annual load for the second year of the Grassland Bypass 

Channel Project, WY 1998, was 9,130 lbs selenium. The 

annual selenium load target was exceeded by 37 percent which 

could have incurred a fee of $174,400, if the load was left 

unadjusted for flooding during the higher than normal rainfall 

in 1998 (note, 1998 was an El Nino year). The WY 1998 flood 

load was estimated at 487 lbs selenium, with 350 lbs documented in overflow to wetland channels. The average selenium 

concentration for the discharge for WY 1998 was 67 μg/L and 

the total volume was 45,858 acre-ft. This annual selenium load 

represents 0.094 lbs selenium per acre or 0.199 lbs selenium 

per acre-feet for the Grassland Area. 

Table B9. Grassland Bypass Channel Project (reuse of a 28-mile portion of the San Luis Drain) WY 1997 drainage, selenium 

concentrations, selenium loads, and selenium load targets for regulatory purposes. 

[Data source: USBR and others, 1998 and ongoing]

WY 1997

Drainage

(average monthly 

acre-ft)

Selenium

(average monthly 

μg/L)

Selenium load

(average monthly 

lbs)

Negotiated selenium 

load targets

(lbs)

Incentive fee

(dollars)

Sept. 23–30, 1996 − − 55a − −

October 1996 1,274 60.8 

(58.6)

202 348 $0

November 1996 1,566 58.3 252 348 $0

December 1996 1,943 51.5 285 389 $0

January 1997 3,696 59.5 599b 533 $2,800

February 1997 4,166 76.6 878b 866 $700

March 1997 4,867 84.2 1,119 1,066 $700

April 1997 4,446 105.5 1,280 799 $2,800

May 1997 4,208 75.7 849 666 $2,800

June 1997 3,451 64.3 611 599 $700

July 1997 3,271 48.1 428 599 $0

August 1997 3,153 40.6 348 533 $0

September 1997 1,442 25.3 109 350 $0

TOTAL (monthly) 37,483 − 6,960 7,096 

(monthly)

$10,500

TOTAL (yearly) 37,483 62.5

(average)

6,960 6,660 

(yearly)

$50,000

Storm discharge (lower watershed, Agatha Canal)− − 137b − −

TOTAL

(project plus storm 

discharge)

− − 7,097 − $60,500

a

Estimated and not counted in total.

b89 lbs selenium in January and 48 lbs selenium in February discharged to wetland sloughs (Agatha Canal) during San Luis Drain overflow events 

due to storms in January and February, 1997.
Appendix B. San Joaquin Valley Agricultural Drainage Projections 123

Westlands Subarea in Combination with 

Grassland Subarea

An analysis of discharge by the USBR in 1983 included 

the San Luis Unit and Delta-Mendota Services Areas, which 

encompasses both the Grassland and Westlands subareas. 

Taking a potential worst-case scenario for the year 2020, the 

amount of drainage from the San Luis Unit Service Area is 

135,240 acre-ft and from the Delta-Mendota Service Area is 

65,783 acre-ft. Using assigned selenium concentrations of 

50, 150, and 300 μg/L applied to these amounts of drainage, 

the range of selenium loads from San Luis Unit Service Area 

is from 18,393 to 110,356 lbs per year; and for the DeltaMendota Service Area is from 8,946 to 53,679 lbs per year. 

The range of combined selenium loads is from 27,339 to 

164,035 lbs per year.

Evidentiary hearings (Westlands Water District, 1996) 

included a scenario in which the Grassland Area drainage 

discharged to the San Joaquin River would be discharged to 

the San Luis Drain, along with the Westlands Water District 

discharges. However, under current agreements, the Grassland 

Bypass Channel Project would terminate if Westlands Water 

District is given permission to use the San Luis Drain (USBR, 

1995). Additional drainage from the Grassland Area (30,000 

to 40,000 acre-ft) is hypothesized here to be of better quality 

than that of water discharged to Kesterson Reservoir. Using 

a measured WY-1997 average concentration of 62.5 μg/L 

applied to these volumes, the projected selenium load is 5,100 

to 6,800 lbs per year (table B2). Under a combined Grassland/

Westlands scenario, the range of total annual loads is 13,518 

to 15,273 lbs per year selenium, if Westlands Water District 

drainage contains a concentration of 50 μg/L selenium. Total 

annual loads increase to 30,355 to 32,218 lbs selenium if 

Westlands Water District drainage contains a concentration 

of 150 μg/L; and 55,610 to 57,637 lbs per year if Westlands 

Water District drainage contains a concentration of 300 μg/L. 

Table B10. Grassland Bypass Channel Project (reuse of a 28-mile portion of the San Luis Drain) WY 1998 drainage, selenium 

concentrations, selenium loads, and selenium load targets for regulatory purposes. 

[Data source: USBR and others, 1998 and ongoing]

WY 1998

Drainage

(average monthly 

acre-ft)

Selenium

(average monthly 

μg/L)

Selenium load

(average 

monthly lbs)

Negotiated selenium 

load targets

(lbs)

Incentive fee

(dollars)

October 1997 1,753 51.9 248 348 $0

November 1997 1,555 48.9 207 348 $0

December 1997 1,403 48.7 178 389 $0

January 1998 1,419 85.0 335 533 $0

February 1998 6,980 52.5 965a 866 $4,200b

March 1998 7,094 83.3 1,600 1,066 $4,200b

April 1998 5,517 105.4 1,554 

(1,560)

799 $4,200b 

May 1998 4,881 104.5 1,371 666 $4,200b

June 1998 3,629 82.1 807 599 $4,200b

July 1998 4,564 49.7 615 599 $1,200

August 1998 3,876 47.5 500 533 $0

September 1998 3,187 43.1 388 350 $2,200

TOTAL

(monthly)

45,858 − − 7,096 

(monthly)

−

TOTAL

(yearly)

45,858 66.9 

(average)

8,768 6,660 

(yearly)

$150,000b

Storm discharge (lower watershed, Agatha Canal))− − 350a − −

TOTAL (project plus storm 

discharge)

− − 9,118 − $174,400

($3,400 paid)

a

350 lbs selenium discharged to wetland sloughs (Agatha Canal) during San Luis Drain overflow events due to storms in February, 1998.

b

Fees waived because of above average rainfall for WY 1998.
124 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Projections from Drainage Program 

Management Options

Data for acreage and drainage volumes for each of the 

five subareas used by the Drainage Program for planning 

purposes is given in tables B11 through B17. Two possible 

alternative futures were defined by the Drainage Program: (1) 

no implementation of a management plan, 0.60 to 0.75 acre-ft 

per acre per year generated drainage, namely, without future; 

and (2) with implementation of a management plan, 0.40 

acre-ft per acre per year generated drainage, namely, with 

future (Drainage Program 1989 and 1990a). A third condition defined here is called with targeted future. The targeted 

future condition applies a factor of 0.20 acre-ft per acre per 

year of generated drainage, exemplifying the lowest, although 

probably not realistic, irrigation water return. Like earlier 

plans, the Drainage Program did not calculate concentrations 

of selenium in drainage water or selenium loads directly, but 

rather focused on estimating the volume of drainage and the 

affected acreage for subareas. Assigning selenium concentrations of 50, 150, and 300 μg/L to these volumes, gives the 

general magnitude of expected selenium loads. 

Table B18 gives selenium load details from each of 

the five subareas based on estimates given by the Drainage 

Program for year 2000 and assigned selenium concentrations 

of 50, 150, and 300 μg/L. This summary gives ranges of acrefeet of drainage and projected annual loads of selenium using 

assigned concentrations. Figures B1a, b, and c depict the 

ranges of agricultural loads for assigned selenium concentrations of 50, 150, and 300 μg/L, if all subareas are considered 

discharging to a valleywide drain. Considered on a subarea 

basis, the selenium loads are (table B18):

Northern subarea. Discharge from the Northern 

subarea is to the San Joaquin River. The range of projections of annual selenium loads from the Northern 

subarea is 925 to 3,536 lbs selenium using an assigned 

concentration of 50 μg/L; 2,774 to 10,608 lbs per year 

using an assigned concentration of 150 μg/L; and 

5,549 to 21,216 lbs per year using an assigned concentration of 300 μg/L.

Grassland subarea. Discharge from the Grassland 

subarea is to the San Joaquin River. The range of 

projections of annual selenium loads from the Grassland subarea is 2,938 to 11,696 lbs per year using an 

assigned concentration of 50 μg/L; 8,813 to 35,088 lbs 

per year using an assigned concentration of 150 μg/L; 

and 17,626 to 70,176 lbs per year using an assigned 

concentration of 300 μg/L.

Westlands subarea. Westlands Water District (encompassing the Westlands subarea) is currently asking 

to extend the San Luis Drain to the Bay-Delta as a 

drainage outlet. The range of projections of annual 

selenium loads from the Westlands subarea is 1,877 to 

11,016 lb per year using an assigned concentration of 

50 μg/L; 5,630 to 33,048 lb per year using an assigned 

•

•

•

concentration of 150 μg/L; and 11,261 to 66,096 lb 

per year using an assigned concentration of 300 μg/L.

Tulare subarea. Tulare subarea currently discharges 

to privately owned evaporation ponds. The range of 

projections of annual selenium loads from the Tulare 

subarea is 2,611 to 10,200 lbs per year using an 

assigned concentration of 50 μg/L; 7,834 to 30,600 lbs 

per year using an assigned concentration of 150 μg/L; 

and 15,667 to 61,200 lbs per year using an assigned 

concentration of 300 μg/L selenium.

Kern subarea. Kern subarea currently discharges 

to privately owned evaporation ponds. The range 

of projections of annual selenium loads from the 

Kern subarea is 1,088 to 6,256 lbs per year using an 

assigned concentration of 50 μg/L; 3,264 to 18,768 lbs 

per year using an assigned concentration of 150 μg/L; 

and 6,528 to 37,536 lbs per year using an assigned 

concentration of 300 μg/L.

Projections from Currently Available Data

Tables B1, B2, B9, B10, B19, B20, and B21 give the 

derivation and details of specific loads projected here for 

each subarea based on a compilation of currently available 

data for problem acreage, drainage volume, and selenium 

concentration. These data have become available since the 

Drainage Program was completed in 1990. Depending on the 

type of data available from each subarea, projections are made 

regarding concentration and load. Because of limited data and 

broad ranges of management alternatives across the subareas, 

maximum and minimum selenium concentrations are given 

to bracket possible load scenarios using specific volumes of 

drainage for each subarea. Although site-specific in nature, 

these projections address only the present discharge to manage 

the annual imbalance, and not general amounts of problem 

water. Projections for the five subareas are:

Northern subarea. Discharge from the Northern 

subarea is to the San Joaquin River. The projected 

selenium concentration range is 5 to 10 μg/L for the 

Northern subarea. The Northern subarea minimum 

projection is based on a nominal 5 μg/L selenium 

concentration applied to adhere to a 5 μg/L USEPA 

criterion for the San Joaquin River. Because management options were not recommended for the Northern 

subarea, the assumed drainage volume is that estimated 

by the Drainage Program for year 2000 without implementation of a management plan (Drainage Program, 

1990a) (tables B13 through B17). The range of projected annual selenium loads for the Northern subarea 

is 350 to 750 lbs per year, if a maximum concentration 

of 10 μg/L is applied to the same drainage volume.

Grassland subarea. Discharge from the Grassland 

subarea is to the San Joaquin River. The projected 

•

•

•

•
Appendix B. San Joaquin Valley Agricultural Drainage Projections 125

selenium concentration range is 68 to 152 μg/L for the 

Grassland subarea. The Grassland subarea projection is 

based on the Grassland Bypass Channel Project measured volume of discharge in WY 1997 (tables B9 and 

B10). The projected Grassland subarea minimum load 

is 6,960 lbs per year. The projected Grassland maximum load is 15,500 lbs per year, a load similar to that 

measured for the San Joaquin River at Crows Landing 

in an extremely wet year (WY 1998). The maximum 

load attempts to represent a load that includes upstream 

San Joaquin River loads of selenium and recycled selenium loads from the Delta-Mendota Canal. 

Westlands subarea. Westlands subarea (or Westlands 

Water District ) currently recycles its drainage and 

therefore no discharge data is available. The projected 

selenium concentration range is 49 to 150 μg/L for the 

Westlands subarea (note, no current data, only testimony on acreage is available). The Westlands Water 

District subarea minimum acre-feet discharge and load 

are for conditions presented as evidence for Westlands 

Water District (60,000 acre-ft at 49 μg/L selenium, 

Westlands Water District, 1996) (tables B1 and B2). 

The maximum load is based on a selenium concentration of 150 μg/L (163 μg/L median and a USBR 

conservative estimate of at least 150 μg/L) applied to 

60,000 acre-ft. The projected range of annual selenium 

loads for Westlands Water District is 8,000 to 24,480 

lbs per year.

Tulare subarea. Tulare subarea currently discharges 

to privately owned evaporation ponds. The Tulare 

subarea projections are based on measurements for 

volume and selenium concentration from 1993 to1997 

(Anthony Toto, Central Valley Board, personal commun., January, 1998, ). A compilation of available 

data from discharges in the Tulare subarea is given 

in tables B19 and B20. Concentration and volume 

data for 1988, 1989, 1994, and 1996 are shown for 

comparison, although sets of data are not available in 

order to calculate load. An average volume is used in 

the projections in conjunction with the minimum and 

maximum selenium loads. From the sparse data available from the Tulare subarea for 1993, 1995, and 1997, 

•

•

0

4,000

8,000

12,000

50 μgL

Tulare

Kern

Northern

Westlands

Grassland

0

10,000

20,000

30,000

0 20,000 40,000 60,000 80,000

Drainage discharge, in acre-feet per year

Selenium load, in lbs per year

0

20,000

40,000

60,000

150 μgL

300 μgL

Tulare

Kern

Northern

Westlands

Grassland

Kern

Northern

Northern

Westlands

Grassland

Tulare

Westlands

Grassland

a

b

c

Figure B1. Annual selenium load projections at (a) 50, (b) 150 and 

(c) 300 μg/L selenium for drainage discharges from the Northern, 

Grassland, Westlands, Tulare, and Kern subareas.

Table B11. Acreage used by the Drainage Program for 

planning purposes in 1985 −1990 (Drainage Program 1989, 

Table 1−1).

Subarea Total 

acreage

(acres)

Irrigable 

acreagea

(acres)

Irrigated 

acreagea

(acres)

Drained 

acreage

(acres)

Northern 236,000 165,000 157,000 26,000

Grasslanda 707,000 345,000 311,000b 51,000

Westlands 770,000 640,000 576,000 5,000

Tulare 883,000 562,000 506,000b 42,000

Kern 1,210,000 762,000 686,000 11,000

Total 3,806,000 2,474,000 2,235,000 135,000

a

A factor of 90 to 95 percent was used to calculate irrigated acres 

from irrigable acres (Drainage Program, 1990a, Table 11).

bEstimates differ from 1989 to 1990 (Drainage Program, 1990a, 

Table 11, Grassland subarea 329,000 acres; Tulare subarea 551,000 

acres). 
126 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table B12. Acreage (irrigated, abandoned, and problem), problem water, and annualized cost (problem water reduction and management 

plan implementation) used by the Drainage Program (1990a).

[The without future alternative (no implementation of a management plan) includes abandonment of lands due to salinization.] 

Subarea

Irrigated

acreage 

for 1990a

(acres)

Irrigated

acreage

without 

future

for 2000a

(acres)

Abandoned

acreage

without 

future

for 2000a

(acres)

Problem 

acreage 

without 

future

for 2000b

(acres)

Factor

(problem 

water

generationc

)

(acre-ft/acre)

Problem 

water

generated 

by 2000d

(acre-ft)

Problem 

water

generated by 

2040d

(acre-ft) 

Annualized 

cost/acre for 

problem water 

reductione

(dollars)

Annualized

cost for management plan

 implementatione

(dollars)

Northern 157,000 152,000 0 34,000 0.70–0.75 26,000 38,000 − −

Grasslandf 329,000 325,000 0 116,000 0.70–0.75 86,000 155,000 $107 $12,412,000

Westlands 576,000 551,000 28,000 108,000 0.60 81,000 153,000 $136 $14,688,000

Tulare 551,000 517,000 38,000 125,000 0.70–0.75 75,000 209,000 $104 $13,000,000

Kern 686,000 665,000 18,000 61,000 0.71 46,000 111,000 $137 $ 8,357,000

Total 2,299,000 2,210,000 84,000 444,000 − 314,000 666,000 − $48,457,000

a

Drainage Program (1990a), table 11.

bDrainage Program (1990a), table 9.

c

Drainage Program (1990a) page 76.

dDrainage Program (1990a) table 10.

e

A 50-year planning period and problem acreage for 2000 were used (Drainage Program, 1990a: pages 5, 143, 148, 153, and 156; approximately $42,000,000, 

page 5). Cost/acre includes the cost of fish and wildlife components.

f

The Grassland subarea total acreage is 707,000 with 329,000 irrigated acres (90% of irrigable lands). The Grassland Area/Drainage Problem Area within the 

subarea is approximately 100,000 acres.

Table B13. Projected drainage using Drainage Program (1990a) tile-drained acreage for 1990, 2000, and 2040.

[No drainage improvement is considered as 0.75 acre-ft/acre/year and minimal improvement is considered as 0.55 acre-ft/acre/year. The without future (no 

implementation of a management plan) includes abandonment of lands due to salinization. An additional calculation is made for the Westlands subarea based 

on upslope contributions from non-tile drained acreage to tile-drained acreage (State Board, 1985).]

Subarea 

Tiledrained 

acreage 

for 1990a

(acres)

Factor 

(acre-ft/

acre/year)

Drainage 

for 1990b

(acre-ft)

Tile-drained

acreage 

without 

future for 

2000a

 (acres)

Factor

(acre-ft/ 

acre/year)

Drainage 

without

future

for 2000b

(acre-ft)

Tiledrained

acreage 

without

future

for 2040a

(acres)

Factor

(acre-ft/ acre/

year)

Drainage 

without future

for 2040b

(acre-ft)

Northern 24,000 0.75 18,000 34,000 –c 26,000 51,000 0.75 38,000d

Grassland 50,000 0.75 38,000 85,000 –c 54,000 152,000 0.55 84,000d

Westlands 5,000 0.75 4,000 50,000 –c 28,000 49,000 0.55 27,000

Westlands 42,000e 0.75 31,500e − –c − − − −

Tulare 43,000 0.60 32,000 86,000 –c 47,000 94,000 0.55 52,000

Kern 11,000 0.75 8,000 14,000 –c 8,000 40,000 0.55 22,000

Total 133,000 − 100,000 269,000 –c 163,000 386,000 − 223,000

a

Drainage Program (1990a), table 11.

bDrainage Program (1990a), table 13.

c

No factor given in table 13 (Drainage Program, 1990a)

dTable 13 shows 37,000 and 105,000 acre-ft (Drainage Program, 1990a). 

e

Not included in total.
Appendix B. San Joaquin Valley Agricultural Drainage Projections 127

the projected selenium concentration range is 1.7 to 

9.8 μg/L. The range of projected annual loads for the 

Tulare subarea is 91 lbs to 519 lbs per year, with the 

majority of the discharge to the Tulare Lake Drainage 

District ponds. A main point of these calculations is to 

compare the magnitude of loading from subareas even 

in view of limited data. The projected annual selenium 

load from this area is small relative to that projected 

from Westlands Water District and Grassland subarea, 

largely because the projected selenium concentrations are relatively low in managed drainage from the 

Tulare subarea.

Kern subarea. Kern subarea currently discharges to 

privately owned evaporation ponds. A compilation of 

available data from discharges in the Kern subarea is 

given in table B21. Kern subarea projections are based 

on measurements for volume and selenium concentration from 1993 to 1997 (Anthony Toto, Central 

Valley Board, personal commun., January, 1998). An 

average volume is used in the projections in conjunction with minimum and maximum selenium loads. 

From the sparse data available, the projected selenium 

concentration range is 175 to 254 μg /L for Kern 

subarea. Projected annual selenium loads from the 

Kern subarea range from a total of 1,089 to 1,586 lbs. 

A main point of these calculations is to compare the 

magnitude of loading from subareas even in view of 

limited data. The projected annual selenium load from 

this area is small relative to that from Westlands Water 

District and Grassland subarea, largely because the 

projected volumes of drainage are relatively low. 

•

 A selenium load summary based on the currently 

available data compiled here is shown in table 7. In addition, sets of graphs in figures B2 and B3 compare generalized projections from Drainage Project volumes (table B18) 

with those based on currently available data. Ranges of 

drainage volume and annual selenium loads are presented for 

each assigned concentration, specifically, 50, 150, and 300 

μg/L for each subarea (figs. B2a to e). Ranges of projected 

drainage volumes and annual selenium loads are presented for 

minimum and maximum concentrations derived from current 

data (figs. B3a to e). In general, these graphical techniques 

enable a prediction or projection of an annual selenium load 

for any assigned concentration or current condition given 

a specific drainage volume. Again, the ranges are due to 

varying estimates of predicted problem water and subsurface drainage under different management alternatives. The 

comparisons show the relative contribution of load from each 

subarea in the event that all subareas discharge to a proposed 

San Luis Drain extension. The graphical technique also shows 

patterns of selenium concentration and load that are indicative 

of the geology, hydrology, and chosen management options 

for each subarea. 

Table B14. Projected drainage using a drainage improvement factor of 0.40 acre-ft/acre/year and Drainage Program (1990a) data.

[The with future alternative specifies implementation of a management plan (Drainage Program, 1990a). An additional calculation is made for Westlands 

based on upslope contributions from non-tile drained acreage to tile drained acreage (State Board, 1985).]

Subarea Tiledrained 

acreage 

for 1990a

(acres)

Factorb

(acre-ft/

acre/

year)

Projected 

drainage 

with future 

for 1990 

(acre-ft)

Tile-drained

acreage with 

future for 

2000a (acres)

Factorb

(acre-ft/ 

acre/year)

Projected 

drainage 

with future

for 2000 

(acre-ft)

Tile-drained

acreage with

future for 

2040a (acres)

Factorb

(acre-ft/ 

acre/year)

Projected 

drainage with

 future for 2040 

(acre-ft)

Northernc 24,000 0.40 9,600 34,000 0.40 13,600 44,000 0.40 17,600

Grassland 50,000 0.40 20,000 108,000 0.40 43,200 192,000 0.40 76,800

Westlands 5,000 0.40 2,000 69,000 0.40 27,600 140,000 0.40 56,000

Westlands 42,000d 0.40 16,800d − − − − − −

Tulare 43,000 0.40 17,200 96,000 0.40 38,400 277,000 0.40 110,800

Kern 11,000 0.40 4,400 53,000 0.40 21,200 106,000 0.40 42,400

Total 133,000 − 53,200 360,000 − 144,000 759,000 − 303,600

a

Drainage Program (1990a), table 27.

bFactor applied from table 26 (Drainage Program, 1990a).

c

No management plan recommended for Northern subarea (Drainage Program, 1990a).

dNot included in total.
128 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table B15a. Projections of annual selenium loads per subarea using Drainage Program problem water estimates for 2000 (without

future alternative, 0.60 to 0.75 acre-ft/acre/year) and a 50 μg/L selenium concentration in drainage.

[Data source: Drainage Program, 1990a.]

Subarea

Problem acreage for 2000a

(acres)

Factor (problem 

water generation 

acre-ft/acre/year)b

Problem water

for 2000c

(acre-ft)

Projected 

selenium

(μg/L)

Projected 

selenium load 

(lbs/year)

Factor

(lbs/acre)

Factor

(lbs/acre-ft)

Northern 34,000 0.70–0.75 26,000 50 3,536 0.1 0.136

Grassland 116,000 0.70–0.75 86,000 50 11,696 0.1 0.136

Westlands 108,000 0.70–0.75 81,000 50 11,016 0.1 0.136

Tulare 125,000 0.60 75,000 50 10,200 0.08 0.136

Kern 61,000 0.70–0.75 46,000 50 6,256 0.1 0.136

TOTAL 444,000 0.71 314,000 50 42,704 0.096 0.136

Table B15b. Projections of annual selenium loads per subarea using Drainage Program problem water estimates for 2000 (without

future alternative, 0.60 to 0.75 acre-ft/acre/year) and a 150 μg/L selenium concentration in drainage. 

[Data source: Drainage Program, 1990a.]

Subarea

Problem acreage for 2000a

(acres)

Factor (problem 

water generation 

acre-ft/acre/year)b

Problem water 

for 2000c

(acre-ft)

Projected 

selenium

(μg/L)

Projected 

selenium load 

(lbs/year)

Factor

(lbs/acre)

Factor

(lbs/acre-ft)

Northern 34,000 0.70–0.75 26,000 150 10,608 0.31 0.408

Grassland 116,000 0.70–0.75 86,000 150 35,088 0.31 0.408

Westlands 108,000 0.70–0.75 81,000 150 33,048 0.31 0.408

Tulare 125,000 0.60 75,000 150 30,600 0.24 0.408

Kern 61,000 0.70–0.75 46,000 150 18,768 0.31 0.408

TOTAL 444,000 0.71 314,000 150 128,112 0.29 0.408

Table B15c. Projections of annual selenium loads per subarea using Drainage Program problem water estimates for 2000 (without

future alternative, 0.60 to 0.75 acre-ft/acre/year) and a 300 μg/L selenium concentration in drainage. 

[Data source: Drainage Program, 1990a.]

Subarea

Problem acreage for 2000a

(acres)

Factor (problem 

water generation 

acre-ft/acre/year)b

Problem water 

for 2000c

(acre-ft)

Projected 

selenium

(μg/L)

Projected 

selenium load 

(lbs/year)

Factor

(lbs/acre)

Factor

(lbs/acre-ft)

Northern 34,000 0.70–0.75 26,000 300 21,216 0.31 0.816

Grassland 116,000 0.70–0.75 86,000 300 70,176 0.31 0.816

Westlands 108,000 0.70–0.75 81,000 300 66,096 0.31 0.816

Tulare 125,000 0.60 75,000 300 61,200 0.24 0.816

Kern 61,000 0.70–0.75 46,000 300 37,536 0.31 0.816

TOTAL 444,000 0.71 314,000 300 256,224 0.29 0.816

a

Drainage Program (1990a), table 9.

bDrainage Program (1990a), page 76.

c

Drainage Program (1990a), table 10.
Appendix B. San Joaquin Valley Agricultural Drainage Projections 129

Table B16a. Projections of annual selenium loads per subarea using Drainage Program subsurface drainage volumes for 2000 (without

future alternative, 0.60 to 0.75 acre-ft/acre/year) and selenium concentrations of 50, 150, and 300 μg/L. 

[Data source: Drainage Program, 1990a.]

Subarea

Drained acreage without 

futurea

(acres)

Subsurface 

drainage for 2000 

without futureb

(acre-ft)

Projected 

selenium

(μg/L)

Projected 

selenium load 

(lbs/year)

Projected 

selenium

(μg/L)

Projected 

selenium 

load

(lbs/year)

Projected 

selenium 

(μg/L)

Projected 

selenium 

load

(lbs/year)

Northern 34,000 26,000 50 3,536 150 10,608 300 21,216

Grassland 85,000 54,000 50 7,344 150 22,032 300 44,064

Westlands 50,000 28,000 50 3,808 150 11,424 300 22,848

Tulare 86,000 47,000 50 6,392 150 19,176 300 38,352

Kern 14,000 8,000 50 1,088 150 3,264 300 6,528

TOTAL 269,000 163,000 50 22,168 150 66,504 300 133,008

Table B16b. Projections of annual selenium loading per subarea using Drainage Program subsurface drainage volumes for 2000 (with

future alternative, 0.40 acre-ft/acre/year) and selenium concentrations of 50, 150, and 300 μg/L.

[Data source: Drainage Program, 1990a.]

Subarea

Drained 

acreage with 

futurea

(acres)

Subsurface drainage for 2000 with 

futureb

(acre-ft)

Projected 

selenium

(μg/L)

Projected 

selenium load 

(lbs/year)

Projected 

selenium

(μg/L)

Projected 

selenium 

load

(lbs/year)

Projected 

selenium 

(μg/L)

Projected 

selenium 

load

(lbs/year)

Northern 34,000 13,600 50 1,850 150 5,549 300 11,098

Grassland 108,000 43,200 50 5,875 150 17,625 300 35,251

Westlands 69,000 27,600 50 3,754 150 11,261 300 22,522

Tulare 96,000 38,400 50 5,222 150 15,667 300 31,334

Kern 53,000 21,200 50 2,883 150 8,650 300 17,299

TOTAL 360,000 144,000 50 19,584 150 58,752 300 117,504

Table B16c. Projections of annual selenium loading per subarea for 2000 using Drainage Program subsurface drainage volumes, with

targeted future alternative (0.20 acre-ft/acre/year), and selenium concentrations of 50, 150, and 300 μg/L. 

[Data source: Drainage Program, 1990a.]

Subarea

Drained acreage with targeted futurea

(acres)

Subsurface drainage for 2000 with 

targeted futurec

(acre-ft)

Projected 

selenium

(μg/L)

Projected 

selenium load 

(lbs/year)

Projected 

selenium

(μg/L)

Projected 

selenium 

load

(lbs/year)

Projected 

selenium 

(μg/L)

Projected 

selenium 

load

(lbs/year)

Northern 34,000 6,800 50 925 150 2,774 300 5,549

Grassland 108,000 21,600 50 2,938 150 8,813 300 17,626

Westlands 69,000 13,800 50 1,877 150 5,630 300 11,261

Tulare 96,000 19,200 50 2,611 150 7,834 300 15,667

Kern 53,000 10,600 50 1,442 150 4,325 300 8,650

TOTAL 360,000 72,000 50 9,793 150 29,376 300 58,753

a

Drainage Program (1990a), table 11.

bDrainage Program (1990a), table 13.

c

Applied factor of 0.20 acre-ft/acre (see text).
130 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Table B17. Projections of annual selenium loads per subarea using Drainage Program drainage estimates (subsurface drainage, problem water, drainage without future, drainage with future, and drainage with a targeted future) and selenium concentrations of 50, 150, and 300 μg/L. [In the targeted future projection, a factor of 0.2 acre-ft/acre/year is applied. Se, selenium. Data source: Drainage Program, 1990a.] Subarea Subsurface drainage for 1990 Projected problem water for 2000a Projected drainage for 2000 without futureb Projected drainage for 2000 with futurec Projected drainage with targeted futured (acre-ft/ year)

(μg /L 

Se)

Se loads 

(lbs/ year)

 (acre-ft/

year)

(μg /L 

Se)

Se loads 

(lbs/year)

 (acre-ft/

year)

(μg /L 

Se)

Se loads 

(lbs/year)

 (acre-ft/

year)

(μg /L 

Se)

Se loads 

(lbs/year)

 (acre-ft/

year)

(μg /L 

Se)

Se loads 

(lbs/year)

Northern 18,000 50 2,448 26,000 50 3,536 26,000 50 3,536 13,600 50 1,850 6,800 50 925Grassland 38,000 50 5,168 86,000 50 11,696 54,000 50 7,344 43,200 50 5,875 21,600 50 2,938

Westlands 4,000 50 544 81,000 50 11,016 28,000 50 3,808 27,600 50 3,754 13,800 50 1,877

Tulare 32,000 50 4,352 75,000 50 10,200 47,000 50 6,392 38,400 50 5,222 19,200 50 2,611

Kern 8,000 50 1,088 46,000 50 6,256 8,000 50 1,088 21,200 50 2,883 10,600 50 1,442

TOTAL 100,000

− 13,600 314,000

− 42,704 163,000

− 22,168 144,000

− 19,584 72,000

− 9,793

Northern 18,000 150 7,344 26,000 150 10,608 26,000 150 10,608 13,600 150 5,549 6,800 150 2,774

Grassland 38,000 150 15,504 86,000 150 35,088 54,000 150 22,032 43,200 150 17,625 21,600 150 8,813

Westlands 4,000 150 1,632 81,000 150 33,048 28,000 150 11,424 27,600 150 11,260 13,800 150 5,630

Tulare 32,000 150 13,056 75,000 150 30,600 47,000 150 19,176 38,400 150 15,667 19,200 150 7,834

Kern 8,000 150 3,264 46,000 150 18,768 8,000 150 3,264 21,200 150 8,650 10,600 150 4,325

TOTAL 100,000

− 40,800 314,000

− 128,112 163,000

− 66,504 144,000

− 58,751 72,000

− 29,376

Northern 18,000 300 14,688 26,000 300 21,216 26,000 300 21,216 13,600 300 11,098 6,800 300 5,549

Grassland 38,000 300 31,008 86,000 300 70.176 54,000 300 44,064 43,200 300 35,251 21,600 300 17,626

Westlands 4,000 300 3,264 81,000 300 66,096 28,000 300 22,848 27,600 300 22,522 13,800 300 11,261

Tulare 32,000 300 26,112 75,000 300 61,200 47,000 300 38,352 38,400 300 31,334 19,200 300 15,667

Kern 8,000 300 6.528 46,000 300 37,536 8,000 300 6,528 21,200 300 17,299 10,600 300 8,650

TOTAL 100,000

− 81,600 314,000

− 256,224 163,000

− 133,008 144,000

− 117,504 72,000

− 58,753

aDrainage Program (1990a), table 10.bDrainage Program (1990a), table 13.cSee calculation this report, Table B14. In general, see tables 27 and 26 for acreage and factors, respectively (Drainage Program, 1990a).dSee this report, Table B15.
Appendix B. San Joaquin Valley Agricultural Drainage Projections 131

Table B18. Summary of projections of annual selenium 

loads per subarea using Drainage Program (1990a) 

estimates of drainage volume and different assigned 

selenium concentrations (50, 150, 300 μg/L). 

[Total drainage/year from all subareas is from 69,400 to 314,000 acreft. Data source: Drainage Program, 1990a.] 

Subarea drainage 

(acre-ft/year)

Selenium load (lbs/year)

50 μg/La 150 μg/Lb 300 μg/Lc

Northern 6,800 925 2,774 5,549

Northern 13,600 1,850 5,549 11,098

Northern 26,000 3,536 10,608 21,216

Grassland 21,600 2,938 8,813 17,626

Grassland 43,200 5,875 17,625 35,251

Grassland 54,000 7,344 22,032 44,064

Grassland 86,000 11,696 35,088 70,176

Westlands 13,800 1,877 5,630 11,261

Westlands 27,600 3,754 11,260 22,522

Westlands 28,000 3,808 11,424 22,848

Westlands 81,000 11,016 33,048 66,096

Tulare 8,400 2,611 7,834 15,667

Tulare 19,200 5,222 15,667 31,334

Tulare 47,000 6,392 19,176 38,382

Tulare 75,000 10,200 30,600 61,200

Kern 8,000 1,088 3,264 6,528

Kern 10,600 1,442 4,325 8,650

Kern 21,200 2,883 8,650 17,299

Kern 46,000 6,256 18,768 37,536

Total selenium load/year (all subareas)

Minimum 9,439 28,315 56,631

Min w/o Northern 8,514 25,541 51,082

Maximum 42,704 128,112 256,224

Max w/o Northern 39,168 117,504 235,008

a

Equivalent to 0.136 lbs selenium/acre-ft.

b

Equivalent to 0.408 lbs selenium/acre-ft.

c

Equivalent to 0.817 lbs selenium/acre-ft.

Table B19. Tulare subarea drainage and selenium 

concentrations in 1988 and 1989 for privately owned 

evaporation basins. 

[Data sources: discharge, Anthony Toto, Central Valley Board, 

personal commun., January, 1998; selenium (Central Valley Board, 

1990a).]

Evaporation 

basin or drainage 

district

Drainage 

(acre-ft/year)

Selenium 

(μg/L)

Selenium 

load

(lbs/year)

1988

Tulare Lake 14,294 − (see text)

 North − 2.6

 Hacienda − −

 South − 30

Westlake − 1−1.1

Meyer − 1

Stone − 1.6–4.3

Britz − −

Others − 9.6–757

1989

Tulare Lake 13,705 − (see text)

 North − −

 Hacienda − 2.0

 South − −

Westlake − 21

Meyer − 0.4–6.5

Stone − 0.8

Britz − 2.3–7.4

Others − −
132 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Evaporation 

basin or drainage 

district

Drainage 

(acre-ft/year)

Selenium 

(μg/L)

Selenium 

load

(lbs/year)

1993

Subarea (total) 17,899−18,955 – 91−97

Tulare Lake 12,497 (net) 

(13,553)a

1.9 average 65−71

 North − 1.4 −

 Hacienda − 2.1 −

 South − 2.0 −

Westlake 4,309 1.3 15

Meyer − − −

Stone 1,093 3.6 10.7

Britz − 124 −

1994

Subarea (total) 19,468 − −

Tulare Lake 14,601 − −

 North 1,432 1.8 7.0

 Hacienda 4,226 − −

 South 8,943 12.6 306

Westlake 3,478 1.2 11.6

Meyer − − −

Stone 1,213 3.7 2.2

Britz 186 15−50 7.6−25.3

1995

Subarea (total) 20,403 − 494−519

Tulare Lake 14,751 − 461

 North 1,373 2.5 9.3

 Hacienda 4,754 13.2 171

 South 8,624 12.0 281

Westlake 3,478 2.25 average 21

Meyer 327 0.76 0.7

Stone 1,665 2.4 10.9

Britz 182 15−50 7.4−25

Evaporation 

basin or drainage 

district

Drainage 

(acre-ft/year)

Selenium 

(μg/L)

Selenium 

load

(lbs/year)

1996

Subarea (total) 19,160 − −

Tulare Lake 13,676 − −

 North 918 2.5 6.2

 Hacienda 4,515 − –

 South 8,243 8.3 186

Westlake 5,152 − −

Meyer 332 0.99 0.894

Stone − − −

Britz − − −

1997

Subarea (total) 20,005 252–442

Tulare Lake 15,605 − 240–430

 North 1,199 2.1/1.8b 6.8−5.9

 Hacienda 5,238 −/5.9 84

 South 9,168 13.6/6.0 339–150

Westlake 4,400 2.27 avg 12

Meyer − − −

Stone − − −

Britz − − −

a

Net=gross minus interceptor seepage.

bTwo samplings for WY 1997 (June and September, 1997).

Table B20. Tulare subarea drainage and selenium concentrations from 1993 to 1997 for privately owned evaporation basins. 

[Data sources: discharge, Anthony Toto, Central Valley Board, personal commun., January, 1998; selenium (Central Valley Board, 1990a).]
Appendix B. San Joaquin Valley Agricultural Drainage Projections 133

Table B21. Kern subarea drainage and selenium concentrations 

in 1988, 1989, and 1993 through 1997. 

[Data sources: Anthony Toto, Central Valley Board, personal commun., 

January, 1998, except for selenium concentrations for 1988 and 1989 which 

are from Central Valley Board, 1990a). 

Evaporation basin or 

drainage district 

Drainage 

(acre-ft/year)

Selenium 

(μg/L)

Selenium 

load

(lbs/year)

1988

Total − − −

Lost Hills Water District 2,452 142 947

Rainbow Ranch − − −

Lost Hills Ranch − 2.4 −

1989

Total − − −

Lost Hills Water District 3,831 83−671 865−6,992

Rainbow Ranch − 212 −

Lost Hills Ranch − 2.1 −

1993

Total 2,467 − 1,426

Lost Hills Water District 1,854 220 1,109

Rainbow Ranch 613 190 317

1994

Total 2,318 − 1,586

Lost Hills Water District 1,739 208 948

Rainbow Ranch 579 405 638

1995

Total 2,237 − 1,410

Lost Hills Water District 1,549 240 1011

Rainbow Ranch 688 213 399

1996

Total 2,365 − 1,407

Lost Hills Water District 1,501 238 972

Rainbow Ranch 864 185 435

1997

Total 2,072 − 1,089

Lost Hills Water District 1,620 195 859

Rainbow Ranch 452 187 230

Table B22. Selenium load scenarios using planned capacities of 

the San Luis Drain or valley-wide drain and assigned selenium 

concentrations of 50, 150, and 300 μg/L. 

San Luis Drain design capacity Selenium load (lbs/year)

50 μg/L 150 μg/L 300 μg/L

300 ft3/s or 216,810 acre-ft/

year (USBR, 1955) planned 

capacity Bakersfield to Mendota section

29,486 88,458 176,917

450 ft3

/s or 325,215 acre-ft/

year (USBR, 1955) planned 

capacity Kesterson Reservoir 

to Bay/Delta section

44,229 132,688 265,375

144,200 acre-ft/year (USBR, 

1955) initially needed

19,611 58,834 117,667

154,100 acre-ft/year maximum 

after 50 years (range 3,100 to 

154,100 acre-ft/year (USBR, 

1978)

20,958 62,873 125,746

201,025 acre-ft/year after 

25 years (range 84,525 to 

279,270 acre-ft/year (USBR, 

1983)

27,339 82,018 164,036

60,000 to 100,000 acre-ft/year 

(Barcellos Judgment, 1986; 

USBR,1992)

8,160−

 13,600 

24,480−

 40,800 

48,960− 

81,600

60,000 acre-ft/year (Westlands 

Water District, 1996)

8,160 24,480 48,960

375,000 acre-ft/year (400,000-

500,000 acre-ft/year needed 

capacity for drainage in San 

Francisco ocean out-fall, 

Montgomery Watson, 1993)

51,000 153,000 306,000
134 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table B23a. Projected selenium loads using Drainage Program (1990a) data (problem water and subsurface 

drainage) and daily fluxes from the western San Joaquin Valley to a proposed San Luis Drain extension. 

[A selenium concentration of 50 μg/L selenium is hypothesized to be attainable with treatment. A selenium concentration of 150 

μg/L is assigned to subsurface drainage.] 

Drainage from all subareas 

(acre-ft) 

Selenium load

(lbs/year)

Selenium load

(kstsa

/year) 

Selenium load

(lbs/day)

Selenium

(μg/L)

Factor

(lbs/acre-ft)

314,000

(problem water at 50 μg/L 

selenium)

42,704 2.45 117 50 0.136

144,000−163,000

(subsurface drainage at 150 

μg/L selenium)

58,752−66,504 3.4−3.8 161−182 150 0.408

Table B23b. Projected low-range selenium loads and daily fluxes from the western San Joaquin Valley to a San 

Luis Drain extension. 

[See table 7 for derivation of selenium concentrations.]

Subareas Selenium load

(lbs/year)

Selenium load

(kstsa/year) 

Selenium load

(lbs/day)

Selenium

(μg/L)

Factor

(lbs/acre-ft)

Northern 350 0.02 0.95 5 0.0135

Grassland 6,960 0.40 19 68 0.186

Westlands 8,000 0.46 22 49 0.133

Tulare 91 0.005 0.25 1.7 0.0047

Kern 1,089 0.062 3.0 175 0.475

Total 16,490 0.95 45.2 − −

Table B23c. Projected high-range selenium loads and daily fluxes from the western San Joaquin Valley to a 

San Luis Drain extension. 

[See table 7 for derivation of selenium concentrations.]

Subareas Selenium load

(lbs/year)

Selenium load

(kstsa

/year) 

Selenium load

(lbs/day)

Selenium

(μg/L)

Factor

(lbs/acre-ft)

Northern 700 0.04 1.9 10 0.027

Grassland 15,500 0.89 42 152 0.414

Westlands 24,480 1.4 67 150 0.408

Tulare 519 0.03 1.4 9.8 0.0266

Kern 1,586 0.09 4.3 254 0.692

Total 42,785 2.46 117 − −

a

One kesterson (kst) = 17,400 lbs selenium.
Appendix B. San Joaquin Valley Agricultural Drainage Projections 135

Estimates of Capacity of Drainage Conveyance 

(proposed San Luis Drain extension)

As a final check of the magnitude of the load projections, 

various design capacities of the San Luis Drain or a drain 

extension are combined with assigned selenium concentrations to calculate load (table B22). The concentration is held 

constant to simulate a constant discharge from a constructed 

conveyance system as opposed to a seasonally impacted 

conveyance system such as the San Joaquin River. The San 

Luis Drain design capacity is assumed to be 300 ft3/s (as 

suggested as early as 1955 and recently), which is equivalent to 216,810 acre-ft per year (USBR, 1955, 1962, 1978; 

State Board, 1999a). At a selenium concentration of 50 μg/L, 

the annual projected selenium load is 29,486 lbs. Using an 

assigned concentration of 150 μg/L, the annual projected load 

is 88,458 lbs. For a 300 μg/L discharge, the annual projected 

load is 176,917 lbs. Other historical estimates of annual 

discharge for the San Luis Drain (for example, 144,200 acre-ft 

per year in early planning; 150,000 estimated during 1975– 77 

for 50 to 100 years of drainage; and 84,525 to 279,270 acreft estimated in 1983 for the period 1995–2095) also can 

be used to estimate loads by applying assigned concentrations to discharge capacity. An estimate used in the 1990s of 

drainage available from the San Joaquin Valley for discharge 

to a proposed San Francisco ocean outfall, which was a part 

of recycling efforts to meet water-quality objectives, showed 

a 375,000 acre-ft annual drainage discharge and a 400,000 

to 500,000 acre-ft capacity drainage facility (MontgomeryWatson, 1993). Hence, most estimates show a need for a drain 

of greater than 200,000 acre-ft per year. 

Total flux from Agricultural Drainage Discharge 

(lbs selenium per day)

It is also useful to present here projected selenium 

loads from the western San Joaquin Valley to the Bay-Delta 

in terms of rates (lbs selenium per year and lbs selenium per 

day) and in terms of cumulative load expressed in kestersons 

(ksts) (Presser and Piper, 1998). The kst unit is the cumulative 

total of 17,400 lbs selenium, which when released directly into 

Kesterson Reservoir caused ecotoxicity and visible ecological 

damage. It is used here as a measure of potential ecological 

damage based on selenium load. Table B23a shows the range 

of projected selenium loads (2.4 to 3.8 ksts per year) from the 

Valley through a San Luis Drain extension based on generalized 

Drainage Program data (314,000 acre-ft of problem water with 

an assigned concentration of 50 μg/L selenium, or 144,000 to 

163,000 acre-ft of subsurface drainage with an assigned concentration of 150 μg/L selenium). The flux of selenium from the 

drain to the Bay-Delta is projected to range from 117 to 182 lbs 

selenium per day. Tables B23b and B23c and figures B4a and 

B4b show a projected selenium rate (lbs selenium per day) from 

each of the five designated subareas of the western San Joaquin 

Valley using the minimum and maximum scenarios defined 

a

b

c

d

e

0 2,500 5,000 7,500 Note: all

ppb = μg/L 

Drainage (acre-ft) selenium

Kern Subarea

300 ppb

150 ppb

50 ppb

2,292 acre-ft acre-ft

1,870 lbs

 935 lbs

 312 lbs

0 15000 30,000 45,000 60,000

Tulare Subarea

300 ppb

150 ppb

50 ppb

15,906 lbs

 7,953 lbs

 2,651 lbs

19,493 acre-ft acre-ft

0 15,000 30,000 45,000 60,000 75,000 90,000

Westlands Subarea

48,960 lbs

24,480 lbs

 8,160 lbs

60,000 acre-ft acre-ft 300 ppb

150 ppb

50 ppb

0 15,000 30,000 45,000 60,000 75,000 90,000

Grassland Subarea

300 ppb

150 ppb

50 ppb

 30,587 lbs

 15,293 lbs

 5,097 lbs

37,483 acre-ft 37,483 acre-ft

0

2,500

5,000

0

20,000

40,000

0

20,000

40,000

60,000

Selenium (lbs)

0

20,000

40,000

60,000

0

250

500

750

1,000

1,250

0 10,000 20,000 30,000 40,000

Northern Subarea

26,000 acre-ft acre-ft

700 lbs

350 lbs

10 ppb

 5 ppb

Figure B2. Projected drainage volume and annual selenium loads 

for variable selenium concentrations (50, 150, 300 μg/L) for 

(a) Northern subarea, (b) Grassland subarea, (c) Westlands 

subarea, (d ) Tulare subarea, and (e) Kern subarea.
136 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

earlier from currently available data (figure B3). The projected 

range of selenium flux from each subarea is: Northern, 0.95 to 

1.9 lbs per day; Grassland, 19 to 42 lbs per day; Westlands, 22 

to 67 lbs per day; Tulare, 0.25 to 1.4 lbs per day; and Kern, 3.0 

to 4.3 lbs per day. The projected total selenium flux is 45 to 117 

lbs per day under the assumed conditions. Westlands and Grassland subareas are projected to account for the largest proportion 

of selenium load (figs. B4a and B4b). The projected range of 

combined loads from the Grassland and Westlands subareas 

is 0.86 to 2.29 ksts per year. For comparison, the current State 

limitation for the Grassland subarea to the San Joaquin River is 

8,000 lbs per year or 0.46 ksts per year.

Total = 117

Grassland

42

Kern

4.3

Tulare

1.4

Northern

1.9

Westlands

67

Total = 45.2 

Grassland

19

Kern

3.0

Tulare

0.25

Northern

0.95

Minimum (lbs/day) Maximum (lbs/day)

Westlands

22

a b

10 ppb

0 10,000 20,000 30,000 40,000 50,000 60,000

Northern Subarea

26,000 acre-ft

37,483 acre-ft

26,000 acre-ft

5 ppb

350 lbs

700 lbs

500

0

1,000

1,500

2,000

5,000

0

10,000

15,000

20,000

25,000

30,000

0 10,000 20,000 30,000 40,000 50,000 60,000

Grassland Subarea

37,483 acre-ft

152 ppb

15,500 lbs

 6,960 lbs 68 ppb

5,000

0

10,000

15,000

20,000

25,000

30,000

0 20,000 40,000 60,000 80,000

Westlands Subarea

24,480 lbs

 8,000 lbs

60,000 acre-ft

150 ppb

49 ppb

0

500

1,000

1,500

2,000

Selenium (lbs)

0 10,000 20,000 30,000 40,000 50,000 60,000

19,493 acre-ft acre-ft

9.8 ppb

 91 lbs 1.7 ppb

519 lbs

500

0

1,000

1,500

2,000

0 2,000 4,000 6,000 8,000 10,000

Kern Subarea

1,586 lbs

1,089 lbs 175 ppb

254 ppb

2,292 acre-ft 2,292 acre-ft

Tulare Subarea

a

b

c

d

e

Drainage (acre-ft)

Note: all

ppb = μg/L 

selenium

Figure B4. Projected (a) minimum and (b) maximum selenium flux 

(lbs per day) for the Northern, Grassland, Westlands, Tulare, and 

Kern subareas.

Figure B3. Projected drainage volume and annual selenium loads 

for select minimum and maximum selenium concentrations (a) 

Northern subarea, (b ) Grassland subarea, (c) Westlands subarea, 

(d ) Tulare subarea, and (e) Kern subarea.
Appendix C. Agricultural Drainage Discharge to the San Joaquin River 137

Contents

Models of discharge to the San Joaquin River .............................................................................................................................................138

Figures

Figure C1. Number of selenium water quality exceedance months (U.S. EPA criterion) for the San Joaquin River 

at Crows Landing during WY 1986 through WY 1997..................................................................................................................144

Figure C2. Comparison of wet, dry, and critically dry years (TMDL model) for 5 μg/L, 4-day average, 1 out of 3 year 

exceedance.......................................................................................................................................................................................144

Figure C3. Comparison of TMDL and TMML model projections during a wet year for 5 μg/L, 4-day average, 1 out of 3 year 

exceedance.......................................................................................................................................................................................144

Figure C4. Comparison of TMDL and TMML model projections during a dry year for 5 μg/L, 4-day average, 1 out of 3 year 

exceedance.......................................................................................................................................................................................144

Figure C5. Comparison of TMDL model projections at Crows Landing during critically dry years for (a) 5 μg/L, 4-day 

average, 1 out of 3 year exceedance, (b) 5 μg/L, monthly average, 1 out of 3 year exceedance, and (c) 5 μg/L, 

4-day average, 1 out of 5 month exceedance..............................................................................................................................145

Figure C6. Comparison of TMDL model projections at Crows Landing during dry and below normal years for (a) 5 μg/L, 

4-day average, 1 out of 3 year exceedance, (b) 5 μg/L, monthly average, 1 out of 3 year exceedance, and 

(c) 5 μg/L, 4-day average, 1 out of 5 month exceedance...........................................................................................................145

Figure C7. Comparison of TMDL model projections at Crows Landing during above normal and wet years for (a) 5 μg/L, 

4-day average, 1 out of 3 year exceedance, (b) 5 μg/L, monthly average, 1 out of 3 year exceedance, and 

(c) 5 μg/L, 4-day average, 1 out of 5 month exceedance...........................................................................................................145

Figure C8. TMML model projection at Crows Landing for 8 μg/L and 1 out of 3 year exceedance .......................................................145

Figure C9. Comparison of TMML model projections during a dry year at Crows Landing for (a) 5 μg/L and 4-day average, 

1 out 3 years exceedance and (b) 5 μg/L and monthly mean, 1 out of 3 years exceedance ...............................................146

Figure C10.Comparison of TMML model projections during a wet year at Crows Landing for (a) 5 μg/L, monthly 

average, 1 out of 3 years exceedance, and (b) 5 μg/L, 4-day average, 1 out of 3 year exceedance.................................146

Figure C11.Monthly selenium loads for a dynamic real time model during a wet year using a 5 μg/L input .......................................146

Tables

Table C1. Modeled annual selenium load allocation and discharge from the Grassland Drainage Problem Area to the San Joaquin 

River using various models (Total Maximum Daily Load Model, Total Maximum Monthly Load Model, and Dynamic 

Real-Time Model), water-year types (critically dry; dry/below normal; above normal/wet, dry; or wet), averaging periods 

(4-day or monthly), and violation frequencies (1 in 3 year or 1 in 5 month) to achieve a 5 μg/L selenium objective for 

San Joaquin River................................................................................................................................................................................141

Table C2. Modeled annual selenium load allowance from the Grassland Area to the San Joaquin River and modeled flow 

for the San Joaquin River at Crows Landing/Patterson using the Total Maximum Monthly Load Model under various 

water-year types (critically dry; dry/below normal; or above normal/ wet), averaging periods (4-day or monthly), and 

violation frequencies (1 in 3 year or 1 in 5 month) to achieve a 5 μg/L selenium objective for San Joaquin River.....................142

Table C3. Modeled annual selenium load allowances from the Grassland Area to the San Joaquin River and modeled flow for the 

San Joaquin River at Crows Landing/Patterson using various models (Total Maximum Monthly Load or Dynamic Real-Time), 

water-year types (critically dry/dry/below normal; above normal/wet; or wet), averaging periods (4-day or monthly), and 

violation frequencies (1 in 3 year) to achieve either a 8 or 5 μg/L selenium objective for San Joaquin River............................143

Appendix C. Agricultural Drainage Discharge to the San Joaquin River
138 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Models of Discharge to the San Joaquin River 

In 1991 and 1992, the State acknowledged elevated levels 

of selenium in the San Joaquin River and parts of the BayDelta by designating specific segments or water bodies as 

water-quality limited or impaired (State Board, 2002). These 

include the lower 130-mile reach of the San Joaquin River, 

Suisun Bay, Carquinez Strait, San Pablo Bay, Central Bay, 

South Bay and the Delta. Discharge of selenium to the San 

Joaquin River has continued based on an agreement to implement a regulatory control program for selenium discharges, 

including recent adoption of selenium load limits and targets 

(State Board, 1985 and 1987; USBR, 1995 and 2001). Figure 

C1 shows the number of months per year that the USEPA’s 5 

μg/L selenium criterion was violated at the State compliance 

point for the San Joaquin River (San Joaquin River at Crows 

Landing) from 1986 to 1997. The number of violations is 

based on a monthly average of a varying number of collected 

grab samples (Central Valley Board, 1998d, e, f, g, h). Additionally in 1999, the State designated the San Joaquin River 

and parts of Bay-Delta as a high priority in the Consolidated 

Toxic Hot Spot Cleanup Plan (State Board, 1999c). Violations 

of the State annual selenium load limit (8,000 lbs selenium) 

have occurred at the San Joaquin River at Crows Landing from 

WY 1995 through 1998, when 14,291 lbs, 10,868 lbs, 8,667 

lbs, and 13,445 lbs selenium, respectively, were discharged.

The Clean Water Act as amended in 1987 [section 303 

(d)(l)(c)] requires that water-quality standards be converted 

into Total Maximum Daily Loads (TMDLs) in water-quality 

impaired water bodies like the lower reach of the San Joaquin 

River. A TMDL approach allows a State to implement waterquality control measures where beneficial uses are known to 

be impaired, but the resource is not being regulated because 

of lack of adequate data. In the case of selenium, both the 

existing record and developed models for the San Joaquin 

River have important limitations (Presser and Piper, 1998). 

From that record, it is difficult to ascertain if progress is being 

made, especially towards protecting the river (Westcot and 

others, 1996; Presser and Piper, 1998). 

TMDL models used for the San Joaquin River are 

conservative-element dilution models that do not consider 

the potential for selenium to bioaccumulate in ecosystems 

(Environmental Defense Fund, 1994; Karkoski, 1996). The 

assimilative capacity of the river in existing models is defined 

only by flow (i.e., dilution capacity). In one derivation of a 

TMDL model, acknowledgement is made of the shortcomings of the approach by stating that, if in the future, load limits 

are derived based on the capacity of the ecosystem to safely 

absorb pollutants, the methodology to derive the load allowances would change, but implementation issues for the agricultural dischargers would remain the same (Environmental 

Defense Fund, 1994). Implementation issues may include a 

requirement for an economic justification of continued impairment of the beneficial uses of the river as prescribed by antidegradation policies (Code of Federal Regulations 40:131.12; 

Clean Water Act Section 303(d) as amended, 1987). Hydrologic-economic models for the San Joaquin Valley and 

information regarding the cost/benefit of agriculture in the San 

Joaquin Valley have been developed and compiled at various 

stages of planning for irrigation and drainage projects (see, for 

example, Interagency Drainage Program, 1979a, b; Department of Water Resources, 1982; Horner, 1986; Willey, 1990; 

Dinar and Zilberman, 1991; Environmental Defense Fund, 

1994; Central Board, 1996c). Monthly selenium concentrations greater than 5 μg/L have not occurred further downstream in the San Joaquin River at Vernalis, the entrance to the 

Bay-Delta. 

Models that Target Load Reduction

Models were constructed in 1994 to calculate a load of 

selenium that might be discharged to the San Joaquin River 

with the goal of meeting a Federal 5 μg/L selenium criterion or 

a State 8 μg/L selenium objective. USEPA rejected the 8 μg/L 

objective for the San Joaquin River in 1992 and promulgated 

a 5 μg/L selenium criterion for the San Joaquin River and 

a 2 μg/L criterion for associated wetland channels (wildlife 

refuge supply channels) (USEPA, 1992). A TMDL model 

was developed by the Environmental Defense Fund and an 

alternative model named the Total Maximum Monthly Load 

(TMML) model was developed by the State (Central Valley 

Board, 1994b; Environmental Defense Fund, 1994). The 

Environmental Defense Fund model was a test case for agricultural non-point source pollution control that applied point 

source control regulation methodology. The model focuses on 

pollution sources, a program of load reductions, and economic 

incentives which include tradable discharge permits and 

tiered water pricing (Environmental Defense Fund, 1994). A 

modified version of a TMDL model for the San Joaquin River 

was adopted as part of a State waste discharge permit for the 

Grassland subarea in 1998 (Central Valley Board, 1998a). 

The choice of a compliance site for load models and 

waste discharge permits has critical implications for the 

perception of water quality in the San Joaquin River. Little 

fresh water flows into the San Joaquin River upstream of 

Crows Landing due to regulation of the river by Friant Dam. 

Most of the San Joaquin River flow is diverted south through 

the Friant-Kern Canal, leaving agricultural drainage as the 

dominant source of flow in the river above its confluence 

with the Merced River. A compliance site upstream of the 

Merced River would be the most precautionary. It would 

closely reflect drainage quality and be indicative of conditions 

in the upstream 22 miles. A compliance site below confluence with the Merced River would be influenced by dilution 

water provided by the Merced River and leave the upstream 

segments unprotected. However, a downstream site is probably more indicative of water quality in the longer downstream 

segment. 

The current compliance point for the San Joaquin River 

is designated as Crows Landing, downstream of the Merced 

River. The State permit for discharge to the San Joaquin River 

allows for a twelve-year compliance schedule. Full compli-
Appendix C. Agricultural Drainage Discharge to the San Joaquin River 139

ance for the San Joaquin River above and below the Merced 

River with a selenium water quality objective of 5 μg/L (4-day 

average) is scheduled for October 2010.

 Variables considered in deriving selenium load allocations from TMDL-type models were:

water-year type,

water quality objective,

averaging period,

exceedance frequency, and

flow derivation.

Table C1 and figures C2 to C4 give a summary of load 

allocations calculated from TMDL and TMML models using 

different types of water years. Figure C2 shows TMDL model 

loads for all water-year types (normal/wet, dry/below normal, 

and critically dry) for the case of a 5 μg/L objective, 4-day 

average, and a one-in-three-year violation rate. Figure C3 

shows a comparison of TMDL and TMML model loads for 

a wet-year allocation under the same conditions as above. 

Figure C4 shows a comparison of TMDL and TMML model 

loads for a dry-year allocation under the same conditions as 

above. Tables C2 and C3 and figures C5 to C10 document in 

more detail load allocations for the San Joaquin River calculated for several different combinations of model assumptions 

using selenium water quality objectives of 8 or 5 μg/L. These 

data are compiled from documentation for TMDL and TMML 

models (Central Valley Board, 1994b and Environmental 

Defense Fund, 1994).

The base case for the San Joaquin River TMDL was a 

single design flow of about 92,000 acre-ft at 5 μg/L selenium. 

The model allocated a load of 1,248 lbs selenium (table C2) 

(Environmental Defense Fund, 1994). A quasi-static type 

TMDL model has three water-year classifications for the San 

Joaquin River (critically dry, dry/below normal, and above 

normal/wet; table C2 and figures C5 to C7). The TMML 

model, as submitted to USEPA for approval, derives loads for 

only two types of water years (critically dry/dry/below normal 

and above normal/wet; table C3 and figures C8 to C10).

 Figures C5 to C10 also depict the seasonal nature of 

the models, with the greatest loads being discharged from 

December through May. Within a specific model, greater loads 

are allowed when dry-year water years are replaced by wetyear water years. Load allocations also increase when 4-day 

averages are replaced by monthly averages, and when allowable 

frequencies of violations of once-in-three-years are replaced 

by a frequency of once-in-five-months (figures C5 to C10). 

The TMDL model allows annual discharges to the San Joaquin 

River at Crows Landing/Patterson of 1,394 to 4,458 lbs selenium in dry years (critically dry, dry, and below normal years, 

table C1), within the ranges of options and excursion frequencies. The TMML model allows selenium discharges of 1,240 to 

1,809 lbs per year in dry years. In wet years, the TMDL model 

allows selenium loads of 3,165 to 6,547 lbs per year and the 

TMML model allows loads of 3,760 to 5,334 lbs per year. 

•

•

•

•

•

The Clean Water Act requires a margin of safety be 

considered in regulatory load models which are based solely 

on dilution. The purpose is to take into account uncertainties 

in the data or any lack of knowledge concerning the relation of 

effluent limitations and water quality (Environmental Defense 

Fund, 1994). Tables C1 to C3 show selenium loads used as 1) 

a margin of safety (a nominal 10 percent); and 2) estimated 

background loads from tributary rivers and wetlands. Margin 

of safety selenium loads range from 123 to 448 lbs per year 

in dry years and 317 to 534 lbs per year in wet years. Background selenium loads range from 91 to 273 lbs per year in 

dry years and 250 to 428 lbs per year in wet years. These 

loads were added to the modeled TMDL allowances for the 

dischargers, thereby increasing the modeled discharge to the 

San Joaquin River at Crows Landing (tables C1 to C3), but 

leaving in doubt protection of the San Joaquin River.

Models that Maximize Allowed Selenium Loads by 

Targeting Concentration

An alternative approach is to define a concentration 

target in a receiving water and manage selenium discharges 

to maintain that concentration under different flow conditions. Such a model, the dynamic real-time (DRT) model as 

suggested by the State, is designed to manage selenium loads 

using dynamic drainage effluent limits based on the real-time

dilution ca­pacity of the San Joaquin River (Karkoski, 1996; 

State Board, 1999a). The DRT approach depends on shortterm forecasts of flow and concentrations. In this management 

approach, selenium load reduction is deferred to a plan of 

temporal storage and timed release of concentrated effluent to 

match dilution by tributary flows to obtain compliance with a 

5 μg/L selenium objective. Timed-release of selenium-laden 

drainage takes maximum advantage of the dilution capacity 

of the river to maintain a given water quality objective (for 

example, the selenium concentration in the San Joaquin River 

will be maintained at 5 μg/L at all times). Note additionally for 

this approach that salinity measurements would need to act as 

surrogates for selenium measurements because technology is 

not available to assess selenium on a real-time basis.

Figure C11 shows an example, from limited data, of 

the DRT model loads for wet-year conditions using a 5 μg/L 

objective (Karkoski, 1996). Table C1 compares selenium loads 

allowed by a DRT model to those allocated by TMDL and 

TMML models, for a minimum, mean, and maximum amount 

of allowable loads of selenium discharged per month in a wet 

year. Figure C11 shows that an order-of-magnitude higher 

loads occurs in some months than that allowed by TMDL or 

TMML models (such as, 400 lbs selenium compared with 

4,000 lbs). The selenium loads discharged for a wet year range 

from 2,605 to 17,605 lbs per year, with a mean of 7,347 lbs 

per year. A more recent reference to the DRT model shows the 

wet year load to be approximately that referenced in 1996 for 

a wet year (7,401 lbs per year) and a dry year value of 4,631 

lbs per year (Drainage Implementation Program, 1999b). 

With real-time drainage management, ponds for flow

regulation would be necessary in order to maximize release 
140 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

of selenium loads during variable flow conditions in the river. 

The holding pond concept is reminiscent of planning for 

the San Luis Drain in the 1970s when Kesterson Reservoir 

ponds were to be used as holding reservoirs to regulate flows 

until the San Luis Drain was completed to the Bay-Delta. 

As mentioned earlier, more sophisticated storage, control, 

and timing are envisioned by managers and State regulators. 

Nevertheless, the ecological consequences of the ponds themselves need to be considered. 

Managing a constant concentration in receiving waters, 

although in response to a TMDL requirement, is the goal of 

the dynamic-effluent-type of modeling. It is unclear whether 

this deviation from a load model target was the intended use 

of concentration-dependent water quality standards defined 

by USEPA. The DRT approach uses a receiving water body’s 

dilution capacity to provide water to maximize disposal of 

selenium. Regulation of loads based on dynamic effluent 

limits provides no certainty for the amount discharged per 

month or year, nor for an assessment of the long-term progress toward selenium load reduction. The focus of TMDL and 

TMML models is to reduce or minimize selenium loads by 

establishing a load target. With real-time drainage management, the focus is shifted to a concentration target that, in 

essence, maximizes selenium loads by adjusting the timing of 

discharges to coincide with dilution capacity. As a result, the 

allowed selenium load would increase over that allocated by 

TMDL or TMML models. A DRT approach is best applied to 

maintaining a designated level of quality in the San Joaquin 

River as a receiving water. It is of less value in regulating 

the San Joaquin River as a source water for the Bay-Delta. 

In terms of ecosystem protection, this type of management 

could simulate a hydrologic system similar to a lake (lentic), 

rather than that of a flowing system (lotic), thus potentially 

expanding opportunities for selenium bioaccumulation.

Some additional practical considerations add complexity 

to applying a DRT concept. These include identifying a regulatory authority responsible for implementation of real time

regulation. Uncertainty also exists about choice of a target 

concentration. Different agencies and stakeholders have called 

for revisions of the selenium objective upward from 5 μg/L to 

8 μg /L, or downward to 2 μg/L. The choice of a compliance 

point (San Joaquin River at Patterson or Crows Landing or 

San Luis Drain at Mud Slough) will have a strong influence on 

the river, and therefore, is critical to determining an allowed 

load (as described above). Uncertainties about the type of 

conveyance used for drainage (wetland channels or the San 

Luis Drain) could have implications for concentrations. Since 

agricultural drainage is regulated as non-point source pollution, a 5 μg /L effluent stream from the discharger has not been 

required in the past. It is unclear how this would be integrated 

into a regulatory control program. Finally, refinement of the 

assimilative capacity operations plan using real-time management needs to include data collection to assess the assimilative 

capacity of the San Joaquin River based on the bioaccumulative nature of selenium (Grassland Area Farmers and San Luis 

and Delta-Mendota Water Authority, 1998; Presser and Piper, 

1998). Understanding sources of selenium and how selenium 

moves through an agricultural discharge system becomes 

important in a strategy that maximizes loads to meet concentration objectives. 

A second reason for modeling the influence of timed 

releases of agricultural discharges to the San Joaquin River 

is to help determine how to meet salinity objectives for the 

San Joaquin River at Vernalis (State Board, 1994, 1997, and 

1999a; EA Engineering, Science, and Technology, 1999). 

The State model predicted that controlled timing of wetland 

releases (or a combination of drainage and wetland releases) 

did not achieve compliance with that standard. Focus then 

shifted toward taking advantage of additional seasonally available downstream dilution by releasing dilution water from the 

New Melones Reservoir on the Stanislaus River. Control of 

drainage release to the San Joaquin River also includes implementation of a system of storage including recycling facilities, evaporation ponds, and in-field subsurface storage (State 

Board, 1997). Despite several opportunities for manipulating 

the massively engineered Central Valley Project water supply, 

the ultimate alternative for salinity control seems to depend on 

managing the same lands that need drainage and that discharge 

selenium, but the State plan does not include an analysis of 

selenium effects.
Appendix C. Agricultural Drainage Discharge to the San Joaquin River 141 Table C1. Modeled annual selenium load allocation and discharge from the Grassland Drainage Problem Area to the San Joaquin River using various models (Total Maximum Daily Load Model, Total Maximum Monthly Load Model, and Dynamic Real-Time Model), water-year types (critically dry; dry/below normal; above normal/wet, dry; or wet), averaging periods (4-day or monthly), and violation frequencies (1 in 3 year or 1 in 5 month) to achieve a 5 μg/L selenium objective for San Joaquin River. Model and water year type Irrigated/ drained acres Range used to model selenium discharge (San Joaquin River at Crows Landing) (acre-ft/year) Range of modeled selenium load allocations (lbs/year) Range of modeled selenium background (lbs/year) Range of modeled selenium margin of safety (lbs/year) Range of modeled selenium discharge to San Joaquin R. at Crows Landing (lbs/year) Total Maximum Daily Load Model, TMDL (5 μg/L selenium objective for San Joaquin River; 4-day or monthly averaging period; 1 in 3 year or 1 in 5 month violation rate) TMDLa 93,390/49,273

−

−

−

−

−

Critically dry b

− 104,030−260,859 1,163−3,060 91−129 140−352 1,394−3,541

Dry/Below normalb − 225,995−328,002 2,504−3,737 257−273 305−448 3,066−4,458

Above normal/wetb − 233,186−481,934 2,598−5,463 250−428 317−656 3,165−6,547

Total Maximum Monthly Load Model, TMML (5 μg/L selenium objective for San Joaquin River; 4-day or monthly averaging period; 1 in 3 year violation frequency)

TMMLc 90,620/44,860

−

−

−

−

−

Dryb − 91,255−133,210 1,001−1,514 114−116 123−179 1,240−1,809

Wetb − 276,772−392,570 3,088−4,451 294−362 381−534 3,760−5,334

Dynamic Real-Time Model, DRT (5 μg/L selenium objective for San Joaquin River)

DRT d wet b

−

− 2,605−17,605

(7,347 mean)

−

−

−

aEnvironmental Defense Fund, 1994; Central Valley Board, 1994b.bCritically dry (< 2.1 million acre-ft); dry (2.1-2.5 million acre-ft); (below normal 2.5-3.1 million acre-ft); above normal (3.1-3.8 million acre-ft); and wet (>3.8 million acre-ft) (Central Valley Board, 

1994b, Table 7); referenced to San Joaquin River Index threshold (Central Valley Board, 1994b).

cDraft submittal to USEPA from Central Valley Board, 1996a.dCalculated effluent limits for wet year based on 22 year period of record (Karkoski, 1996).
142 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Table C2. Modeled annual selenium load allowance from the Grassland Area to the San Joaquin River and modeled flow for the San Joaquin River at Crows Landing/ Patterson using the Total Maximum Monthly Load Model under various water-year types (critically dry; dry/below normal; or above normal/ wet), averaging periods (4-day or monthly), and violation frequencies (1 in 3 year or 1 in 5 month) to achieve a 5 μg/L selenium objective for San Joaquin River. [The Total Maximum Daily Load Model was developed by the Environmental Defense Fund (1994) and the Central Valley Board (1994b). Modeled effluent load data from October, 1985 to December, 1988. Modeled San Joaquin River flow at Crows Landing and Patterson from WY 1970 to 1991. Note: flow record for Crows Landing is from 1970-1972; the remainder of the data used in the model for the San Joaquin River at Crows Landing was reconstructed from flow data collected at San Joaquin River at Patterson. Data also was adjusted for averaging period because record is incomplete (Central Valley Board, 1994b; Karkoski, 1996).] Selenium performance goal or regulation scenario Irrigated/drained acreagea (acres) Modeled selenium load allocation (lbs/year) Modeled selenium background (lbs/year) Modeled selenium margin of safety (lbs/year) Modeled selenium dis- charge to San Joaquin River at Crows Landing/ Patterson (lbs/year) Modeled flow of San Joaquin River at Crows Landing/ Patterson) (acre-ft/year Total Maximum Daily Load Model, TMDL (single design flow; 5 μg/L selenium objective for San Joaquin River; 4-day average; 1 in 3 year violation frequency) TMDL 93,390/49,273 1,248

−

−

− 92,363

Total Maximum Daily Load Model, TMDL (5 μg/L selenium objective for San Joaquin River; 4-day average; 1 in 3 year violation frequency)

TMDL 93,390/49,273

−

−

−

−

−

Critically dryb − 1,163 110 140 1,415 104,030

Dry/below normalb − 2,504 257 305 3,069 225,995

Above normal/wetb − 2,598 250 317 3,166 233,186

Total Maximum Daily Load Model, TMDL (5 μg/L selenium objective for San Joaquin River; monthly average; 1 in 3 year violation frequency)

TMDL 93,390/49,273

−

−

−

−

−

Critically dryb − 1,676 119 200 1,994 147,029

Dry/Below normalb − 3,036 265 366 3,666 270,000Above normal/wetb − 3,374 280 405 4,061 299,049

Total Maximum Daily Load Model, TMDL (5 μg/L selenium objective for San Joaquin River; 4-day average; 1 in 5 month violation frequency)

TMDL 93,390/49,273

−

−

−

−

−

Critically dryb − 3,060 129 352 3,546 260,859

Dry/Below normalb − 3,737 273 448 4,454 328,002Above normal/wetb − 5,463 428 656 6,549 481,934

aTable II-4, Baseline Data for Pollution Allocation Subtotal (Environmental Defense Fund, 1994). Acreage does not include 10,000 irrigated acres and 5,276 drained acres as noted in total acreage taken 

from water district data for various years (1987-1990) and Central Valley Board data.

bCritically dry (< 2.1 million acre-ft); dry (2.1-2.5 million acre-ft); (below normal 2.5-3.1 million acre-ft); above normal (3.1-3.8 million acre-ft); and wet (>3.8 million acre-ft) (Central Valley Board, 

1994b, Table 7); referenced to San Joaquin River Index threshold (Central Valley Board, 1994b).
Appendix C. Agricultural Drainage Discharge to the San Joaquin River 143 Table C3. Modeled annual selenium load allowances from the Grassland Area to the San Joaquin River and modeled flow for the San Joaquin River at Crows Landing/ Patterson using various models (Total Maximum Monthly Load or Dynamic Real-Time), water-year types (critically dry/dry/below normal; above normal/wet; or wet), averaging periods (4-day or monthly), and violation frequencies (1 in 3 year) to achieve either a 8 or 5 μg/L selenium objective for San Joaquin River. [Modeled effluent load data from October, 1985 to December, 1988. Modeled San Joaquin River flow at Crows Landing and Patterson from WY 1970 to 1991. Note: flow record for Crows Landing is from 1970-1972; the remainder of the data used in the model for the San Joaquin River at Crows Landing was reconstructed from flow data collected at San Joaquin River at Patterson. Data also was adjusted for averaging period because record is incomplete (Central Valley Board, 1994b; Karkoski, 1996).] Selenium performance goal or regulation scenario Irrigated/drained acreagea (acres) Modeled selenium load allocation (lbs/year) Modeled selenium background (lbs/year) Modeled selenium margin of safety (lbs/year) Modeled selenium dis- charge to San Joaquin R. at Crows Landing/ Patterson (lbs/year) Modeled flow San Joaquin River at Crows Landing/ Patterson (acre-ft/year) Total Maximum Monthly Load Model, TMML (8 μg/L selenium objective for San Joaquin River; monthly mean; 1 in 3 year violation frequency) TMMLb 90,620/44,860 − − − − − Critically dry/dry/below normal − 2,491 114 290 2,896 133,210 Total Maximum Monthly Load Model, TMML (5 μg/L selenium objective for San Joaquin River; 4-day average; 1 in 3 year violation frequency) TMMLb 90,620/44,860 Critically dry/dry/below normal − 1,001 116 123 1,240 91,255 Above normal/wet − 3,088 294 381 3,760 276,772 Total Maximum Monthly Load Model, TMML (5 μg/L selenium objective for San Joaquin River; monthly average; 1 in 3 year violation frequency) TMMLb 90,620/44,860 − − − − − Critically dry/dry/below normal − 1,514 114 179 1,809 133,210 Above normal/wet − 4,451 362 534 5,334 392,570 Dynamic Real-Time Model, DRT DRT c − − − − − − Wet (mean) − 7,347 − − − − Wet (minimum) − 2,605 − − − − Wet (maximum) − 17,605 − − − − aTable 1 (Central Valley Board, 1994b). bDraft submittal of TMML Model to USEPA (Central Valley Board, 1996a). cKarkoski, 1996.
144 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

0

2

4

6

8

10

Number of months

86 87 88 89 90 91 92 93 94 95 96 97

Water year

0

5,000

10,000

15,000

20,000

25,000

30,000

35,000

SJR flow at Crows L. (acre-ft)

0

100

200

300

400

500

Selenium (lbs)

O N D J F M A M J J A S

Month

Comparison of Wet, Dry, Critically Dry

Years, 5 ppb Se, 4 Day average,1/3 yr

Normal/Wet

Dry/Below Normal

Critically dry

Discharge

(acre-ft)

Se

(lbs)

5,000

0

10,000

15,000

20,000

25,000

30,000

35,000

SJR flow at Crows L. (acre-ft)

0

50

100

150

200

250

300

350

400

450

Selenium (lbs)

Normal/Wet

Wet

Discharge

(acre-ft)

Se

(lbs)

NO D J F M A M J J A S

Month

SJR flow at Crows L. (acre-ft)

0

100

200

300

400

Selenium (lbs)

Comparison of TMML & TMDL, Dry

5 ppb Se, 4 Day average, 1/3 yr

Dry

Critically Dry

Dry/Below Normal

5,000

0

10,000

15,000

20,000

25,000

30,000 Discharge

(acre-ft)

Se

(lbs)

O N D J F M A M J J A S

Month

Figure C4. Comparison of TMDL and TMML model projections 

during a dry year for 5 μg/L, 4-day average, 1 out of 3 year 

exceedance.

Figure C3. Comparison of TMDL and TMML model projections 

during a wet year for 5 μg/L, 4-day average, 1 out of 3 year 

exceedance.

Figure C2. Comparison of wet, dry, and critically dry years (TMDL 

model) for 5 μg/L, 4-day average, 1 out of 3 year exceedance.

Figure C1. Number of selenium water quality exceedance months 

(U.S. EPA criterion) for the San Joaquin River at Crows Landing 

during WY 1986 through WY 1997.
Appendix C. Agricultural Drainage Discharge to the San Joaquin River 145

0

10,000

20,000

30,000

40,000

SJR flow at Crows L. (acre-ft)

0

100

200

300

400

500

600

Selenium (lbs)

4-day, 1/5 month annual load

SJR at Crows Landing

= 4,454 lbs Se

= 328,002 acre-ft.

Monthly, 1/3 yr

annual load

SJR at Crows Landing

= 3,666 lbs Se

= 270,000 acre-ft.

4-day, 1/3 yr annual load

SJR at Crows Landing

= 3,069 lbs Se

= 225,995 acre-ft.

Discharge

(acre-feet)

Se

(lbs)

b)

c)

a)

O N D J F M A M J J A S

Month

SJR flow at Crows L. (acre-ft)

0

50

100

150

200

250

300

350

400

Selenium (lbs)

0

5,000

10,000

15,000

20,000

25,000

30,000

Monthly, 1/3 yr

annual load

SJR at Crows Landing

= 1,994 lbs Se

= 147,029 acre-ft.

O N D J F M A M J J A S

Month

b)

c)

4-day, 1/3 yr annual load

SJR at Crows Landing

= 1,415 lbs Se

= 104,030 acre-ft.

4-day, 1/5 month

annual load

SJR at Crows Landing

= 3,546 lbs Se

= 260,859 acre-ft.

a)

Discharge

(acre-ft)

Se

(lbs)

Figure C5. Comparison of TMDL model projections at Crows 

Landing during critically dry years for (a) 5 μg/L, 4-day average, 1 

out of 3 year exceedance, (b) 5 μg/L, monthly average, 1 out of 3 

year exceedance, and (c) 5 μg/L, 4-day average, 1 out of 5 month 

exceedance.

Figure C6. Comparison of TMDL model projections at Crows 

Landing during dry and below normal years for (a) 5 μg/L, 4-day 

average, 1 out of 3 year exceedance, (b) 5 μg/L, monthly average, 

1 out of 3 year exceedance, and (c) 5 μg/L, 4-day average, 1 out of 

5 month exceedance.

0

10,000

20,000

30,000

40,000

50,000

60,000

SJR flow at Crows L. (acre-ft)

0

100

200

300

400

500

600

700

800

Selenium (lbs)

Monthly, 1/3 yr annual load

SJR at Crows Landing

= 4,061 lbs Se

= 299,049 acre-ft.

4-day, 1/3 yr annual load

SJR at Crows Landing

= 3,166 lbs Se

= 233,186 acre-ft.

Monthly, 1/5 month annual load

SJR at Crows Landing

= 6,549 lbs Se

= 481,934 acre-ft.

Discharge

(acre-feet)

Se

(lbs)

b)

c)

a)

O N D J F M A M J J A S

Month

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

SJR flow at Crows L. (acre-ft)

0

50

100

150

200

250

300

350

Selenium (lbs)

Discharge (acre-ft)

Se (lbs)

1/3 yr annual discharge

SJR@Crows Landing

= 2,896 lbs selenium

= 133,210 acre-ft.

O N D J F M A M J J A S

Month

Figure C7. Comparison of TMDL model projections at Crows 

Landing during above normal and wet years for (a) 5 μg/L, 4-day 

average, 1 out of 3 year exceedance, (b) 5 μg/L, monthly average, 

1 out of 3 year exceedance, and (c) 5 μg/L, 4-day average, 1 out of 

5 month exceedance.

Figure C8. TMML model projection at Crows Landing for 8 μg/L 

and 1 out of 3 year exceedance.
146 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Figure C9. Comparison of TMML model projections during a dry 

year at Crows Landing for (a) 5 μg/L, 4-day average inputs, 1 out of 

3 years exceedance, and (b) 5 μg/L and monthly average, 1 out of 

3 years exceedance.

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

SJR flow at Crows L. (acre-ft)

0

50

100

150

200

4-day avg,1/3 yr

Selenium (lbs)

annual discharge

SJR@Crows Landing

= 1,240 lbs Se

= 133,210 acre-ft.

Monthly,1/3 yr

annual discharge

SJR@Crows Landing

= 1,809 lbs Se

= 133,210 acre-ft.

Discharge

(acre-ft)

Se

 (lbs) 

b)

a)

O N D J F M A M J J A S

Month

10,000

0

20,000

30,000

40,000

SJR flow at Crows L. (acre-ft)

0

100

200

300

400

500

Selenium (lbs)

4-day,1/3 yr

annual discharge

SJR@Crows Landing

= 3,760 lbs Se

= 276,772 acre-ft.

Monthly,1/3 yr

annual discharge

SJR at Crows Landing

= 5,334 lbs Se

= 392,570 acre-ft.

Discharge

(acre-ft)

Se

 (lbs) 

b)

a)

O N D J F M A M J J A S

Month

Figure C10. Comparison of TMML model projections during a wet 

year at Crows Landing for (a) 5 μg/L, monthly average, 1 out of 3 

years exceedance, and (b) 5 μg/L, 4-day average, 1 out of 3 year 

exceedance.

0

1,000

2,000

3,000

4,000

5,000

Selenium (lbs)

Minimum (2,605 lbs Se/yr)

Mean (7,347 lbs Se/yr)

Maximum (17,605 lbs Se/yr)

O N D J F M A M J J A S

Month

Figure C11. Monthly selenium loads for a dynamic real time (DRT) 

model during a wet year using a 5 μg/L input.
Appendix D. Temporal and Spatial Variability in Selenium Load 147

Appendix D. Temporal and Spatial Variability in Selenium Load

Contents

Introduction............................................................................................................................................................................................................149

Temporal Variability ..............................................................................................................................................................................................149

Spatial Variability ..................................................................................................................................................................................................152

Prediction of Short-Term Selenium Reservoirs ...............................................................................................................................................155

Figures

Figure D1. Relation between flow and (a) selenium concentration; (b) selenium load; (c) salt concentration; and (d  ) salt 

load on a monthly basis for site B (San Luis Drain outflow to Mud Slough) during WY 1997 .............................................150

Figure D2. Relation between flow and (a) selenium concentration; (b) selenium load; (c ) salt concentration; 

and (d  ) salt load on a monthly basis for site B (San Luis Drain outflow to Mud Slough) during WY 1998 ........................150

Figure D3. Daily variation of (a) flow; (b) selenium concentration; (c) specific conductance; 

(d  ) total dissolved solids; (e) selenium load; and (f ) salt load for site B (San Luis Drain outflow

to Mud Slough) during WY 1997.....................................................................................................................................................150

Figure D4. Daily variation of (a) flow; (b) selenium concentration; (c) specific conductance; 

(d  ) total dissolved solids; (e) selenium load; and (f ) salt load for site B (San Luis Drain outflow 

to Mud Slough) during WY 1998.....................................................................................................................................................151

Figure D5. Relations between electrical conductance and selenium concentrations on an hourly basis for site B 

(San Luis Drain outflow to Mud Slough).......................................................................................................................................151

Figure D6. Relation between selenium concentration and load for the San Joaquin R. at Crows Landing 

during (a) WY 1997 and (b ) WY 1998 .............................................................................................................................................151

Figure D7. Relation between salt concentration and load for the San Joaquin River at Crows Landing 

during (a) WY 1997 and (b) WY 1998 .............................................................................................................................................152

Figure D8. Daily variation of (a) flow; (b) selenium concentration; (c) specific conductance; 

(d  ) total dissolved solids; (e) selenium load; and (f ) salt load for the San Joaquin River at Crows 

Landing during WY 1997 ..................................................................................................................................................................152

Figure D9. Daily variation of (a) flow; (b ) selenium concentration; (c) specific conductance; 

(d  ) total dissolved solids; (e) selenium load; and (f ) salt load for the San Joaquin River at Crows 

Landing during WY 1998 ..................................................................................................................................................................153

Figure D10.Percent selenium load (normalized to the selenium load at the San Joaquin River at Vernalis)

for the Drainage Problem Area (DPA); combined Mud and Salt Sloughs (MS+SS); and the San 

Joaquin River at Crows Landing-Patterson (CL-PATT) for WY 1986 through WY 1997.........................................................154

Figure D11.Percent salt load (normalized to the salt load at the San Joaquin River at Vernalis) for Drainage 

Problem Area (DPA); combined Mud and Salt Sloughs (MS+SS); and the San Joaquin River at 

Crows Landing-Patterson (CL-PATT) for WY 1986 through WY 1997 .......................................................................................155

Figure D12.Relation between total water applied and drainage discharge for the Drainage Problem Area 

(DPA) during WY 1986 through WY 1997 ......................................................................................................................................155

Figure D13.Relation among (a) total water applied, selenium concentration, and total dissolved solids 

concentration; (b) total water applied, selenium load, and salt load for the Drainage Problem 

Area (DPA) during WY 1986 through WY 1997 .............................................................................................................................155

Figure D14.Relation among (a) drain discharge, selenium concentration, and total dissolved solids 

concentration; (b) drain discharge, selenium load, and salt load for the Drainage Problem 

Area (DPA) during WY 1986 through WY 1997 .............................................................................................................................156
148 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Figure D15. Relation among flow, selenium concentration, and selenium load on a daily basis at site B 

San Luis Drain outflow to Mud Slough) for WY 1997 ...............................................................................................................156

Figure D16. Relation among flow, selenium concentration, and selenium load on a daily basis at site B 

(San Luis Drain outflow to Mud Slough) for WY 1998 ..............................................................................................................156

Figure D17. Relation among drainage discharge and applied water (irrigation/precipitation combined) and 

(a ) selenium concentration; or (b) selenium load on a monthly basis at site B 

(San Luis Drain outflow to Mud Slough) during WY 1997 .......................................................................................................157

Figure D18. Relation among drainage discharge and applied water (irrigation/precipitation combined) and 

(a) selenium concentration; or (b) selenium load on a monthly basis at site B (San Luis Drain 

outflow to Mud Slough) during WY 1998 ....................................................................................................................................157

Figure D19. Relation among drainage discharge and applied water (irrigation/precipitation combined) and 

(a) selenium concentration; or (b) selenium load on a monthly basis at site B (San Luis Drain 

outflow to Mud Slough) for base average WY 1986 through WY 1994 .................................................................................157

Figure D20. Relation among drainage discharge and applied water (irrigation/precipitation combined) and 

(a) salt concentration; or (b) salt load on a monthly basis at site B (San Luis Drain outflow to 

Mud Slough) during WY 1997 .......................................................................................................................................................157

Figure D21. Relation among drainage discharge and applied water irrigation/precipitation combined and 

(a) salt concentration; or (b) salt load on a monthly basis at site B (San Luis Drain outflow to 

Mud Slough) during WY 1998 .......................................................................................................................................................157

Tables

Table D1. Selenium loads from the Grassland Drainage Problem Area, Mud and Salt Sloughs, and 

the San Joaquin River at Crows Landing-Patterson as a percentage of selenium loads at the 

San Joaquin River at Vernalis ........................................................................................................................................................153

Table D2. Salt loads (Total Dissolved Solids) from the Grassland Drainage Problem Area, Mud and 

Salt Sloughs, and the San Joaquin River at Crows Landing-Patterson as a percentage of salt 

loads at the San Joaquin River at Vernalis ..................................................................................................................................154
Appendix D. Temporal and Spatial Variability in Selenium Load 149

Introduction

Estimates of selenium loads in this report contain some 

substantial uncertainties that have not yet been discussed. 

The most important of these are associated with the temporal 

and spatial dependence of selenium loads or the ways those 

loads are determined. Given here are a series of graphs based 

on available data that document the variability in the quality 

of agricultural drainage that is discharged to the San Joaquin 

River and a 28-mile portion of the San Luis Drain re-opened 

as part of the Grassland Bypass Channel Project. Flow and 

concentration data also are compiled and graphed as determinants of load. Compilations such as these could be useful in 

helping to design monitoring plans to collect data suitable for 

more detailed projections, which are essential in the future. 

Data from the Grassland Drainage Problem Area (DPA) 

and the San Luis Drain outflow to Mud Slough (site B) characterize drainage from a source area (farmland sumps or agricultural drainage canals). Sites downstream from the source 

area and the San Luis Drain outflow are Mud Slough (MS); 

Salt Slough (SS); the San Joaquin River at Crows Landing/

Patterson below the confluence with the Merced River (CL/

PATT, about 50 miles downstream from farm sumps); and the 

San Joaquin River at Vernalis (VERN, about 130 miles downstream from agricultural discharges). 

Data sets mainly encompass WY 1986 to WY 1998. 

Focus here is on WYs 1997 and 1998 data sets because these 

were the first years in which data were collected at greater 

frequency than had been the case historically.

Temporal Variability

Seasonal and inter-annual variability

Salt imbalance in the San Joaquin Valley is also a driving 

force for management activities. Selenium loads are compared 

to salt loads to elucidate the behavior of a non-conservative 

element (selenium) to that of a conservative element (salt). 

Total dissolved solids concentrations or specific conductance 

is used here as a surrogate for salt concentrations. Salt concentrations are calculated from specific conductance by using the 

equation:

Specific conductance × 0.65 = mg/L total dissolved solids 

(TDS) or salt

Salt or TDS load (in tons) is calculated using the equation: 

[salt or TDS concentration (mg/L) × drainage volume 

(acre-ft)] × 0.00136 = salt or TDS load (tons), 

where 0.00136 tons salt or TDS per acre-foot is equal to a 

concentration of 1 mg/L salt or TDS. Pounds can be converted 

to tons using the conversion factor: tons = lbs ÷ 2,000. Conversion factors used for salt and selenium were compiled previously (see main text table 4).

Monthly, Daily and Hourly Measurements

Monitoring for the Grassland Bypass Channel Project 

provides for frequent measurements of flow and concentrations in the re-opened 28-mile portion of the San Luis Drain 

(USBR and others, 1996). Salt and selenium loads for the 

Grassland Drainage Problem Area were measured at the San 

Luis Drain outflow to Mud Slough (site B) for WYs 1997 and 

1998 (also see appendix B, tables B8 and B9) (USBR and 

others, 1998 and ongoing). Figures D1 and D2 show the variation for WYs 1997 and 1998 in monthly San Luis Drain flow 

(averages of daily flow measurements), monthly selenium 

concentrations (averages of daily measurements), monthly 

salt concentrations [averages of daily specific conductance 

converted to total dissolved solids or salt concentration], and 

calculated monthly selenium and salt loads. For the Grassland 

Bypass Channel Project, drainage management is aimed at 

meeting monthly selenium load targets that are based on the 

seasonal nature of drainage generation (listed in appendix 

B, tables A8 and A9 and shown in appendix A, figure A11). 

Maximum pre-irrigation occurs in February, maximum irrigation in July, and maximum discharge in February or March. 

Ranges of monthly variation for WY 1997 are: flow, 1,274 

to 4,867 acre-ft; selenium concentration 25 to 105 μg/L; 

salt concentration 2,175 to 3,255 mg/L; selenium load 109 

to 1,278 lbs; and salt load 4,325 to 20,091 tons. Ranges of 

monthly variation for WY 1998 are: flow, 1,403 to 7,094 acreft; selenium concentration 43 to 105 μg/L; salt concentration 

2,391 to 3,704 mg/L; selenium load 178 to 1,598 lbs; and salt 

load 5,563 to 31,182 tons. 

Figures D3 and D4 show the daily variation for WYs 

1997 and 1998 in San Luis Drain flow (continuous monitoring based on 20-minute interval measurements), selenium 

concentrations, TDS or salt concentrations (based on specific 

conductance measurements), selenium loads, and salt loads 

(USBR and others, 1998 and ongoing). Ranges of daily 

variation for WY 1997 are: flow 21 to 181 acre-ft; selenium 

concentration 15 to 116 μg/L; and salt concentration 1,703 to 

3,671 mg/L. Daily loads vary from 1.1 to 54 lbs selenium and 

66 to 860 tons salt. Ranges of daily variation for WY 1998 

are: flow 20 to 288 acre-ft; selenium concentration 20 to 128 

μg/L; and salt concentration 4,114 to 2,230 mg/L. Daily loads 

vary from 2.7 to 69 lbs selenium and 83 to 1,218 tons salt. 

Figure D5 shows the hourly variation in selenium 

concentration and conductivity for the San Luis Drain 

discharge during a 24-hour interval (Rudy Schnagl, Central 

Valley Board, personal commun., June, 1998). Ranges of 

hourly variations are: selenium concentration 47 to 78 μg/L; 

and conductivity 4,280 to 4,675 μmhos/cm (equivalent to 

2,782 to 3,039 mg/L total dissolved solids).

Figure D6 compares monthly selenium load and concentration data for the San Joaquin River at Crows Landing 
150 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

0

2,000

4,000

6,000

0

400

800

1200

1600

2,000

0

4,000

6,000

0

8,000

16,000

24,000

32,000

0

2,000

4,000

6,000

0

20

40

60

80

100

120

0

2,000

4,000

6,000

0

800

1,600

2,400

3,200

Se (lbs)

Salt (tons)

Se (μg/L) Salt (mg/L)

Flow

Flow

Flow

Flow

Selenium

Selenium

Salt

Salt

Flow (acre-ft) Flow (acre-ft)

Flow (acre-ft) Flow (acre-ft)

a b

c d

O N D J F M A M J J A S

Month

WY 1997

O N D J F M A M J J A S

Month

WY 1997

0

2,000

4,000

6,000

0

400

800

1200

1600

2,000

0

4,000

6,000

0

8,000

16,000

24,000

32,000

0

2,000

4,000

6,000

Flow (acre-ft) Flow (acre-ft)

Flow (acre-ft) Flow (acre-ft)

0

20

40

60

80

100

120

0

2,000

4,000

6,000

0

800

1600

2,400

3,200

Se (lbs) Salt (tons)

Se (μg/L) Salt (mg/L)

Flow

Flow

Flow

Flow

Selenium

Selenium

Salt

Salt

a b

c d

O N D J F M A M J J A S

Month

WY 1998

O N D J F M A M J J A S

Month

WY 1998

0

40

80

120

160

0

40

80

120

Se (μg/L) Salt (mg/L) Salt (tons/day)

0

2000

4000

6000

0

1000

2000

3000

4000

0

20

40

60

0

400

800

1200

Flow (ft3/s) Specific conductance (μS/cm) Se (lbs)

O N D J F M A M J J A S O N D J F M A M J J A S

a b

c d

e f

Month

WY 1997

Month

WY 1997

Figure D1. Relation between flow and (a) 

selenium concentration; (b) selenium load; 

(c) salt concentration; and (d) salt load on 

a monthly basis for site B (San Luis Drain 

outflow to Mud Slough) during WY 1997.

Figure D2. Relation between flow and (a) 

selenium concentration; (b) selenium load; 

(c) salt concentration; and (d ) salt load on 

a monthly basis for site B (San Luis Drain 

outflow to Mud Slough) during WY 1998.

Figure D3. Daily variation of (a) flow; 

(b) selenium concentration; (c) specific 

conductance; (d ) total dissolved solids; 

(e) selenium load; and (f) salt load for site 

B (San Luis Drain outflow to Mud Slough) 

during WY 1997. 
Appendix D. Temporal and Spatial Variability in Selenium Load 151

downstream of the San Luis Drain discharge for WYs 1997 

and 1998 (USBR and others, 1998 and ongoing). In WY 

1997, selenium concentrations were lower compared to 

those of WY 1998. Flow in the San Joaquin River below the 

Merced River was sustained at a higher level for a longer 

period in WY 1998 than in WY 1997 due to increased snowmelt flowing in the Merced River. The competing seasonal 

effects of increased source load due to increased applied 

water and dilution afforded by the Merced River resulted in a 

selenium load of 9,054 lbs for WY 1997; and 15,884 lbs for 

WY 1998. Violation of the 5 μg/L selenium criterion occurred 

at this site in WY 1997, but not in WY 1998. Figure D7 

compares salt load and concentration data for the San Joaquin 

River at Crows Landing for WYs 1997 and 1998. Salt load 

and concentration patterns generally follow those for selenium load and concentration in WY 1997, but the salt concentration pattern deviates from that of selenium concentration 

in WY 1998. Ranges of monthly variation for WY 1997 are: 

flow 28,761 to 1,212,948 acre-ft; selenium concentration, 

0.36 to 6.8 μg/L; salt concentration 109 to 952 mg/L; selenium load, 149 to 1,533 lbs; and salt load, 24,563 to 242,735 

tons. Ranges of monthly variation for WY 1998 are: flow 

0

40

80

120

160

0

40

80

120

Se (μg/L) Salt (mg/L) Salt (tons/day)

0

2000

4000

6000

0

1000

2000

3000

4000

0

20

40

60

0

400

800

1200

Flow (ft3/s) Specific conductance (μS/cm) Se (lbs)

O N D J F M A M J J A S O N D J F M A M J J A S

a b

c d

e f

Month

WY 1998

Month

WY 1998

Figure D4. Daily variation of (a) flow; 

(b) selenium concentration; (c) specific 

conductance; (d ) total dissolved solids; 

(e) selenium load; and (f ) salt load for site 

B (San Luis Drain outflow to Mud Slough) 

during WY 1998. 

4200

4300

4400

4500

4600

4700

Lab EC (μS/cm)

45

50

55

60

65

70

75

80

Se (μg/L)

0 2 4 6 8 10 12 14 16 18 20 22

Time (hours)

Lab EC

Selenium

SPECIAL STUDY—SAN LUIS DRAIN

6/26/97

0

800

1,600

2,400

3,200

0

2

4

6

0

2

4

6

μg/L

μg/L

lbs

lbs

0

800

1,600

2,400

3,200

Se (lbs)

Se (μg/L)

O N D J F M A M J J A S

a

b

Month Figure D5. Relations between electrical conductance and 

selenium concentrations on an hourly basis for site B (San Luis 

Drain outflow to Mud Slough).

Figure D6. Relation 

between selenium 

concentration and 

load for the San 

Joaquin River at 

Crows Landing during 

(a) WY 1997 and 

(b ) WY 1998.
152 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

40,200 to 998,158 acre-ft; selenium concentration, 0.69 to 

2.6 μg/L; salt concentration 108 to 934 mg/L; selenium load, 

262 to 3,133 lbs; and salt load, 37,006 to 284,356 tons.

Daily measurements of salt and selenium also were taken 

during WYs 1997 and 1998 for the San Joaquin River at Crows 

Landing (USBR and others, 1998 and ongoing). Figure D8 

shows the WY 1997 daily variation of flow, concentration, and 

load. Ranges of daily variation for WY 1997 are: flow 818 to 

73,458 acre-feet; selenium concentration 0.1 to 9.7 μg/L; salt 

concentration 82 to 1,165 mg/L; selenium load 1.3 to 183 lbs; 

and salt load 500 to 15,956 tons. Figure D9 shows the WY 

1998 daily variation of flow, selenium and salt concentrations, 

and calculated daily selenium and salt loads. Ranges of daily 

variation for WY 1998 are: flow 483 to 24,200 cfs or 956 to 

47,916 acre-feet; selenium concentration 0.5 to 4.1 μg/L; salt 

concentration 79 to 1,165 mg/L; selenium load 3.4 to 183 lbs; 

and salt load 809 to 15,482 tons. 

Spatial Variability 

Tables D1 and D2 show the percentage of input selenium 

(non-conservative element) and salt (conservative element) 

loads to the discharged load of selenium and salt for the San 

Joaquin River at Vernalis, which is the entrance to the BayDelta (Central Valley Board, 1996a, b, 1998d, e, f, g, h). These 

0

100,000

200,000

300,000

Salt (tons)

Salt (mg/L)

O N D J F M A M J J A S

Month

0

400

800

0

100,000

200,000

300,000

Salt (tons)

Salt (mg/L)

O N D J F M A M J J A S

0

400

800

tons

tons

mg/L

a

b

mg/L

0

10,000

20,000

30,000

40,000

0

4

2

6

8

10

Se (μg/L)

0

400

800

1200

1600

0

50

100

150

200

Flow (ft3/s) Specific conductance (μS/cm) Se (lbs)

O N D J F M A M J J A S

Month

WY 1997

Month

WY 1997

Salt (mg/L) Salt (tons)

0

400

800

1200

0

4,000

8,000

12,000

16,000

O N D J F M A M J J A S

a b

e f

c d

Figure D7. Relation between salt concentration 

and load for the San Joaquin River at Crows 

Landing during (a) WY 1997 and (b) WY 1998.

Figure D8. Daily variation 

of (a) flow; (b) selenium 

concentration; (c) specific 

conductance; (d ) total 

dissolved solids; (e) selenium 

load; and (f ) salt load for the 

San Joaquin River at Crows 

Landing during WY 1997. 
Appendix D. Temporal and Spatial Variability in Selenium Load 153

data for WYs 1986 to 1997 show that 62 to 162 percent of the 

San Joaquin River selenium load is discharged above or at the 

Merced River inflow to the river, which would include loads 

from both slough and river sources (the San Joaquin River 

is the only outlet from the San Joaquin Valley). The Merced 

River inflow to the San Joaquin River is about 60 miles above 

Vernalis. Between the Merced River confluence and Vernalis, 

the Tuolumne and Stanislaus Rivers flow into the San Joaquin 

River. About 68 to 87 percent of the San Joaquin River salt 

load is discharged above or at the Merced River inflow to 

the river. Figure D10 shows the percent of the selenium load 

from the Drainage Problem Area, combined Mud and Salt 

Sloughs, and Crows Landing/Patterson normalized to the selenium load at the San Joaquin River at Vernalis. Figure D11 

shows the percent of the salt load from the Drainage Problem 

Area, combined Mud and Salt Sloughs, and Crows Landing/

Patterson normalized to the salt load at the San Joaquin River 

at Vernalis. The pattern of behavior of non-conservative selenium is different from that of conservative salt. The selenium 

loads measured as the input to the system (primary drainage 

canals, Drainage Problem Area) are perpetually different from 

those measured as the outputs from the system (downstream 

in wetland sloughs or the San Joaquin River). Downstream 

selenium loads show both decreases (measured at Salt and 

Mud Sloughs) and increases (San Joaquin River at Crows 

Landing and Vernalis) (also see appendix B, tables B4 to B7). 

Table D1. Selenium loads from the Grassland Drainage Problem 

Area, Mud and Salt Sloughs, and the San Joaquin River at Crows 

Landing-Patterson as a percentage of selenium loads at the San 

Joaquin River at Vernalis.

Selenium 

(lbs/

year)

Grassland Drainage Problem 

Area/San Joaquin 

R. at 

Vernalis (%)

Mud and Salt 

Sloughs/San 

Joaquin R. at 

Vernalis (%)

San Joaquin R. at 

Crows LandingPatterson/San 

Joaquin R.

at Vernalis (%)

1986 65 46 72

1987 126 88 101

1988 120 96 110

1989 100 93 85

1990 99 103 82

1991 162 108 98

1992 143 82 86

1993 99 77 92

1994 109 102 94

1995 69 62 83

1996 88 83 94

1997 62 69 77

0

10,000

20,000

30,000

40,000

0

4

2

6

8

10

Se (μg/L)

0

400

800

1200

1600

0

50

100

150

200

Flow (ft3/s) Specific conductance (μS/cm) Se (lbs)

O N D J F M A M J J A S

Month

WY 1998

Month

WY 1998

Salt (mg/L) Salt (tons)

0

400

800

1200

0

4,000

8,000

12,000

16,000

O N D J F M A M J J A S

a b

e f

c d Figure D9. Daily variation 

of (a) flow; (b) selenium 

concentration; (c) specific 

conductance; (d) total 

dissolved solids; (e) selenium 

load; and (f) salt load for the 

San Joaquin River at Crows 

Landing during WY 1998. 
154 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

In the absence of the San Luis Drain extension to the BayDelta, which would provide a single source of selenium at a 

single discharge point, loads discharged from the San Joaquin 

River at Vernalis are not likely to equal loads discharged into 

the river from the drainage source area. 

As noted in appendix B, selenium is persistently 

discharged from the Grassland area to the San Joaquin River, 

but selenium loads are dependent on monitoring site location 

within the Grassland area (also see main text table 5; appendix 

B, tables B4 to B7; appendix A, figures A9 and A10). The 

upstream discharge represents managed components of 

flow and load. Data for WYs 1986 to 1998 generally can be 

related to physical variables that affect drainage conditions 

(for example, drought in 1987 through 1992; California Coast 

Range flooding in 1995; and Sierra Nevada flooding in winter 

1997–1998; also see appendix A, fig. A10). Ranges of yearly 

variation for WYs 1986 to 1997 for the Drainage Problem 

Area are: flow, 24,533 to 67,006 acre-ft; selenium concentration 52 to 80 μg/L; selenium load 5,083 to 10,959 lbs. Ranges 

of yearly variation are for Mud and Salt Sloughs are: flow, 

85,428 to 288,253 acre-ft; selenium concentration 10 to 16 

μg/L; selenium load 2,919 to 10,694 lbs. Combining the data 

for Mud and Salt sloughs dampens the variation seen in each 

slough when influenced by agricultural discharge. Ranges of 

yearly variation for the San Joaquin River at Crows Landing/

Patterson are: flow, 0.29 to 4.18 million acre-ft per year; 

selenium concentration 1 to 6.3 μg/L; and selenium load 3,064 

to 14,291 lbs per year. Ranges of yearly variation for the San 

Joaquin River at Vernalis are: flow, 0.66 to 6.77 million acre-ft 

per year; selenium concentration 0.6 to 3.0 μg/L; and selenium 

load 3,611 to 17,238 lbs per year. 

Except for WY 1990, selenium input loads (upstream 

drainage canals, Drainage Problem Area, appendix B, 

table B4) from 1986 to 1995 are higher than output loads 

(downstream of Mud and Salt Sloughs, appendix B, table 

B5). Comprehensive monitoring data are not available to 

adequately determine selenium loss (that amount of load 

unaccounted for) after transit through the Grasslands wetlands 

(estimated annual maximum potential attenuation of 50 

percent) (Presser and Piper, 1998).

Loads farther downstream in the San Joaquin River at 

Crows Landing/Patterson (table 5; appendix B, Table B6) 

and Vernalis (table 5; appendix B, table B7) show increases 

over loads measured at Mud and Salt Sloughs, and in some 

cases, over loads measured furthest upstream (Drainage 

Problem Area). The increases may be due to other sources of 

selenium entering the San Joaquin River or errors introduced 

through limitations of the data as noted above. During WYs 

1986 to 1998, the loads in the San Joaquin River at Crows 

Landing/Patterson range from 3,064 to 15,501 lbs selenium 

with the maximum occurring in WY 1998 (appendix B, table 

B6). Selenium loads for the San Joaquin River at Vernalis from 

WYs 1986 to 1997 range from 3,558 to 17,238 lbs, with the 

Table D2. Salt loads (Total Dissolved Solids) from the Grassland 

Drainage Problem Area, Mud and Salt Sloughs, and the San 

Joaquin River at Crows Landing-Patterson as a percentage of salt 

loads at the San Joaquin River at Vernalis.

Salt 

(tons/

year)

Grassland Drainage 

Problem Area/San 

Joaquin R. at 

Vernalis (%)

Mud and Salt 

Sloughs/San 

Joaquin R. at 

Vernalis (%)

San Joaquin R. 

at Crows Landing-Patterson/

San Joaquin R.

at Vernalis (%)

1986 17 17 78

1987 27 27 79

1988 28 28 86

1989 28 28 75

1990 25 25 79

1991 27 27 87

1992 24 24 85

1993 21 21 78

1994 24 24 84

1995 17 17 87

1996 17 17 68

1997 10 10 74 Selenium load (%) (% at various locations/Vernalis)

Year

Drainage Problem Area

Mud and Salt Sloughs

Crows Landing – Patterson

0

50

100

150

86 87 88 89 90 91 92 93 94 95 96 97 98a 98b

Figure D10. Percent selenium load 

(normalized to the selenium load at the 

San Joaquin River at Vernalis) for the 

Drainage Problem Area (DPA); combined 

Mud and Salt Sloughs (MS+SS); and the 

San Joaquin River at Crows LandingPatterson (CL-PATT) for WY 1986 through 

WY 1997.
Appendix D. Temporal and Spatial Variability in Selenium Load 155

two highest values occurring in 1986 and 1995 (appendix B, 

table B7). Two different load values were calculated for the San 

Joaquin River at Crows Landing for WY 1998 (15,501 lbs and 

13,445 lbs) depending on sets of flow data. For WY 1998 for 

the San Joaquin River at Vernalis, the reported value is 15,810 

lbs per year which is less than or similar to the value measured 

for the San Joaquin River at Crows Landing. A State limit for 

drainage of 8,000 lbs selenium from the Grassland Area was 

enacted in 1996. 

Prediction of Short-Term Selenium Reservoirs

Data from WYs 1986 to 1994 from the Grassland area (or 

generically, the drainage source area) are given as an example 

of a managed agricultural drainage discharge system (Central 

Valley Board, 1996a, b, 1998d, e, f, g, h; Grassland Area 

Farmers, 1998b). Measurements for the drainage problem area 

are referenced to agricultural drainage canals for WYs 1986 to 

1996 and site B (San Luis Drain discharge into Mud Slough) 

for WYs 1997 and 1998. Figures D12 through D14 show, 

using data from WYs 1986 to 1997, general relations among 

annualized amounts of:

irrigation water applied to the drainage source area; 

flow generated from the drainage source area;

•

•

Salt load (%)

(% at various locations/Vernalis)

Year

0

20

40

60

80

86 87 88 89 90 91 92 93 94 95 96 97

Drainage Problem Area

Mud and Salt Sloughs

Crows Landing – Patterson

Figure D11. Percent salt load (normalized 

to the salt load at the San Joaquin River at 

Vernalis) for Drainage Problem Area (DPA); 

combined Mud and Salt Sloughs (MS+SS); 

and the San Joaquin River at Crows 

Landing-Patterson (CL-PATT) for WY 1986 

through WY 1997.

80,000

60,000

40,000

20,000

0

Discharge (acre-ft)

180,000 220,000 260,000 300,000 340,000

Total water (acre-ft)

Figure D12. Relation between total water applied and 

drainage discharge for the Drainage Problem Area 

(DPA) during WY 1986 through WY 1997. 

3,200

2,400

1600

800

Selenium

Selenium

TDS TDS

0

80

60

40

20

0 0

4,000

8,000

12,000

TDS (mg/L)

Se (μg/L)

Se (lbs)

180,000 220,000 260,000 300,000 340,000 180,000 220,000 260,000 300,000 340,000

Total water (acre-ft)

240,000

160,000

80,000

0

TDS (tons)

Total water (acre-ft)

a b

Figure D13. Relation among (a) total water applied, selenium concentration, and total dissolved solids 

concentration; (b) total water applied, selenium load, and salt load for the Drainage Problem Area (DPA) 

during WY 1986 through WY 1997. 
156 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

concentration of selenium in the generated discharge; 

and

loads of salt and selenium generated from the drainage 

source area. 

This series of figures illustrates some of the variables that 

affect load generation, but do not address the comprehensive 

processes controlling the distribution and transport of selenium and salt. Based on annualized data, figure D12 shows 

that as total water (applied irrigation water plus precipitation) 

increases, flow from the drainage source area increases. Figure 

D13 shows that as total applied water increases, selenium 

and salt concentrations in the discharge decrease. Figure D13 

shows that as total applied water increases, selenium and salt 

loads from the drainage source area increase. Figure D14 

shows that as flow from the drainage source area increases, 

selenium and salt concentrations decreases. Figure D14 shows 

that as flow from the drainage source area increases, selenium 

load increases. 

However, based on monthly and daily data these annual 

relations change. Figures D15 and D16 show the relation 

among flow, concentration, and load using daily measurements 

for WYs 1997 and 1998 at the San Luis Drain discharge to 

Mud Slough (site B) (USBR and others, 1998, and ongoing). In 

WY 1997, selenium load and concentration increase with flow. 

In WY 1998 however, concentration and load decrease at flows 

greater than about 100 ft3

/s, thus showing some drainage relief 

through dilution at the higher flows during storms in February 

1998 (an El Nino year). [Note: These data have been generalized in the main text (fig. 6) to help denote the characteristics 

of source water in comparison to receiving water (also see 

discussion in main text)]. 

Figures D17 to D21 are a series of graphs that depict the 

relation between load, concentration, applied water, and flow 

for the San Luis Drain (site B) on a monthly basis. Figures D17 

and D18 summarize monthly averages of flow, selenium load, 

and selenium concentration along with amounts of applied 

water (irrigation and precipitation) for WYs 1997 and 1998. 

•

•

3,200

2,400

1,600

800

TDS

0

80

60

40

20

0

TDS (mg/L)

Se (μg/L)

Se (lbs)

20,000 40,000 60,000 80,000

Discharge (acre-ft)

Selenium

Selenium

TDS

0

4,000

8,000

12,000

20,000 40,000 60,000 80,000

240,000

160,000

80,000

0

TDS (tons)

Discharge (acre-ft)

a b

Figure D14. Relation among (a) drain discharge, selenium concentration, and total dissolved solids 

concentration; (b) drain discharge, selenium load, and salt load for the Drainage Problem Area 

(DPA) during WY 1986 through WY 1997. 

0

20

40

60

80

100

120

140

10 30 50 70 90 110 130

Flow (ft3

/s)

lbs

μg/L

Se (μg/L or lbs)

Se (μg/L or lbs)

0

20

40

60

80

100

120

140

10 30 50 70 90 110 130

Flow (ft3

/s)

lbs

μg/L

Figure D15. Relation among flow, selenium concentration, and 

selenium load on a daily basis at site B (San Luis Drain outflow to 

Mud Slough) for WY 1997.

Figure D16. Relation among flow, selenium concentration, and 

selenium load on a daily basis at site B (San Luis Drain outflow to 

Mud Slough) for WY 1998.
Appendix D. Temporal and Spatial Variability in Selenium Load 157

10,000

0

20,000

30,000

40,000

50,000

10,000

0

20,000

30,000

40,000

50,000

Discharge (acre-ft)

Discharge (acre-ft)

0

20

40

60

80

100

120

Se (μg/L)

O D F A J A

0

400

800

1200

1600

2,000

Se (lbs)

Month

O D F A J A

Month

Discharge Applied water Selenium or salt

a b

10,000

0

20,000

30,000

40,000

50,000

10,000

0

20,000

30,000

40,000

50,000

0

20

40

60

80

100

120

Se (μg/L)

0

400

800

1200

1600

2,000

Se (lbs)

a b

Discharge (acre-ft)

Discharge (acre-ft)

O D F A J A

Month

O D F A J A

Month

Figure D17. Relation among 

drainage discharge, 

applied water (irrigation/

precipitation combined), and 

(a) selenium concentration; 

or (b) selenium load on a 

monthly basis at site B (San 

Luis Drain outflow to Mud 

Slough) during WY 1997. 

Figure D18. Relation among 

drainage discharge, applied 

water (irrigation/precipitation 

combined), and (a) selenium 

concentration; or (b) 

selenium load on a monthly 

basis at site B (San Luis 

Drain outflow to Mud Slough) 

during WY 1998. 

10,000

0

20,000

30,000

40,000

50,000

0

800

1600

2,400

3,200

Salt (mg/L)

0

10,000

20,000

30,000

40,000

50,000

0

10,000

20,000

30,000

Salt (tons)

Discharge (acre-ft)

Discharge (acre-ft)

O D F A J A

Month

O D F A J A

Month

a b

Figure D19. Relation among 

drainage discharge, applied 

water (irrigation/precipitation 

combined), and (a) selenium 

concentration; or (b) 

selenium load on a monthly 

basis at site B (San Luis 

Drain outflow to Mud Slough) 

for base average WY 1986 

through WY 1994.

Figure D20. Relation among 

drainage discharge, 

applied water (irrigation/

precipitation combined), and 

(a) salt concentration; or (b) 

salt load on a monthly basis 

at site B (San Luis Drain 

outflow to Mud Slough) 

during WY 1997. 

10,000

0

20,000

30,000

40,000

50,000

10,000

0

20,000

30,000

40,000

50,000

0

20

40

60

80

100

120

Se (μg/L, average)

0

400

800

1200

1600

2,000

Se (lbs, average)

Discharge (acre-ft)

Discharge (acre-ft)

O D F A J A

Month

O D F A J A

Month

a b

10,000

0

20,000

30,000

40,000

50,000

0

800

1600

2,400

3,200

Salt (mg/L)

0

10,000

20,000

30,000

40,000

50,000

0

10,000

20,000

30,000

Salt (tons)

Discharge (acre-ft)

Discharge (acre-ft)

O D F A J A

Month

O D F A J A

Month

a b

Figure D21. Relation among 

drainage discharge, applied 

water (irrigation/precipitation 

combined), and (a) salt 

concentration; or (b) salt load 

on a monthly basis at site B 

(San Luis Drain outflow to 

Mud Slough) during WY 1998. 
158 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Figure D19 shows monthly averages for WYs 1986 through 

1994 (the base year average used for generating Grassland 

Bypass Channel Project load targets, see appendix B, figure 

B1) for the same parameters. For comparison, figures D20 

and D21 summarize salt load and salt concentrations for the 

San Luis Drain (site B) in a similar series of graphs to that for 

selenium load in WYs 1997 and 1998. Patterns for the San 

Luis Drain discharge are similar through the series of graphs, 

showing peak selenium loads and concentrations during the 

months of March or April. Maximum application of water 

occurs in June, July, and August. Winter rainfall peaks can be 

seen especially in WY 1998 during February. 
Appendix E. Sediment Quantity and Quality Tables 159

Appendix E. Sediment Quantity and Quality Tables

Table E1. Quantity of sediment (bed and suspended), selenium concentrations, and selenium loads in bed sediment of the original San 

Luis Drain.

San Luis Drain sediment 

survey (segment and 

date) 

Deposition (tons/

year, dry 

weight)

Volume

(cubic yards, 

dry weight)

Selenium 

load

(lbs) 

Selenium

range/

average

(μg/g, dry 

weight)

Suspended

sediment

(average 

input) 

(mg/L) 

Suspended

sediment

(average 

output) 

(mg/L)

Reference

28-mile segment, 1984 − 80,583 − − − − USBR, 1986

85-mile segment, 

compilation of five 

surveys since August, 

1984

− 211,000 5,280 5−190/84 − − USBR, 1986

Compilation of five 

surveys, 1984-1993

− − − 1.4−210/55 − − Presser and others, 1996

28-mile segment, 1987

28-mile segment, 1997

28-mile segment, 1998

28-mile segment, 1999

28-mile segment, 2000

28-mile segment, 2001

28-mile segment, 2002

− 58,094

60,594

82,406

88,621 

114,368 

135,809 

158,489

− − − − USBR and others, 1998 

and ongoing 

Segments 1 and 10; 

February and May, 

1994

− − − 2.4-94/39 Presser and others, 1996; 

Presser and Piper, 

1998

Segments 1, 10, 17, 24; 

August, 1994

− − − 3.2−110/43 − − Presser and others, 1996; 

Presser and Piper, 

1998

Segments 1/2, 10/11, 

15/16, 27/28; September, 1994

− − − 11−94/44 − − Presser and others, 1996; 

Presser and Piper, 

1998

28-mile segment, 1995 − 55,788 4,500a − − − Presser and Piper, 1998

85-mile segment, 1995 − 177,900 14,400a − − − Presser and Piper, 1998

28-mile segment, 1997 − 60,593 − 2.9−100/30 

(whole core 

average except 

0.1 value)

− − USBR and others, 1998 

and ongoing

Estimated from suspended solids, wateryear 1997465 308 (1.8 

g/cm3)

213 (2.6 

g/cm3)

− − 102 28 USBR and others, 1998 

and ongoing

a

Calculated using an average selenium concentration in bed sediment of 44 μg/g dry weight (see 1994 data above).
160 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Location, date, 

and reference

Bed sediment

 (μg/g)

Suspended 

sediment (μg/g)

Plankton

(μg/g)

Salt Slough near highway 165 (Department of Fish and Game)

1987 0.31−1.3 1.4 −

1988 1.1−1.4 1.2−2.6 0.17−4.2

1989 1.5 2.0 5.0

Salt Slough (USFWS; USBR; USBR and others)

1992–1993 0.2−0.45 − −

1993−September, 

1995

0.2−1.3 − −

Water-year 1997 0.12−0.94 − −

San Joaquin River at Lander Avenue (upstream of discharge) (Department of Fish and Game)

1987 0.01 0.98 −

1988 0.04−<0.18 1.0−1.8 <0.08−0.16

1989 <0.18 2.0 0.23

San Joaquin River at or below Merced River (Department of Fish 

and Game)

1987 0.19−0.75 1.7 −

1988 <0.18−0.56 1.3−2.2 0.33−2.0

1989 0.18 1.9 2.5

San Joaquin River at Vernalis (Airport Blvd.; Maze Blvd; all below 

Stanislaus River) (Department of Fish and Game)

1987 0.25−1.2 1.2 −

1988 <0.18−5.2 0.91−2.4 0.11−2.1

1989 − 1.4 1.2

a

The San Luis Drain was not in use (inactive) from July 1,1986 to September 23, 1996. 

bData from 2002 through 2003 indicate selenium concentrations in bed 

sediment (0-3 cm) of 5 to 8.5 μg/g dry weight in a seasonal backwater (site 

I2) of the Grassland Bypass Channel Project (USBR and others, 1998 and 

ongoing).

Location, date, 

and reference

Bed sediment

 (μg/g)

Suspended 

sediment (μg/g)

Plankton

(μg/g)

Agatha Canal (Department of Fish and Game)

1988 1.0 1.4 3.8

Camp 13 Slough (Department of Fish and Game)

1987 0.79 − −

1988 0.71−.4 1.6−2.6 0.54−3.6

1989 0.89 3.2 3.2

East Big Lake impoundment (USFWS)

1992−1993 1.0−1.8 − −

Mud Slough , 200m downstream of San Luis Drain (inactive)a (Department of Fish and Game)

1987 0.32−1.3 2.1 −

1988 0.31−1.8 1.2−6.7 0.19−3.4

1989 1.1 2.4 3.8

Mud Slough, 600 yards upstream of San Luis Drain (SLD) discharge; 

immediately downstream (120 m) of SLD (inactive) a; 6.6 miles downstream of SLD (inactive) a (USFWS)

1992−1993 

(average of all 

sites)

0.15−0.75 − −

Mud Slough upstream of San Luis Drain discharge (USBR)

1993−September, 1995

<0.1−0.3 − −

Water-year 1997 <0.10−0.44 − −

Mud Slough immediately downstream of San Luis Drain (USBR; 

Department of Fish and Game)

1993−-September, 1995 

(inactive)a 

<0.1−0.4 − −

Water-year 1997 <0.10−0.76 −

Mud Slough 6.6 miles downstream of San Luis Drain (Department of 

Fish and Game; USBR and others)

1993−September, 1996 

(inactive)a

<0.1−0.7 − −

Water-year 1997 0.70−1.9 − −

Mud Slough 6.6 miles downstream of San Luis Drain (Department of 

Fish and Game; USBR and others)

1993−1995 0.3−0.6 − −

March, 1997 0.4−1.5 − −

Table E2. Selenium in sediment (bed and suspended) and plankton in natural channels.

[All values are dry weight. Natural channels are subjected to intermittent agricultural drainage discharge from the Grassland Drainage Problem Area through: 

(a) the Agatha Canal and Camp 13 Slough from the 1950s to September 1996; and (b) the San Luis Drain from October 1996 and continuing. Data sources: 

Department of Fish and Game = White and others, 1987, 1988, 1989; Urquhart and Regalado, 1991; USFWS = Henderson and others, 1995; USBR = 1995; 

USBR and others, 1998 and ongoing.]
Appendix F. Supplemental Spreadsheets 161

Tables

Table F1. Forecasts of monthly composite freshwater endmember concentrations of selenium assuming that all 

San Joaquin River inflow enters the Bay-Delta, all freshwater exports are from the Sacramento River, and

a selenium concentration of 2 μg/L is maintained in the San Joaquin River............................................................................162

Table F2. Forecasts of monthly composite freshwater endmember concentrations of selenium assuming that all 

San Joaquin River inflow enters the Bay-Delta, all freshwater exports are from the Sacramento River, and 

a selenium concentration of 1 μg/L is maintained in the San Joaquin River............................................................................165

Table F3. Forecasts of particulate selenium concentration for a wet year in a high flow season under load scenarios

for conveyance of agricultural drainage either through a San Luis Drain extension or the San Joaquin River................168

Table F4. Forecasts of particulate selenium concentration for a wet year in a low flow season under load scenarios

for conveyance of agricultural drainage either through a San Luis Drain extension or the San Joaquin River. ..............169

Table F5. Forecasts of particulate selenium concentration for a critically dry year in a low flow season under load 

scenarios for conveyance of agricultural drainage either through a San Luis Drain extension or the 

San Joaquin River...............................................................................................................................................................................170

Table F6. Bioaccumulation of selenium by a generic bivalve (ingestion rate, IR=0.25 g food/g tissue/day; efflux rate, 

ke=0.03/day) for a wet year in a high flow season under various load scenarios, partitioning coefficients 

(Kd=1,000; 3,000; 10,000), particulate selenium concentrations, and assimilation efficiencies (AE1=0.35; 

AE2 = 0.55; AE3 =0.63; AE4=0.8)........................................................................................................................................................171

Table F7. Bioaccumulation of selenium by a generic bivalve (ingestion rate, IR=0.25g food/g tissue/day; efflux rate, 

ke=0.03/day) for a wet year in a low flow season under various load scenarios, partitioning coefficients 

(Kd=1,000; 3,000; 10,000), particulate selenium concentrations, and assimilation efficiencies (AE1=0.35; 

AE2 = 0.55; AE3 =0.63; AE4=0.8)........................................................................................................................................................172

Table F8. Bioaccumulation of selenium by a generic bivalve (ingestion rate, IR=0.25 g food/g tissue/day; efflux rate, 

ke=0.03/day) for a critically dry year in a low flow season under various load scenarios, partitioning coefficients 

(Kd=1,000; 3,000; 10,000), particulate selenium concentrations, and assimilation efficiencies (AE1=0.35; 

AE2 = 0.55; AE3 =0.63; AE4=0.8)........................................................................................................................................................173

Table F9. Bioaccumulation of selenium by a generic bivalve (ingestion rate, IR=0.25 g food/g tissue/day; efflux rate, 

ke=0.03/day) for a targeted San Joaquin River load scenario (approximately 7,000 lbs selenium annually or 

3,400 or 3,590 lbs selenium in six months depending on flow season) for a critically dry year in a low flow 

season, a wet year in a low flow season, and a wet year in a high flow season under various partitioning 

coefficients (Kd=1,000; 3,000; 10,000), particulate selenium concentrations, and assimilation efficiencies 

(AE1= 0.35; AE2= 0.55; AE3= 0.63; AE4 =0.8) ...................................................................................................................................174

Appendix F. Supplemental Spreadsheets
162 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table F1. Forecasts of monthly composite freshwater endmember concentrations of selenium assuming that all San Joaquin River 

inflow enters the Bay-Delta, all freshwater exports are from the Sacramento River, and a selenium concentration of 2 μg/L is 

maintained in the San Joaquin River.

[A total of 36,848 lbs selenium is released annually. Flow data are from 1997. This table is a representation of a spreadsheet.]

Restoration

scenario

Volume

(average

ft3

/s)

Volume

(million 

acre-ft)

Volume

(billion 

liters)

Selenium

Concentration

(μg/L)

Load 

(billion 

μg)

Load

(lbs per six 

months)

Freshwater 

endmember

(μg/L)

Carquinez 

Strait (17.5 psu) 

(μg/L)

January

Total outflow index 256,565

Sacramento River 224,096 13.31 16,412.84 0.04 657 1,448

San Joaquin River 32,469 1.93 2,378.04 2 4,756 10,492

San Luis Drain 0 0.00 0.00 62.5 0 0

Refineries – 0.00 1.03 50 51 113

Total 12,054 0.29 0.15

February

Total outflow index 119,090

Sacramento River 86,950 5.16 6,368.24 0.04 255 562

San Joaquin River 32,140 1.91 2,353.94 2 4,708 10,386

San Luis Drain 0 0.00 0.00 62.5 0 0

Refineries – 0.00 1.03 50 51 113

Total 11,061 0.57 0.29

March

Total outflow index 33,831

Sacramento River 20,944 1.24 1,533.94 0.04 61 135

San Joaquin River 12,887 0.77 943.85 2 1,888 4,164

San Luis Drain 0 0.00 0.00 62.5 0 0

Refineries – 0.00 1.03 50 51 113

Total 4,413 0.81 0.40

April

Total outflow index 13,734

Sacramento River 9,811 0.58 718.56 0.04 29 63

San Joaquin River 3,923 0.23 287.32 2 575 1,268

San Luis Drain 0 0.00 0.00 62.5 0 0

Refineries – 0.00 1.03 50 51 113

Total 1,444 0.65 0.33

May

Total outflow index 12,261

Sacramento River 7,210 0.43 528.06 0.04 21 47

San Joaquin River 5,051 0.30 369.94 2 740 1,632

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 1,792 0.90 0.45
Appendix F. Supplemental Spreadsheets 163

Table F1. Forecasts of monthly composite freshwater endmember concentrations of selenium assuming that all San Joaquin River 

inflow enters the Bay-Delta, all freshwater exports are from the Sacramento River, and a selenium concentration of 2 μg/L is 

maintained in the San Joaquin River—Continued.

[A total of 36,848 lbs selenium is released annually. Flow data are from 1997. This table is a representation of a spreadsheet.]

Restoration

scenario

Volume

(average

ft3

/s)

Volume

(million 

acre-ft)

Volume

(billion 

liters)

Selenium

Concentration

(μg/L)

Load 

(billion 

μg)

Load

(lbs per six 

months)

Freshwater 

endmember

(μg/L)

Carquinez 

Strait (17.5 psu) 

(μg/L)

June

Total outflow index 8,762

Sacramento River 5,550 0.33 406.48 0.04 16 36

San Joaquin River 3,212 0.19 235.25 2 470 1,038

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 1,187 0.84 0.42

July

Total outflow index 9,350

Sacramento River 7,326 0.44 536.56 0.04 21 47

San Joaquin River 2,024 0.12 148.24 2 296 654

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 815 0.54 0.27

August

Total outflow index 9,031

Sacramento River 7,378 0.44 540.37 0.04 22 48

San Joaquin River 1,653 0.10 121.07 2 242 534

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 695 0.48 0.24

September

Total outflow index 4,555

Sacramento River 2,633 0.16 192.84 0.04 8 17

San Joaquin River 1,922 0.11 140.77 2 282 621

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 751 1.02 0.51

October

Total outflow index 4,571

Sacramento River 2,237 0.13 163.84 0.04 7 14

San Joaquin River 2,334 0.14 170.94 2 342 754

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 882 1.19 0.60
164 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table F1. Forecasts of monthly composite freshwater endmember concentrations of selenium assuming that all San Joaquin River 

inflow enters the Bay-Delta, all freshwater exports are from the Sacramento River, and a selenium concentration of 2 μg/L is 

maintained in the San Joaquin River—Continued.

[A total of 36,848 lbs selenium is released annually. Flow data are from 1997. This table is a representation of a spreadsheet.]

Restoration

scenario

Volume

(average

ft3

/s)

Volume

(million 

acre-ft)

Volume

(billion 

liters)

Selenium

Concentration

(μg/L)

Load 

(billion 

μg)

Load

(lbs per six 

months)

Freshwater 

endmember

(μg/L)

Carquinez 

Strait (17.5 psu) 

(μg/L)

November

Total outflow index 6,270

Sacramento River 4,095 0.24 299.92 0.04 12 26

San Joaquin River 2,175 0.13 159.30 2 319 703

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – 0.00 1.03 50 51 113

Total 843 0.83 0.41

December

Total outflow index 18,914

Sacramento River 16,780 1.00 1,228.97 0.04 49 108

San Joaquin River 2,134 0.13 156.29 2 313 690

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – 0.00 1.03 50 51 113

Total 911 0.30 0.15

Total Selenium Exported from San Joaquin River (lbs) 36,848
Appendix F. Supplemental Spreadsheets 165

Table F2. Forecasts of monthly composite freshwater endmember concentrations of selenium assuming that all San Joaquin River 

inflow enters the Bay-Delta, all freshwater exports are from the Sacramento River, and a selenium concentration of 1 μg/L is 

maintained in the San Joaquin River.

[A total of 20,380 lbs selenium is released annually. Flow data are from 1997. This table is a representation of a spreadsheet.]

Restoration

scenario

Volume

(average 

ft3

/s)

Volume

(million 

acre-ft)

Volume

(billion 

liters)

Selenium

Concentration

(μg/L)

Load 

(billion 

μg)

Load

(lbs per six 

months)

Freshwater 

endmember

(μg/L)

Carquinez Strait

(17.5 psu)

(μg/L)

January

Total outflow index 256,565

Sacramento River 224,096 13.31 16,412.84 0.04 657 1,448

San Joaquin River 32,469 1.93 2,378.04 1 2,378 5,246

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113 0.16 0.08

Total 6,808

February

Total outflow index 119,090

Sacramento River 86,950 5.16 6,368.24 0.04 255 562

San Joaquin River 32,140 1.91 2,353.94 1 2,354 5,193

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 5,868 0.30 0.15

March

Total outflow index 33,831

Sacramento River 20,944 1.24 1,533.94 0.04 61 135

San Joaquin River 12,887 0.77 943.85 1 944 2,082

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 2,331 0.43 0.21

April

Total outflow index 13,734

Sacramento River 9,811 0.58 718.56 0.04 29 63

San Joaquin River 3,923 0.23 287.32 1 287 634

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 811 0.36 0.18

May

Total outflow index 12,261

Sacramento River 7,210 0.43 528.06 0.04 21 47

San Joaquin River 5,051 0.30 369.94 1 370 816

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 976 0.49 0.25
166 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table F2. Forecasts of monthly composite freshwater endmember concentrations of selenium assuming that all San Joaquin River 

inflow enters the Bay-Delta, all freshwater exports are from the Sacramento River, and a selenium concentration of 1 μg/L is 

maintained in the San Joaquin River—Continued.

[A total of 20,380 lbs selenium is released annually. Flow data are from 1997. This table is a representation of a spreadsheet.]

Restoration

scenario

Volume

(average 

ft3

/s)

Volume

(million 

acre-ft)

Volume

(billion 

liters)

Selenium

Concentration

(μg/L)

Load 

(billion 

μg)

Load

(lbs per six 

months)

Freshwater 

endmember

(μg/L)

Carquinez Strait

(17.5 psu)

(μg/L)

June

Total outflow index 8,762

Sacramento River 5,550 0.33 406.48 0.04 16 36

San Joaquin River 3,212 0.19 235.25 1 235 519

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 668 0.47 0.24

July

Total outflow index 9,350

Sacramento River 7,326 0.44 536.56 0.04 21 47

San Joaquin River 2,024 0.12 148.24 1 148 327

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 488 0.32 0.16

August

Total outflow index 9,031

Sacramento River 7,378 0.44 540.37 0.04 22 48

San Joaquin River 1,653 0.10 121.07 1 121 267

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 428 0.29 0.15

September

Total outflow index 4,555

Sacramento River 2,633 0.16 192.84 0.04 8 17

San Joaquin River 1,922 0.11 140.77 1 141 311

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 441 0.60 0.30

October

Total outflow index 4,571

Sacramento River 2,237 0.13 163.84 0.04 7 14

San Joaquin River 2,334 0.14 170.94 1 171 377

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 505 0.68 0.34
Appendix F. Supplemental Spreadsheets 167

Table F2. Forecasts of monthly composite freshwater endmember concentrations of selenium assuming that all San Joaquin River 

inflow enters the Bay-Delta, all freshwater exports are from the Sacramento River, and a selenium concentration of 1 μg/L is 

maintained in the San Joaquin River—Continued.

[A total of 20,380 lbs selenium is released annually. Flow data are from 1997. This table is a representation of a spreadsheet.]

Restoration

scenario

Volume

(average 

ft3

/s)

Volume

(million 

acre-ft)

Volume

(billion 

liters)

Selenium

Concentration

(μg/L)

Load 

(billion 

μg)

Load

(lbs per six 

months)

Freshwater 

endmember

(μg/L)

Carquinez Strait

(17.5 psu)

(μg/L)

November

Total outflow index 6,270

Sacramento River 4,095 0.24 299.92 0.04 12 26

San Joaquin River 2,175 0.13 159.30 1 159 351

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 491 0.48 0.24

December

Total outflow index 18,914

Sacramento River 16,780 1.00 1,228.97 0.04 49 108

San Joaquin River 2,134 0.13 156.29 1 156 345

San Luis Drain 0 0.00 0.00 0 0 0

Refineries – – 1.03 50 51 113

Total 567 0.19 0.09

Total Selenium Exported from San Joaquin River (lbs) 20,380
168 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Table F3. Forecasts of particulate selenium concentration for a wet year in a high flow season under load scenarios for conveyance of agricultural drainage either through a San Luis Drain extension or the San Joaquin River. [Inputs from the Sacramento River and oil refineries also are considered. Refinery cleanup is assumed in all scenarios. Scenarios using a San Luis Drain extension for conveyance assume a 2 million acre-ft inflow from the San Joaquin River reaches the Bay Delta. The targeted scenario using the San Joaquin River for conveyance assumes no San Luis Drain inflow and a 1.1 million acre ft inflow reaches the Bay- Delta. The restoration scenario assumes greater San Joaquin River inflows with the high flow season conveying 75% of the annual river flow to the Bay-Delta. This table is a representation of a spreadsheet.] Volume (million acre-ft) Selenium Load (lbs per six months) Source con- centration

(μg/L)

Dissolved concentration Particulate concentration

Kd=1,000 Kd= 3,000 Kd=10,000

Endmember

(μg/L)

Carquinez Strait

(μg/L)

Endmember

(μg/L)

Carquinez 

Strait (μg/L)

Endmember

(μg/L)

Carquinez 

Strait (μg/L)

Endmember

(μg/L)

Carquinez 

Strait (μg/L)

Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; refinery cleanup.

Sacramento R. 17 1,850 0.04

San Joaquin R. 2 5,440 1

San Luis Drain 0.05 6,800 50

Refineries 0.005 680 50

0.28 0.14 0.280 0.140 0.840 0.420 2.800 1.400

Load scenario: San Luis Drain extension at 300 ft3/s and 62.5 μg/L for a load of 18,700 lbs per six months; refinery cleanup.

Sacramento R. 17 1,850 0.04

San Joaquin R. 2 5,440 1

San Luis Drain 0.11 18,700 62.5

Refineries 0.005 680 50

0.51 0.26 0.510 0.260 1.530 0.780 5.100 2.600

Load scenario: San Luis Drain extension at 300 ft3/s and 150 μg/L for a load of 44,880 lbs per six months; refinery cleanup.

Sacramento R. 17 1,850 0.04

San Joaquin R. 2 5,440 1

San Luis Drain 0.11 44,820 150

Refineries 0.005 680 50

1.02 0.51 1.020 0.510 3.060 1.530 10.200 5.100

Load scenario: San Luis Drain extension at 300 ft3/s and 300 μg/L for a load of 89,760 lbs per six months; refinery cleanup.

Sacramento R. 17 1,850 0.04

San Joaquin R. 2 5,440 1

San Luis Drain 0.11 89,760 300

Refineries 0.005 680 50

1.88 0.94 1.880 0.940 5.640 2.820 18.800 9.400

Load scenario: Targeted San Joaquin River load of 7,180 lbs annually (3,590 lbs per six months); refinery cleanup.

Sacramento R. 17 1,850 0.04

San Joaquin R. 1.1 3,590 1.2

San Luis Drain 0 0 0

Refineries 0.005 680 50

0.12 0.06 0.120 0.060 0.360 0.180 1.200 0.600

Load scenario: San Joaquin River Restoration (conveys 75% of San Joaquin River inflow); refinery cleanup.

Sacramento R. 17 1,850 0.04

San Joaquin R. 2.25 3,060 0.5

San Luis Drain 0 0 0

Refineries 0.005 680 50

0.11 0.05 0.110 0.050 0.330 0.150 1.100 0.500
Appendix F. Supplemental Spreadsheets 169 Table F4. Forecasts of particulate selenium concentration for a wet year in a low flow season under load scenarios for conveyance of agricultural drainage either through a San Luis Drain extension or the San Joaquin River. [Inputs from the Sacramento River and oil refineries also are considered. Refinery cleanup is assumed in all scenarios. Scenarios using a San Luis Drain extension for conveyance assume a 2 million acre-ft inflow from the San Joaquin River reaches the Bay Delta. The targeted scenario using the San Joaquin River for conveyance assumes no San Luis Drain inflow and a 1.1 million acre ft inflow reaches the Bay- Delta. The restoration scenario assumes greater San Joaquin River inflows with the low flow season conveying 25% of the annual river flow to the Bay-Delta. This table is a representation of a spreadsheet.] Volume (million acre-ft) Selenium Load (lbs per six months) Source con- centration (μg/L) Dissolved concentration Particulate concentration Kd=1,000 Kd= 3,000 Kd=10,000 Endmember (μg/L) Carquinez Strait (μg/L) Endmember (μg/L) Carquinez Strait (μg/L) Endmember (μg/L) Carquinez Strait (μg/L) Endmember (μg/L) Carquinez Strait (μg/L) Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; refinery cleanup. Sacramento R. 2.3 250 0.04 San Joaquin R. 0.001 3 2 San Luis Drain 0.05 6,800 50 Refineries 0.005 680 50 1.21 0.60 1.210 0.600 3.630 1.800 12.100 6.000 Load scenario: San Luis Drain extension at 300 ft3/s and 62.5 μg/L for a load of 18,700 lbs per six months; refinery cleanup. Sacramento R. 2.3 250 0.04 San Joaquin R. 0.001 5 2 San Luis Drain 0.11 18,700 62.5 Refineries 0.005 680 50 2.99 1.49 2.990 1.490 8.970 4.470 29.900 14.900 Load scenario: San Luis Drain extension at 300 ft3/s and 150 μg/L for a load of 44,880 lbs per six months; refinery cleanup. Sacramento R. 2.3 250 0.04 San Joaquin R. 0.001 5 2 San Luis Drain 0.11 44,820 150 Refineries 0.005 680 50 6.97 3.49 6.970 3.490 20.910 10.470 69.700 34.900 Load scenario: San Luis Drain extension at 300 ft3/s and 300 μg/L for a load of 89,760 lbs per six months; refinery cleanup. Sacramento R. 2.3 250 0.04 San Joaquin R. 0.001 5 2 San Luis Drain 0.11 89,760 300 Refineries 0.005 680 50 13.8 6.9 13.800 6.900 41.400 20.700 138.000 69.000 Load scenario: Targeted San Joaquin River load of 6,800 lbs annually (3,400 lbs per six months); refinery cleanup. Sacramento R. 2.3 250 0.04 San Joaquin R. 0.5 3,400 2.5 San Luis Drain 0 0 0 Refineries 0.005 680 50 0.57 0.28 0.570 0.280 1.710 0.840 5.700 2.800 Load scenario: San Joaquin River Restoration (conveys 75% of San Joaquin River inflow); refinery cleanup Sacramento R. 2.3 250 0.04 San Joaquin R. 0.75 1,020 0.5 San Luis Drain 0 0 0

Refineries 0.005 680 50

0.23 0.12 0.230 0.120 0.690 0.360 2.300 1.200
170 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension Table F5. Forecasts of particulate selenium concentration for a critically dry year in a low flow season under load scenarios for conveyance of agricultural drainage either through a San Luis Drain extension or the San Joaquin River. [Inputs from the Sacramento River and oil refineries also are considered. Refinery cleanup is assumed in all scenarios. Scenarios using a San Luis Drain extension for conveyance assume a 2 million acre-ft inflow from the San Joaquin River reaches the Bay Delta. The targeted scenario using the San Joaquin River for conveyance assumes no San Luis Drain inflow and a 0.5 million acre ft inflow reaches the Bay- Delta. The restoration scenario assumes greater San Joaquin River inflows with the low flow season conveying 25% of the annual river flow to the Bay-Delta. This table is a representation of a spreadsheet.] Volume (million acre-ft) Selenium Load (lbs per six months) Source concen- tration

(μg/L)

Dissolved concentration Particulate concentration

Kd=1,000 Kd=3,000 Kd=10,000

Endmember

(μg/L)

Carquinez 

Strait (μg/L)

Endmember

(μg/L)

Carquinez 

Strait (μg/L)

Endmember

(μg/L)

Carquinez 

Strait (μg/L)

Endmember

(μg/L)

Carquinez 

Strait (μg/L)

Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; refinery cleanup.

 Sacramento R. 1.3 141 0.04

San Joaquin R. 0.0005 3 2

San Luis Drain 0.05 6,800 50

Refineries 0.005 680 50

2.07 1.03 2.070 1.030 6.210 3.090 20.700 10.300

Load scenario: San Luis Drain extension at 300 ft3/s and 62.5 μg/L for a load of 18,700 lbs per six months; refinery cleanup.

Sacramento R. 1.3 141 0.04

San Joaquin R. 0.0005 3 2

San Luis Drain 0.11 18,700 62.5

Refineries 0.005 680 50

5.07 2.54 5.070 2.540 15.210 7.620 50.700 25.400

Load scenario: San Luis Drain extension at 300 ft3/s and 150 μg/L for a load of 44,880 lbs per six months; refinery cleanup.

Sacramento R. 1.3 141 0.04

San Joaquin R. 0.001 5 2

San Luis Drain 0.11 44,880 150

Refineries 0.005 680 50

11.87 5.93 11.870 5.930 35.610 17.790 118.700 59.300

Load scenario: San Luis Drain extension at 300 ft3/s and 300 μg/L for a load of 89,760 lbs per six months; refinery cleanup.

Sacramento R. 1.3 141 0.04

San Joaquin R. 0.0005 3 2

San Luis Drain 0.11 89,760 300

Refineries 0.005 680 50

23.53 11.76 23.530 11.760 70.590 35.280 235.300 117.600

Load scenario: Targeted San Joaquin River load of 6,800 lbs annually (3,400 lbs per six months); refinery cleanup.

Sacramento R. 2.3 250 0.04

San Joaquin R. 0.5 3,400 2.5

San Luis Drain 0 0 0

Refineries 0.005 680 50

0.86 0.43 0.860 0.430 2.580 1.290 8.600 4.300

Load scenario: San Joaquin River Restoration (conveys 25% of San Joaquin River inflow); refinery cleanup

Sacramento R. 1.6 174 0.04

San Joaquin R. 0.28 381 0.5

San Luis Drain 0 0 0

Refineries 0.005 680 50

0.24 0.12 0.240 0.120 0.720 0.360 2.400 1.200
Appendix F. Supplemental Spreadsheets 171

Table F6. Bioaccumulation of selenium by a generic bivalve (ingestion rate, IR=0.25 g food/g tissue/day; efflux 

rate, ke=0.03/day) for a wet year in a high flow season under various load scenarios, partitioning coefficients 

(Kd=1,000; 3,000; 10,000), particulate selenium concentrations, and assimilation efficiencies (AE1=0.35; 

AE2=0.55; AE3=0.63; AE4=0.8).

[This table is a representation of a spreadsheet.]

Selenium

Kd =1,000 Kd =3,000 Kd =10,000

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; 

refinery cleanup.

Particles 0.280 0.140 0.840 0.420 2.800 1.400

AE1 0.8 0.4

AE2 3.9 1.9

AE3 14.7 7.4

AE4 18.7 9.3

Load scenario: San Luis Drain extension at 300 ft3

/s and 62.5 μg/L for a load of 18,700 lbs per six months;

 refinery cleanup.

Particles 0.510 0.260 1.530 0.780 5.100 2.600

AE1 1.5 0.8

AE2 7.0 3.6

AE3 26.8 13.7

AE4 34.0 17.3

Load scenario: San Luis Drain extension at 300 ft3

/s and 150 μg/L for a load of 44,880 lbs per six months; 

refinery cleanup.

Particles 1.020 0.510 3.060 1.530 10.200 5.100

AE1 3.0 1.5

AE2 14.0 7.0

AE3 53.6 26.8

AE4 68.0 34.0

Load scenario: Prior to refinery cleanup: no San Luis Drain extension 

Particles 0.220 0.110 0.660 0.330 2.180 1.100

AE1 0.96 0.48

AE2 4.54 2.27

AE3 17.17 8.66

AE4 21.80 11.00
172 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table F7. Bioaccumulation of selenium by a generic bivalve (ingestion rate, IR=0.25g food/g tissue/day; efflux 

rate, ke=0.03/day) for a wet year in a low flow season under various load scenarios, partitioning coefficients 

(Kd=1,000; 3,000; 10,000), particulate selenium concentrations, and assimilation efficiencies (AE1=0.35; AE2=0.55; 

AE3=0.63; AE4=0.8). 

[This table is a representation of a spreadsheet.]

Selenium

Kd =1,000 Kd =3,000 Kd =10,000

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; refinery cleanup.

Particles 1.210 0.600 3.630 1.800 12.100 6.000

AE1 3.5 1.8

AE2 16.6 8.3

AE3 63.5 47.3

AE4 80.7 60.0

Load scenario: San Luis Drain extension at 300 ft3

/s and 62.5 μg/L for a load of 18,700 lbs per six months; refinery cleanup.

Particles 2.990 1.490 8.970 4.470 29.900 14.900

AE1 8.7 4.3

AE2 41.1 20.5

AE3 157.0 117.3

AE4 199.3 149.0

Load scenario: San Luis Drain extension at 300 ft3

/s and 150 μg/L for a load of 44,880 lbs per six months; refinery cleanup.

Particles 6.970 3.490 20.910 10.470 69.700 34.900

AE1 20.3 10.2

AE2 95.8 48.0

AE3 365.9 274.8

AE4 464.7 349.0

Load scenario: Prior to refinery cleanup: no San Luis Drain extension 

Particles 0.390 0.200 1.170 0.600 3.900 2.000

AE1 1.7 0.9

AE2 8.0 4.1

AE3 30.7 15.8

AE4 39.0 20.0
Appendix F. Supplemental Spreadsheets 173

Table F8. Bioaccumulation of selenium by a generic bivalve (ingestion rate, IR=0.25 g food/g tissue/day; efflux 

rate, ke=0.03/day) for a critically dry year in a low flow season under various load scenarios, partitioning 

coefficients (Kd=1,000; 3,000; 10,000), particulate selenium concentrations, and assimilation efficiencies 

(AE1=0.35; AE2=0.55; AE3=0.63; AE4=0.8).

[This table is a representation of a spreadsheet.]

Selenium

Kd =1,000 Kd =3,000 Kd =10,000

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Load scenario: San Luis Drain extension at 150 ft3/s and 50 μg/L for a load of 6,800 lbs per six months; refinery cleanup.

Particles 2.100 1.000 6.200 3.100 20.700 10.300

AE1 6.1 2.9

AE2 28.4 14.2

AE3 108.7 81.1

AE4 138.0 103.0

Load scenario: San Luis Drain extension at 300 ft3

/s and 62.5 μg/L for a load of 18,700 lbs per six months; refinery 

cleanup.

Particles 5.100 2.500 15.200 7.600 50.700 25.400

AE1 14.9 7.3

AE2 69.7 34.8

AE3 266.2 200.0

AE4 338.0 254.0

Load scenario: San Luis Drain extension at 300 ft3

/s and 150 μg/L for a load of 44,880 lbs per six months; refinery 

cleanup.

Particles 11.900 5.900 35.600 17.800 119.000 59.000

AE1 34.7 17.2

AE2 163.2 81.6

AE3 624.8 464.6

AE4 793.3 590.0

Load scenario: Prior to refinery cleanup: no San Luis Drain extension 

Particles 0.530 0.270 1.590 0.810 5.300 2.700

AE1 2.3 1.2

AE2 10.9 5.6

AE3 41.7 21.3

AE4 53.0 27.0
174 Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension

Table F9. Bioaccumulation of selenium by a generic bivalve (ingestion rate, IR=0.25 g food/g tissue/day; 

efflux rate, ke=0.03/day) for a targeted San Joaquin River load scenario (approximately 7,000 lbs selenium 

annually or 3,400 or 3,590 lbs selenium in six months depending on flow season) for a critically dry year in 

a low flow season, a wet year in a low flow season, and a wet year in a high flow season under various 

partitioning coefficients (Kd=1,000; 3,000; 10,000), particulate selenium concentrations, and assimilation 

efficiencies (AE1=0.35; AE2=0.55; AE3=0.63; AE4=0.8).

[This table is a representation of a spreadsheet.]

Selenium

Kd =1,000 Kd =3,000 Kd =10,000

Endmember

(μg/L)

Carquinez 

Strait (μg/L)

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Endmember

(μg/L)

Carquinez Strait 

(μg/L)

Critically dry year in a low flow season

Particles 0.860 0.430 2.580 1.290 8.600 4.300

AE1 2.5 1.3

AE2 11.8 5.9

AE3 45.2 33.9

AE4 57.3 43.0

Wet year in a low flow season

Particles 0.570 0.280 1.710 0.840 5.700 2.800

AE1 1.7 0.8

AE2 7.8 3.9

AE3 29.9 22.1

AE4 38.0 28.0

Wet year in a high flow season

Particles 0.120 0.060 0.360 0.180 1.200 0.600

AE1 0.4 0.2

AE2 1.7 0.8

AE3 6.3 4.7

AE4 8.0 6.0
Acknowledgments 175

Acknowledgments

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. We wish to thank Eugenia McNaughton, 

Gail Louis, Philip Woods, and Mike Boots of the U.S. Environmental Protection Agency (Region 9); John Kopchik of 

Contra Costa County; and Richard Denton of Contra County 

Water District for their support and encouragement throughout 

the development of our model. We wish to thank Keith Kirk, 

U.S. Geological Survey Regional Reports Specialist, for his 

guidance and electronic wizardry that contributed to the overall quality and design of our report. We wish to thank Mark 

Huebner for his concern for detail in all aspects of technical report preparation. We wish to thank David Jones for his 

expertise in illustrating and formatting our report. The longrange vision of T. John Conomos within the U.S. Geological 

Survey and the goals of the National Research Program of the 

Water Resources Discipline have made this report possible. 
176
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