Forecasting Selenium Discharges to the San Francisco Bay-Delta 

Estuary: Ecological Effects of A Proposed San Luis Drain Extension

Open-File Report 00-416 

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

By Samuel N. Luoma 

 Theresa S. Presser 

___________________________________________________________ 

U.S. GEOLOGICAL SURVEY 

Open-File Report 00-416 

Water Resources Division 

National Research Program 

This project has been funded in part by the United States Environmental Protection Agency 

Interagency Agreement DW-14-95534701-4 (Region 9, Water Division) and Joint Funding 

Agreements with Contra Costa County and Contra Costa Water District. The contents of this 

document do not necessarily reflect the views and policies of the U.S. Environmental Protection 

Agency, Contra Costa County, or Contra Costa Water District. 

Menlo Park, California 

2000 

 
U.S. DEPARTMENT OF THE INTERIOR 

BRUCE BABBITT, Secretary 

U.S. GEOLOGICAL SURVEY 

Charles G. Groat, Director

The use of firm, trade, and brand names in this report is for identification purposes only and does not 

constitute endorsement by the U.S. Geological Survey. 

_________________________________________________________________ 

For information write to: Copies of the report can be purchased from: 

Samuel N. Luoma U.S.Geological Survey 

Theresa S. Presser Information Services 

U.S. Geological Survey Box 25286 

345 Middlefield Road Federal Center

Menlo Park, CA 94025 Denver, CO 80225 

 303-202-4200 

ii
CONTENTS 

ABSTRACT 1 

INTRODUCTION 3 

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

Selenium Issues in the Bay-Delta.........................................................................................................9 

ISSUES ARE CHANGING 15 

APPROACH TO UNDERSTANDING CHANGING ISSUES 20 

SOURCES 22 

Inputs of Selenium from Agriculture in the Western San Joaquin Valley.........................................23 

The problem ....................................................................................................................................23 

Prediction of long-term reservoir: how sustainable is discharge? ..................................................24 

Selenium concentrations in source waters......................................................................................25 

Drainage management.....................................................................................................................27 

Forecasting loads of selenium: general consideratons....................................................................28 

How to determine load....................................................................................................................30 

Characteristics of agricultural subareas..........................................................................................32 

Development of forecasts................................................................................................................37

Forecasting selenium loadings using the sum of data from all subareas........................................38 

Forecasting selenium loadings using data from individual subareas..............................................39

Loading scenarios ...........................................................................................................................40 

Scenarios based on the capacity of an extension of the San Luis Drain.........................................42 

The San Joaquin River as a conveyance facility, a de facto drain..................................................43 

Summary .........................................................................................................................................44 

Inputs of Selenium from Oil Refineries .............................................................................................45 

Inputs of Selenium from the Sacramento River .................................................................................46

Summary.............................................................................................................................................47 

HYDRAULIC CONNECTIONS AND CONVEYANCE OF SELENIUM TO THE BAY-DELTA 47 

CONCENTRATIONS OF SELENIUM IN THE BAY-DELTA 49

Interpreting Effects of Source Water Se Loads on Receiving Water Se Concentrations...................49 

Existing Concentrations in the Bay-Delta ..........................................................................................51 

Regional baseline ............................................................................................................................51 

Concentrations observed in the Bay-Delta......................................................................................52 

iii
CHEMICAL FORMS OF SELENIUM (SPECIATION) 54 

PARTICULATE AND SEDIMENT-ASSOCIATED SELENIUM 55 

Processes Affecting Particulate Selenium..........................................................................................55 

Partitioning......................................................................................................................................55 

Transformation................................................................................................................................56 

Range of distribution coefficients (Kd’s)........................................................................................58 

Sources of Particulate Selenium in the Bay-Delta .............................................................................59

Particulate selenium in the San Joaquin River................................................................................59

Particulate selenium in the Delta ....................................................................................................61 

Particulate selenium in existing portion of the San Luis Drain ......................................................61 

Sedimentary selenium in Suisun Bay and San Pablo Bay ..............................................................62 

Suspended particulate selenium in Suisun Bay and San Pablo Bay ...............................................63 

Summary .........................................................................................................................................64 

BIOACCUMULATION OF SELENIUM BY INVERTEBRATES 64 

Processes ............................................................................................................................................64 

Selenium in Invertebrates from the Bay-Delta...................................................................................65 

Summary of Selenium in Invertebrates from the Bay-Delta ..............................................................68 

Modeling Selenium Bioaccumulation in the Bay-Delta: DynBaM....................................................69 

BIOACCUMULATION OF SELENIUM BY PREDATORS 71 

Dietary Exposure................................................................................................................................71 

Existing Selenium Concentrations in Tissues of Birds and Fish in the Bay-Delta ............................73 

EFFECTS OF SELENIUM ON WILDLIFE 76

Relating Selenium Concentrations in Food (Prey) to Effects in Predators........................................78 

Fish..................................................................................................................................................78 

Birds................................................................................................................................................78 

Relating Selenium Concentrations in Tissue to Effects in Predators.................................................79

Fish................................................................................................................................................. 79

Birds................................................................................................................................................81

Comparison to Selenium Hazard Index..............................................................................................83 

FORECASTS 85 

Forecasts of Composite Input Loads and Volumes to the Bay-Delta ................................................85 

Forecasts of Waterborne Selenium Concentrations ...........................................................................89

iv
Calculating composite selenium input (or freshwater endmember) concentrations .......................89

Comparing forecasted selenium concentrations to observed conditions prior to refinery cleanup 90 

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

concentrations .................................................................................................................................91 

Monthly waterborne selenium concentrations................................................................................94 

Summary of forecasts......................................................................................................................96 

Forecasts of Speciation and Transformation......................................................................................98 

Defining speciation, transformation, and bioavailability................................................................99 

Comparison to Bay-Delta conditions prior to refinery cleanup....................................................101 

Forecasts of Particulate Selenium Concentrations...........................................................................101 

Sediment quality guidelines..........................................................................................................101 

Particulate selenium concentrations (all concentrations are in μg Se/g dry weight, dw).............102 

Cumulative summary ....................................................................................................................104 

Other possible scenarios................................................................................................................106 

Forecasts of Bioaccumulation in Consumer Organisms ..................................................................107 

Calculating bioaccumulation in a generic bivalve (modeling) .....................................................107 

Comparing model predictions to Bay-Delta conditions prior to refinery cleanup........................109 

Bivalves as food for predators ......................................................................................................109 

Generic bivalve selenium concentrations (i.e., contamination of prey)........................................110 

Effects on predators based on selenium concentrations in food ...................................................113 

Forecast of Selenium Concentrations in Tissues of Predators.........................................................114 

Choice of predators.......................................................................................................................114 

Relation of selenium concentrations in bivalves to selenium concentrations in predators...........115 

Selenium concentrations in predators...........................................................................................116 

CONCLUSIONS 117 

Cumulative Impacts on the Bay-Delta .............................................................................................117 

Extent and Sustainability of Agricultural Discharge from the San Joaquin Valley.........................120 

Implications and Monitoring Needs.................................................................................................122 

ACKNOWLEDGMENTS 127 

REFERENCES 128 

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

concentrations .................................................................................................................................92 

v
APPENDICES 

APPENDIX A San Joaquin Valley Historic Planning and Geologic Inventory A1-25

APPENDIX B San Joaquin Valley Agricultural Drainage Projections B1-42 

APPENDIX C Agricultural Drainage Discharge to the San Joaquin River C1-20 

APPENDIX D Variability D1-26 

APPENDIX E Sediment Quality and Quantity Tables E1-3 

APPENDIX F Supplemental Spreadsheets F1-12 

FIGURES 

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

activities, receiving waters bodies, and biota at risk. 

2. Conceptual model describing linked factors that determine the effects of selenium on ecosystems. 

The sequence of relations links environmental concentrations to biological effects. The general 

term “bioaccumulation” can be applied to all of the biological levels of selenium transfer through 

the food web, but in this report we use the term explicitly in reference to particulate/invertebrate 

bioaccumulation. 

3. Map of the San Joaquin Valley and the adjacent Coast Ranges and Sierra Nevada. The five 

designated subareas for management of agricultural drainage are shown along with the major 

rivers, supply canals, the San Luis Drain, and Kesterson National Wildlife Refuge. The San 

Joaquin River flows north to the San Francisco Bay-Delta Estuary. Proposed management 

alternatives to sustain agriculture include draining selenium-laden salts into the San Joaquin River 

or a proposed extension of the San Luis Drain. See Figure 5 for details of hydrologic connections 

between the valley and the estuary. See Figure 4 for detailed map of the Bay-Delta and Figure 5 

for details of hydrologic connections between the valley and the estuary. Adapted from Presser and 

Piper, 1998. 

4. Map of the San Francisco Bay-Delta Estuary including locations of oil refineries (filled circles) in 

the North Bay. The North Bay includes Suisun Bay and San Pablo Bay. Adapted from Conomos 

et al., 1985. 

5. Hydrologic connections of the San Francisco Bay-Delta Estuary with the San Joaquin Valley. The 

only natural outlet from the valley is the San Joaquin River. An extension of the San Luis Drain 

would provide a constructed outlet for agricultural drainage from the San Joaquin Valley to the 

Bay-Delta. Filled circles show locations of five major oil refineries. Enlarged arrows are for 

emphasis and are not representational of flow. Not to scale. 

6. Selenium concentration in drainage (i.e., source waters) as a function of flow (i.e., water flux) and 

resultant selenium load. This schematic representation from current data depicts the effect of a 

large reservoir of selenium on subsurface drainage. 

7. Projected high and low range of annual selenium discharges from the five subareas of the western 

San Joaquin Valley using current available data. Discharges are given in kestersons (ksts), where 1 

kst equals 17,400 lbs. The kst unit is the cumulative total of 17,400 lbs Se, 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. 

8. Projected high range of daily selenium discharges from the five subareas shown as proportions of 

total discharge from the western San Joaquin Valley. 

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9. The balance between water diversions (e.g., pumping at Tracy and Clifton Court Forebay), total 

river inflow to the Bay-Delta, and the discharge of the San Joaquin River in a dry year (1994). 

10. The balance between water diversions (e.g., pumping at Tracy and Clifton Court Forebay), total 

river inflow to the Bay-Delta, and the discharge of the San Joaquin River in a wet year (1996). 

11. Hypothetical dilution profiles for selenium in the Bay-Delta. 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 (practical-salinity units, psu). The 

example mixing profile shows the selenium concentration in a hypothetical average freshwater 

endmember as it is diluted by concentrations in the Pacific Ocean. This endmember was calculated 

from loads and volumes in the Sacramento River at 20 million acre-feet (MAF) per year plus 

refinery inputs of approximately 4,000 lbs Se per year (typical of a wet year prior to refinery 

cleanup). 

12. Dissolved selenium profiles as a function of salinity (practical-salinity units, psu) in the Bay-Delta, 

comparing high and low flow seasons in 1986 (4/86 and 9/86) and in 1995-96 (6/95 and 10/96). 

13. Particulate selenium profiles as a function of salinity (practical-salinity units, psu) in the Bay-Delta, 

comparing high and low flow seasons in 1986 (9/86) and in 1995-96 (10/96). 

14. Frequency distributions of selenium concentrations in (a) 129 composite samples of C. fluminea

collected between January 1985 and October 1986; and (b) 62 composite samples of P. amurensis

collected between May 1995 and June 1997 from the Bay-Delta. Concentrations in bivalves from

reference sites also are given. 

15. Selenium concentrations in replicate composite samples of P. amurensis from 1995 through 1997 

as a function of Delta outflow. Flows are averaged on a monthly basis. 

16. Selenium concentrations in replicate composite samples of P. amurensis at 22 locations in the BayDelta during October 1996. Bivalve selenium concentrations are given in μg Se/g dry weight. 

17. Selenium concentrations in fish samples collected from the North Bay during 1986. Data from

California Department of Fish and Game Selenium Verification Study (White et al., 1987; 1988; 

1989; Urquhart and Regalado, 1991). 

18. Average selenium concentrations in bird liver samples collected from Suisun Bay and San Pablo 

Bay from 1986 to 1990. Data from California Department of Fish and Game Selenium Verification 

Study (White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). Species marked with an 

asterisk were collected in Suisun Marsh. 

19. 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. 

20. Forecasts of monthly composite freshwater endmember selenium concentrations under three 

discharge scenarios (San Joaquin River at 1 and 2 μg Se/L; San Luis Drain at 62.5 μg Se/L) 

contrasted to input concentrations and loads of selenium. 

21. Dilution of selenium through the estuary as a function of salinity (practical-salinity units, psu) in 

October 1997 (wet year). Carquinez Strait is assumed to be about half seawater salinity (17.5 

practical-salinity units). The composite freshwater endmember selenium concentrations are 

forecast for the SJR at 1 and 2 μg Se/L and for a SLD extension at 62.5 μg Se/L. 

22. Forecasts of seasonal composite freshwater endmember concentrations under five discharge 

scenarios for the high flow season of a wet year and the low flow seasons of wet and dry years. 

Input agricultural selenium loads released through a SLD conveyance are from 6,800 to 89,760 lbs 

per six months. The SJR forecast releases 3,500 lbs Se per six months. 

vii
23. Calculation of eight composite freshwater endmember selenium concentrations as derived from

different combinations of total input load and total river inflow. River inflows are the composited 

mass of water that reaches the estuary in a six-month period. The range of inflows and input loads 

are typical of different climate regimes (wet year or dry year) during the six-month dry season. 

24. Suspended particulate selenium concentrations as a function of total dissolved selenium

concentrations. Lines describing predicted particulate concentrations using Kd’s of 1 X 103 and 1 

X 104 are superimposed on the plots. 

25. Particulate selenium concentrations as occurring landward (salinity, psu = 0) to seaward (salinity, 

psu = 35) in the Bay-Delta. Three different Kd’s forecast three different trend lines for particulate 

concentrations using dissolved Se concentrations (Figure 24). The observed October 1996 

particulate data is superimposed on the projections. 

26. Relation between bivalve selenium concentrations and selenium concentrations in surf scoter liver. 

Data from California Department of Fish and Game Selenium Verification Study (White et al., 

1987; 1988; 1989; Urquhart and Regalado, 1991). 

27. Relation between bivalve selenium concentrations and selenium concentrations in sturgeon flesh. 

Data from California Department of Fish and Game Selenium Verification Study (White et al., 

1987; 1988; 1989; Urquhart and Regalado, 1991). 

28. Relation between bivalve selenium concentrations and selenium concentrations in sturgeon liver. 

Data from California Department of Fish and Game Selenium Verification Study (White et al., 

1987; 1988; 1989; Urquhart and Regalado, 1991). 

 

TABLES 

1. Chronology of authorizing, planning, regulatory and evidentiary events for construction of a valleywide drain or San Luis Drain. 

2. Chronology of investigative and regulatory events for the San Francisco Bay-Delta Estuary 

concerning selenium. 

3. Measured and estimated selenium concentrations in shallow ground water and subsurface drainage 

in Westlands Water District, Grassland Drainage Problem Area, Tulare subarea and Kern subarea. 

4. Conversion factors for selenium and salt or Total Dissolved Solids (TDS). 

5. Annual acre-feet or million acre-feet (MAF) and selenium loads from the upstream drainage source 

(Drainage Problem Area or Grassland Bypass Channel Project site B) and downstream sites for 

Mud and Salt Sloughs, and the San Joaquin River at Crows Landing (state compliance point for Se 

in the SJR) and at Vernalis. 

6. Load scenarios using data from the SJV Drainage Program (1990a) and 50 ppb, 150 ppb, and 300 

ppb assigned selenium concentrations. 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 our analysis, the 

distinction between problem water and subsurface drainage helps in assigning water-quality. The 

SJVDP defined scenarios of without future (i.e., no implementation of recommended plan) and with 

future (i.e., implementation of recommended plan). A third condition defined for use in our 

projections is called with targeted future which applies a factor of 0.20 acre-feet per acre per year 

of generated drainage, estimating the lowest, although probably not realistic, irrigation water 

return. The year 2000 projection for problem water is calculated here applying a factor of 0.4 acrefeet per acre per year; this projection was not part of the SJV Drainage Program consideration. 

viii
7. Our calculations of selenium concentrations in discharge from SJV Drainage Program subareas 

based on evidence presented by Westlands Water District or currently available ranges of 

measurements for drainage volume (acre-feet) and selenium load (i.e. measured values after the 

SJV Drainage Program database measurements in 1986-1989; see footnotes for source), except for 

Northern subarea where there is no recommended management plan by the SJV Drainage Program

(1990a) (see footnote). Only one set of values for the Westlands Water District drainage volume 

and selenium load was presented in evidence (see minimum). Since no updated measurements are 

available for Westlands Water District, the condition for the maximum load was calculated using 

an assigned* concentration of 150 ppb to the volume of drainage presented in evidence. 

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

scenarios. A kesterson (kst) is 17,400 lbs of Se, the cumulative load that caused visible ecological 

damage when released to a wetland (Kesterson National Wildlife Refuge, California). 

9. Load of Se discharged if a constant concentration is maintained in the SJR and conveyed to the 

Delta under high (3.0 MAF per year) and low (1.1 MAF per year) flow regimes. Approximately 

220,000 acre-feet represent the annual volume of flow from a proposed San Luis Drain extension at 

maximum capacity or a small SJR input to Bay-Delta in a dry year. 

10. Annual and daily oil refinery Se loads for the Bay-Delta for the period 1986 to 1992 and 1999. 

Cleanup of discharges and further permitting was required by 1998. 

11. Partitioning between dissolved Se and particulate or sediment Se in ecosystems for which reliable 

analytical data is available. 

12. Selenium concentrations in fish (μg Se/g dry weight) from the Bay-Delta (North Bay including 

Suisun, San Pablo, Grizzly and Honker Bays) and Humboldt Bay (Selenium Verification Study, 

White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). 

13. Examples of thresholds for Se effects (health, reproductive, teratogenesis, or survival) in fish based 

concentrations of Se in food; the example of massive poisoning at Kesterson Reservoir, California 

also applies to aquatic birds. Selenium concentrations in the most abundant benthic prey (food) 

organism in the Bay-Delta are given for comparison. 

14. Examples of thresholds for Se effects (health, reproductive, teratogenesis, or survival) in fish based 

on Se concentrations in tissues of fish. Selenium concentrations in tissues of white sturgeon from

the Bay-Delta are given for comparison. 

15. Examples of thresholds for Se effects (health, reproductive, teratogenesis, or survival) in birds 

based on Se concentrations in tissues of birds. Thresholds based on diet are also included. 

Selenium concentrations in tissues of bird species from Kesterson Reservoir and the Bay-Delta are 

given for comparison. 

22. Selenium loads employed in forecasts of Se impacts. Loads were calculated for a six-month 

season. Annual loads would be two times higher if Se discharge is continuous (i.e., at a constant 

rate). Agricultural inputs fall into three groups depending on management strategy: supply-driven 

management: (3,000 to 8,000 lbs Se/year); demand-driven load with management of land and/or 

drainage quality (15,000 to 45,000 lbs Se/year; and demand-driven load with minimum 

management (45,000 to 128,000 lbs Se/year). 

17. Comparison of Se hazard in the Bay-Delta and other environments. Values are Se concentrations 

in μg Se/g dry wt. 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. Data 

ix
sources are Lemly, 1995; 1996a; b; 1997a; b; c for western U.S. sites and this report and *Kroll and 

Doroshov, 1991 for the Bay-Delta. 

18. Calculation of a composite freshwater (FW) endmember concentration of Se (μg Se/L) from inputs 

of the Sacramento River (Sac R), the San Joaquin River (SJR), and oil refineries under conditions 

simulating those prior to refinery cleanup. Forecasts contrast wet and dry years: and high and low 

flow seasons. Load is expressed in lbs Se per six months. 

19. Calculation of a composite freshwater (FW) endmember concentration of Se (μg Se/L) from inputs 

of the Sacramento River (Sac R), the San Joaquin River (SJR), a proposed San Luis Drain 

extension, and oil refineries under different load scenarios. Forecasts are for a wet year (1997) 

during the high flow season. Load is expressed in lbs Se per six months. Forecasts 1a through 1d 

use a SLD extension and assume a 2 MAF SJR inflow reaches the Bay-Delta. The final forecast 

assumes no SLD extension and a SJR inflow of 1.1 MAF.

20. Calculation of a composite freshwater (FW) endmember concentration of Se (μg Se/L) from inputs 

of the Sacramento River (Sac R), the San Joaquin River (SJR), a proposed San Luis Drain 

extension, and oil refineries under different load scenarios. Forecasts are for a wet year (1997) 

during the low flow season. Se load is lbs Se per six months. Forecasts 2a through 2d use a SLD 

extension and assume little SJR inflow reaches the Bay-Delta. The final forecast assumes no SLD 

extension and a 0.5 MAF SJR inflow.

21. Calculation of a composite freshwater (FW) endmember concentration of Se (μg Se/L) from inputs 

of the Sacramento River (Sac R), the San Joaquin River (SJR), a proposed San Luis Drain 

extension, and oil refineries under different load scenarios. Forecasts are for a critically dry year 

(1994) during the low flow season. Se load is lbs Se per six months. Forecasts 3a through 3d use a 

SLD extension and assume little SJR inflow reaches the Bay-Delta. The final forecast assumes no 

SLD extension and a 0.5 MAF SJR inflow.

22. Calculation of a composite freshwater (FW) endmember concentration of Se from inputs of the 

Sacramento River (Sac R), the San Joaquin River (SJR), and oil refineries under a “restoration” 

scenario. Se load is lbs Se per six months. Assume greater SJR inflows enter the Bay-Delta to aid 

fish migration and the SJR input is held constant at 0.5 μg Se/L. High flow season conveys 75% of 

the SJR annual flow; low flow season, 25%. 

23. Summary of forecasts of Se concentrations in a composite freshwater endmember entering the BayDelta under different conditions. Load is expressed in lbs per six months. SLD loads are for the 

SLD only; targeted load and “restoration” scenario is for the SJR only. CF is a composite 

concentration in all sources of freshwater at the head of the estuary (i.e. near the discharge point of 

a proposed SLD extension); CE is a composite concentration at 17.5 practical-salinity units (psu), 

usually near Carquinez Strait during the low flow season. 

24. Summary of forecasts of Se concentrations in particulate material under different conditions. Load 

is expressed in lbs Se per six months. SLD scenario loads are for the SLD only; the targeted load 

and “restoration” scenario are for the SJR only. C1 is the concentration forecast at a Kd of 104

, 

typical of suspended sediment; C2 is the concentration forecast at a Kd of 3X103, typical of 

shallow-water bed sediment; C3 is the low reactivity concentration forecast at a Kd of 103

. All 

concentrations are those at the head of the estuary (near the release point of a proposed SLD 

extension). 

25. Forecast of particulate Se concentrations at the head of the Bay-Delta estuary: 

• in years with different climate regimes; 

• in different seasons; and 

x
• for alternative speciation and biogeochemical behavior patterns. 

The scenarios considered are: 

• a SLD extension discharge of 18,700 lbs per six months (full capacity, 62.5 μg Se/L); 

• a SJR discharge of a targeted load of 3,590 lbs per six months for a wet year (1.2 μg Se/L) 

and 3,400 lbs per six months for a dry year (2.5 μg Se/L). 

Forecasts are compared to conditions prior to refinery cleanup. 

26. Laboratory-derived physiological constants for Se bioaccumulation by several species of bivalve 

and composite values for a generic bivalve (data from Luoma et al., 1992; Reinfelder et al., 1997). 

27. Selenium concentrations in a generic bivalve when exposed to different concentrations of 

particulate organo-Se or particulate elemental Se (constants from Luoma et al., 1992 and 

Reinfelder et al., 1997). 

28. Summary of forecasts of Se concentrations in a generic bivalve under different conditions. Load is 

expressed in lbs per six months. SLD scenario loads are for the SLD only. The targeted load and 

“restoration” scenario are for the SJR only. C1 is the concentration forecast at a Kd of 104

, typical of 

suspended sediment; C2 is the concentration forecast at a Kd of 3X103

, typical of shallow-water bed 

sediment; C3 is the low reactivity concentration forecast at a Kd of 103. Four assimilation efficiencies 

have been assumed for each Kd: AE4 = 0.8; AE3 = 0.63; AE2 = 0.55; and AE1 = 0.35. All 

concentrations are those at the head of the estuary (near the release point of a proposed SLD 

extension). 

29. Forecast of Se concentrations bioaccumulated by a generic bivalve at the head of the Bay-Delta 

estuary: 

• in years with different climate regimes; 

• in different seasons; and 

• for alternative speciation and biogeochemical behavior patterns. 

The scenarios considered are: 

• a SLD extension discharge of 18,700 lbs per six months (full capacity, 62.5 μg Se/L); 

• a SJR discharge of a targeted load of 3,590 lbs per six months for a wet year (1.2 μg Se/L) 

and 3,400 lbs per six months for a dry year (2.5 μg Se/L). 

Forecasts are compared to conditions prior to refinery cleanup. 

30. Regression equations for bivalves versus bivalve predators. Data from Selenium Verification Study

(White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991) 

31. Data employed in regression of Se concentrations in bivalves versus Se concentrations in bivalve 

predators. Means from different years are aggregated; North Bay is Suisun Bay and San Pablo 

Bay. Concentrations of Se in both flesh and liver are shown for predators. Bivalves are from

different species (Corbicula fluminea*; Mya arenaria**; Macoma balthica***; and 

Potamocorbula amurensis****) and different studies (White et al., 1987*; 1988*; 1989*; Urquhart 

and Regalado, 1991*; Johns et al., 1988*; Luoma and Linville, 1997****; Linville and Luoma, in 

press****). Selenium as ppm is equivalent to micrograms per gram. All values are for dry weight. 

32. Forecasts of Se concentrations in bivalves and resulting Se concentrations in livers of surf scoter, 

greater and lesser scaup, and white sturgeon under two Se discharge conditions: 1) the SLD 

scenario is for 18,700 lbs per six months (37,400 lbs Se per year) and 2) the SJR scenario is for a 

targeted load of 3,500 lbs per six months (7,000 lbs per year) (SJR conditions defined earlier). All 

forecasts are for six months of discharge during the low flow season of a critically dry year. 

Forecast concentrations are compared to average Se concentrations in these organisms (Corbicula 

fluminea in 1988-1990; Potamocorbula amurensis, 1995-1996; surf scoter, greater and lesser scaup, 

xi
and white sturgeon, 1989-1990) in the Bay-Delta and to thresholds for adverse effects described 

earlier. Forecasts for predators were predicted by extrapolation from regressions between bivalve 

and predator concentrations using data from 1986 to 1990 (Tables 30 and 31). 

33. Relation of Se loads, composite freshwater endmember Se concentrations, particulate Se 

concentrations, Se bioaccumulation by bivalves, Se bioaccumulation by two predators (sturgeon 

and scaup) and Se guidelines or concentrations at which effects are expected. Forecasts are for: 

• discharges from a SLD extension or the SJR; 

• 

• 

concentrations in the North Bay near the site of input (i.e., head of estuary) with 

instantaneous mixing; and 

the low flow season of a dry year. 

Conditions prior to refinery cleanup are given for comparison. 

CONVERSION FACTORS 

By weight: microgram per gram is equivalent to parts per million (ppm) 

1 microgram (μg/g) = 10-6 gram (g) 

For concentration of dissolved solids less than approximately 7,000 mg/L: 

Milligram per liter (mg/L) is equivalent to parts per million 

Microgram per liter (μg/L) is equivalent to parts per billion (ppb) 

1,000 microgram per liter (μg/L) = 1 milligram per liter (mg/L) 

See also Table 4 (in text) which is duplicated below. 

Selenium (Se) Salt or Total Dissolved Solids (TDS) 

1 ppb Se =1 μg Se/L 1 ppm TDS = 1 mg salt/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 μgrams Se/acre-foot at 1 ppb Se 

1.23 grams Se/ acre-foot at 1 ppb Se 1,234 grams salt/acre-foot at 1 ppm salt 

454 grams = 1 lb

0.00272 lbs Se/acre-foot at 1 ppb Se 2.72 lbs salt/acre-foot at 1 ppm salt 

[1 ppb Se = 0.00272 lbs Se/acre-foot] [1 ppm salt= 2.72 lbs salt/acre-foot] 

2000 lbs = 1 ton 

1 ppm salt = 0.00136 tons salt/acre-foot 

VOLUME 

1 cubic foot per second (cfs) = 1.98 acre-feet/day

For those who prefer to use the International System of Units (SI), the conversion factors 

for terms used in this report are listed below. 

Multiply By To obtain

Acre 4,047 square meter (m2) 

Acre 0.4047 hectare (ha)

acre-foot 1,233 cubic meter (m3) 

cubic foot per second (cfs) 0.02832 cubic meters per second (m3/s) 

xii
ABBREVIATIONS 

AF Acre-foot 

AE Assimilation Efficiency 

BAF Bioaccumulation Factor 

BSAF Biota to Sediment Accumulation Factor 

Bay-Delta San Francisco Bay-Delta Estuary 

CALFED A cooperative, interagency effort of fifteen federal and state agencies with 

management and regulatory responsibilities for the Bay-Delta 

CCtF Clifton Court Forebay 

CCVRWQCB California Central Valley Regional Water Quality Control Board 

CDFG California Department of Fish and Game

CDWR California Department of Water Resources 

CSFBRWQCB California San Francisco Bay Regional Water Quality Control Board 

CSWRCB California State Water Resources Control Board 

CVP Central Valley Project 

dw dry weight 

DynBaM Dynamic Multi-path Bioaccumulation Model 

FR Feeding Rate 

GBCP Grassland Bypass Channel Project 

Kd Distribution (partitioning) coefficient 

kst kesterson unit (equals 17,400 lbs Se) 

MAF Million Acre-Feet 

NMFS National Marine Fisheries Service 

psu practical-salinity unit 

Sac R Sacramento River 

SJR San Joaquin River 

SJV San Joaquin Valley 

SJVDP San Joaquin Valley Drainage Program

SLD San Luis Drain 

SLU San Luis Unit 

SWP State Water Project 

TMDL Total Maximum Daily Load 

TMML Total Maximum Monthly Load 

USBR United States Bureau of Reclamation 

USEPA United States Environmental Protection Agency 

USFWS United States Fish and Wildlife Service 

USGS United States Geological Survey 

WWD Westlands Water District

WY Water Year (A water year begins on October 1st) 

xiii
Forecasting Selenium Discharges to the San Francisco Bay-Delta 

Estuary: Ecological Effects of A Proposed San Luis Drain Extension 

Samuel N. Luoma 

Theresa S. Presser 

ABSTRACT 

 During the next few years, federal and state agencies may be required to evaluate proposals and 

discharge permits that could significantly change selenium (Se) inputs to the San Francisco Bay-Delta 

Estuary (Bay-Delta), particularly in the North Bay (i.e., Suisun Bay and San Pablo Bay). These 

decisions may include discharge requirements for an extension of the San Luis Drain (SLD) to the 

estuary to convey subsurface agricultural drainage from the western San Joaquin Valley (SJV), a 

renewal of an agreement to allow the existing portion of the SLD to convey subsurface agricultural 

drainage to a tributary of the San Joaquin River (SJR) (coincident with changes in flow patterns of the 

lower SJR), and refinements to promulgated Se criteria for the protection of aquatic life for the estuary. 

 Understanding the biotransfer of Se is essential to evaluating the fate and impact of proposed 

changes in Se discharges to the Bay-Delta. However, past monitoring programs have not addressed the 

specific protocols necessary for an element that bioaccumulates. Confusion about Se threats in the past 

have stemmed from failure to consider the full complexity of the processes that result in Se toxicity. 

Past studies show that predators are more at risk from Se contamination than their prey, making it 

difficult to use traditional methods to predict risk from environmental concentrations alone. In this 

report, we employ a novel procedure to model the fate of Se under different, potentially realistic load 

scenarios from the SJV. For each potential load, we progressively forecast the resulting environmental 

concentrations, speciation, transformation to particulate form, bioaccumulation by invertebrates, 

trophic transfer to predators, and effects in those predators. Enough is known to establish a first order 

understanding of effects should Se be discharged directly into the North Bay via a conveyance such as 

the SLD. 

 Our approach uses 1) existing knowledge concerning the biogeochemical reactions of Se (e.g., 

1
speciation, partitioning between dissolved and particulate forms, and bivalve assimilation efficiency) 

and 2) site-specific data mainly from 1986 to 1996 on clams and bottom-feeding fish and birds. 

Forecasts of Se loading from oil refineries and agricultural drainage from the SJV enable the 

calculation of a composite freshwater endmember Se concentration at the head of the estuary and at 

Carquinez Strait as a foundation for modeling. Our analysis of effects also takes into account the mode 

of conveyance for agricultural drainage (i.e., the SLD or SJR). The effects of variable flows on a 

seasonal or monthly basis from the Sacramento River and SJR are also considered. 

 The results of our forecasts for external SJV watershed sources of Se mirror predictions made since 

1955 of a worsening salt (and by inference, Se) buildup exacerbated by the arid climate and irrigation 

for agricultural use. We show that the reservoir of Se in the SJV is sufficient to provide loading at an 

annual rate of approximately 42,500 pounds (lbs) of Se to a Bay-Delta disposal point for 63 to 304 

years at the lower range of our projections, even if influx of Se from the California Coast Ranges could 

be curtailed. Disposal of wastewaters on an annual basis outside of the SJV may slow the degradation 

of valley resources, but drainage alone cannot alleviate the salt and Se buildup in the SJV, at least 

within a century. 

 Our forecasts show the different proportions of Se loading to the Bay-Delta. Oil refinery loads from

1986 to 1992 ranged from 11 to 15 lbs Se per day; with treatment and cleanup, loads decreased to 3 lbs 

Se per day in 1999. In contrast, SJV agricultural drainage loads could range from of 45 to 117 lbs Se 

per day across a set of reasonable conditions. Components of this valley-wide load include five source 

subareas (i.e., Grassland, Westlands, Tulare, Kern, and Northern) based on water and drainage 

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

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

0.8 to 10 lbs Se per day. 

 A consistent picture of ecological risk emerges for the Bay-Delta based on concurrent lines of 

evidence. The threat to the estuary is greatest during low flows and dry years. Where Se undergoes 

reactions typical of low flow or longer residence time, highly problematic bioaccumulation in prey 

(food) is forecast to result. The Bay-Delta predators—surf scoter, greater and lesser scaup, and white 

sturgeon—appear to be most at risk because they feed on filter-feeding bivalves. Recent findings add 

Sacramento splittail to that list. During the low flow season of dry years, the lower range of proposed 

protective guidelines for waterborne, particulate, dietary, and predator tissue Se is exceeded under the 

most likely forecast of Se inputs from a proposed SLD extension. Also under low flow conditions, the 

2
upper range of guidelines (i.e., high certainty of adverse effects) is exceeded in all instances except at 

the lowest load considered. High flows afford some protection in the forecast SJR scenarios under 

certain conditions. However, meeting a combined goal of releasing a specific load during maximum

flows and keeping Se concentrations below a certain objective to protect against bioaccumulation may 

not always be attainable. Management of the SJR on a constant concentration basis could also create 

problematic bioaccumulation during a wet year, especially during the low flow season, because high 

flows translate to high loads that are not always offset by seasonal inflows. 

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

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

in livers of diving ducks. During this time, Se concentrations in the Bay-Delta were well below the 

most stringent water quality criteria. Enhanced biogeochemical transformations to bioavailable 

particulate Se and efficient uptake by bivalves and then predators characterized the system. If these 

biogeochemical conditions continue to prevail, the forecasts suggest the risk of adverse effects will be 

difficult to eliminate under an out-of-valley resolution to the Se problem. 

 The forecasts for Se loading present a new tool to evaluate ecological effects based upon the major 

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

site-specific analysis and could provide a framework for developing new protective criteria. We

conclude that credible protective criteria should be based on 1) contaminant concentrations in sources, 

such as particulate material, that most influence bioavailability and 2) concentrations in media and 

organisms relevant to vulnerable food webs. Existing criteria for water, particulate material, and tissue 

of prey and predators should be used in combination to evaluate risk or hazard. Bivalves appear to be 

the most sensitive indicator of Se contamination in the Bay-Delta. 

INTRODUCTION 

 The sources and biogeochemistry of Se 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 et al., 1999; Hamilton, 1999; Eisler, 2000; Hamilton, 2000a]. Selenium is 

especially enriched in organic-rich shales that are source rocks for oil, coal, and phosphate ores (Figure 

1) (Cumbie and Van Horn, 1978; Presser, 1999; Piper et al., 2000). Release of Se to aquatic systems is 

3
a result of weathering and anthropogenic activities such as refining, power production, and mining. 

Selenium is also enriched in the soils and runoff derived from these source sedimentary shales in many 

semi-arid regions exploited for irrigated agriculture, such as in the SJV, California (Presser, 1994a; b; 

Seiler et al., 1999). Salinization of some of these soils is accompanied by Se contamination that 

increases the complexity of problems associated with continued exploitation of such lands (SJV 

Drainage Program, 1990a; Dinar and Zilberman, 1991). Irrigation, leaching, and generation of 

subsurface drainage leads to surface and ground waters being contaminated (Presser and Ohlendorf, 

1987). Treatment technologies for Se have utilized both chemical and biological processes to remove 

Se from the water column, but with little operational success or cost-effectiveness (SJV Drainage 

Program, 1990a; Hanna et al., 1990; SJV Drainage Implementation Program, 1998; 1999a). Use of 

large-scale biological treatment technologies (e.g. wetlands or evaporation ponds) has generated 

serious ecological problems and hazardous Se wastes for disposal (Presser and Piper, 1998; Skorupa, 

1998a; Hamilton, 2000b). Selenium removal is further hampered by the failure of traditional chemical 

methods to reduce Se to levels acceptable for remediation and, in arid regions, by the problem of 

disposal of associated salts (SJV Drainage Program, 1990a). Remediation has not been established 

other than that dependent on dilution in a larger body of water (SJV Drainage Implementation 

Program, 1998; U.S. Department of the Interior’s National Irrigation Water Quality Program, 2000). 

Management plans for the western SJV that include drainage storage and reduction through source 

control have been developed, but systematic and comprehensive implementation has not taken place 

(SJV Drainage Program, 1990a; SJVDP, 1991; SJV Drainage Implementation Program, 1998; 

Environmental Defense Fund, 1994). 

 The biogeochemical cycling of Se and its role as an essential nutrient lead to the dominance of 

biological reactions over thermodynamic reactions in aquatic systems (Shrift, 1964; Stadtman, 1974; 

National Research Council, 1976; Measures and Burton, 1978; Cutter and Bruland, 1984; Lemly, 

1985; Presser and Ohlendorf, 1987; Oremland et al., 1989; Luoma et al., 1992; Maier and Knight, 

1994; Presser, 1994a; Lemly, 1997b; Wang et al., 1996; Luoma and Fisher, 1997; Dowdle and 

Oremland, 1999; Reinfelder et al., 1998). The fate and adverse ecological effects of Se discharges are 

determined by a sequence of linked processes that connect loads, concentrations, speciation, 

bioavailability, trophic transfer, and effects on predators (Luoma et al., 1992; Luoma, 1996; Wang et 

al., 1996; Reinfelder et al., 1997; 1998; Luoma and Fisher, 1997) (Figure 2). Pathway 

bioaccumulation models allow consideration of 1) biotransfer from different types of 

4
suspended/particulate matter (e.g., phytoplankton, seston, and benthos); 2) biotransformation to 

different speciation regimes (selenate, selenite, organo-Se, elemental Se); 3) bioaccumulation via the 

lower trophic food web; and 4) uptake of food by predator species. Because Se concentrations can be 

magnified at each step of food web transfer (e.g., USEPA, 1980; Saiki, 1986; Maier and Knight, 1994), 

upper trophic level species are probably the species most vulnerable to adverse effects from Se 

contamination. Aquatic species potentially at risk from Se contamination (Figure 1) include 

charismatic birds (e.g., ducks, shorebirds, and grebes) and fish (e.g., sturgeon, carp, trout, and sunfish) 

(White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991; Luoma et al., 1992; Lemly, 1993a; 

1998a; b; Skorupa, 1998a). Herps (frogs and snakes) also may be at risk from Se [Skorupa, 1998b; 

U.S. Fish and Wildlife Service (USFWS) and National Marine Fisheries Service (NMFS), 1998 and 

amended, 2000), as may Sacramento splittail (Stewart, et al., in preparation). 

 Analysis of one of the above sets of processes, in isolation, is inadequate to characterize Se 

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 interpretations of Se effects on the environment (e.g., 

O’Toole and Raisbeck, 1998; Hamilton and Lemly, 1999; Chapman, 1999; Lemly, 1999a; Skorupa, 

1998a; 1999). In view of advances in the understanding of Se environmental chemistry, the USEPA 

has recently called for a re-definition of the Se criteria for the protection of aquatic life (USEPA, 1998; 

Renner, 1998). 

 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 et al., 1999). Selenium

issues are of particular concern in the SJR basin (Figure 3) and in the Bay-Delta (Figure 4). Here, Se 

issues are intricately interwoven with issues of water management, urbanization, irrigated agriculture, 

and protection of fish and wildlife resources [Conomos, 1979; Conomos et al., 1985; Cloern and 

Nichols, 1985; Nichols et al., 1986; California State Water Resources Control Board (CSWRCB), 

1994; 1999a; USFWS, 1995; Hollibaugh, 1996; Presser and Piper, 1998; CALFED, 1998a; b; 1999a; 

b; c; d; Thompson et al., 2000]. The SJV has also suffered major losses of crucial habitat for migratory 

birds (Gilmer at al., 1982; Vencil, 1986). 

 The goal of this paper is to introduce a comprehensive approach to forecast the ecological effects of 

Se under an array of scenarios that could result from different resolutions of water and waste 

management issues. We concentrate on analysis of Se inputs based on engineering solutions that 

5
would convey Se-laden salts from the western SJV to the Bay-Delta via a proposed extension of the 

San Luis Drain (SLD) (Barcellos, 1986; Wanger, 1994; CSWRCB, 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, 2000). We also consider using 

the SJR as a conveyance facility (i.e., the SJR as a de facto drain) because it is the only natural outlet 

from the SJV. We present a history of the discussions surrounding the construction of the drain and 

use of the SJR to convey Se outside the SJV. We forecast loads, concentrations, fate, and effects of Se 

on animals in the estuarine food web that could result from projected Se discharges. 

 Our approach involves using existing knowledge, that includes empirical observations from the 

Bay-Delta and models, to convert proposed mass emissions to concentrations in receiving waters under 

several scenarios. Bioaccumulation in lower trophic level consumer organisms (bivalves) is projected 

from a likely range of concentration, partitioning, and speciation scenarios using pathway 

bioaccumulation models. Comparisons of Se concentrations in Bay-Delta clams are made to proposed 

protective dietary Se guidelines for fish and birds. Selenium concentrations in a few key predators are 

predicted from correlations with bivalve tissue concentrations of Se using data from the existing 

literature. Because the relation between tissue concentrations and adverse effects are relatively well 

constrained for Se in wildlife, predictions of tissue residues in waterfowl and fish provide a first order 

estimate of potential adverse effects of Se mass emissions. The specific information—bioaccumulation 

of Se by clams and biotransfer of Se to fish and waterfowl—could be applied to evaluate proposals for 

disposal of Se from the SJV that include discharge to aquatic systems (i.e., using the Bay-Delta as a 

receiving water). Presentation of the process by which we evaluate the ecological effects of Se is as 

important as the specifics of the discussion as applied to the Bay-Delta. The general process of a 

linked bioaccumulation model using a bioindicator organism to assess potential adverse impacts on 

predators can be applied to other ecosystems subjected to Se loading and can help in the development 

of national or site-specific Se criteria for aquatic protection. 

Generic Selenium Issues 

Existing knowledge concerning the biogeochemistry of Se allows the following generalizations: 

1. Geologic sources of Se are widespread (Figure 1). 

2. Exploitation of energy sources (oil and coal), mining of phosphate ore, irrigation of areas 

underlain by organic-rich marine shales, and irrigation of lands where alluvium is derived from

6
such shales, mobilize geologic Se and ultimately result in the contamination problems found 

today (see examples in Figure 1). 

3. Linked biological and geochemical reactions affect the form of Se (Figure 2). Geochemical 

form (speciation) determines how readily the element enters aquatic food webs, initiates food 

web transfer, and cycles through particulate matter, sediments, consumer organisms, and 

predators. 

4. Hydrologic connections also determine the effects of Se. Compartmentalized ecological 

systems can interact at critical hydrologic junctures such as in estuaries. Seemingly harmless 

concentrations of Se in a riverine system may become problematic in downstream

impoundments, marshes, or wetlands, where cycling and bioaccumulation are accentuated 

(Luoma et al., 1992; Skorupa, 1998a; Lemly, 1999b). The geographic scale of Se issues can 

extend beyond local conditions and therefore, an analysis of downstream effects needs to 

follow. 

5. Traditional toxicity tests are problematic because they determine toxicity only via direct waterborne exposures. Direct transfer of Se from solution to animals such as fish and bivalves is a 

small proportion of exposures. Bioaccumulation and uptake via food is the most important 

route of Se transfer to upper trophic level species (Figure 2) (Ohlendorf et al., 1986; Saiki and 

Lowe, 1987; Presser and Ohlendorf, 1987; Lemly, 1985; Luoma et al., 1992; Presser et al., 

1994). 

6. Selenium efficiently bioaccumulates through aquatic food webs, and strongly biomagnifies into 

many components of the food web (Saiki, 1986; Presser and Ohlendorf, 1987; Luoma et al., 

1992; Maier and Knight, 1994). Invertebrates may be the best indicator for monitoring predator 

exposure. Consumer species like bivalves integrate the influences of environmental 

concentrations, speciation, and transformations of Se and are practical to sample. Predators, on 

the other hand, are mobile and impractical to sample in large numbers on a routine basis. A 

predator’s choice of food, which varies widely among species, could result in some trophic 

pathways being more efficient accumulators of Se than others (Lemly, 1982; 1985; Luoma, et 

al., 1992; Luoma and Fisher, 1997; Skorupa, 1998a; CH2M HILL, 1996; 1999a). 

7. Charismatic species (birds and fish) are the first to express the effects of Se contamination due 

to this efficient bioaccumlation in the food web and their sensitivity to exposure to Se 

(Ohlendorf, 1989; Ohlendorf et al., 1989a; Hamilton et al., 1990; Lemly, 1996b; c; Skorupa, 

7
1998a; b; c; Hamilton et al., 2000a; b). Thus, bioaccumulation models must link food sources 

to predator animals to predict biotic effects. 

8. 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 et al., 2000a). In 

contrast to many other contaminants, significant environmental damage due to Se 

contamination has been well documented. Skorupa (1998a) described case studies showing 

different degrees of Se effects in a variety of wetlands and reservoirs impacted by agricultural 

drainage, burning of fossil fuels, or refining of oil. An especially well documented case study 

exists for Belews Lake in North Carolina where Se contamination resulted in local extinctions 

of most fish populations, via reproductive impairment and teratogenesis (Cumbie and Van 

Horn, 1978; Lemly, 1985; 1997a). The most well known case of Se poisoning in a field 

environment was at Kesterson National Wildlife Refuge in the SJV of California (Ohlendorf, et 

al., 1986; Presser and Ohlendorf, 1987; Skorupa and Ohlendorf, 1991). There, teratogenesis 

and reproductive failure were widespread in populations of water birds. 

9. Although extreme Se contamination causes death in adult organisms, the responses of greatest 

concern are impairment of reproductive success (e.g. failure of eggs to hatch) and teratogenesis 

(deformities in juveniles) in birds and fish (Skorupa and Ohlendorf, 1991). Inhibition of 

growth, depressed immune system response, mass wasting, and winter stress syndrome also are 

effects of concern (Ohlendorf, 1989; Lemly, 1993b; 1998a; CH2M HILL, 1997; 1999b; 

USFWS and NMFS, 1998 and amended, 2000; Santolo et al., 1999). Reproductive damage and 

teratogenesis can occur at low concentrations [low micrograms per liter (μg/L)] of 

environmental Se because the window is narrow between the amount of Se that is nutritionally 

beneficial and the amount that is toxic (Wilber, 1983; National Research Council, 1976; 

USEPA, 1980; 1998; Haygarth, 1994; Skorupa, 1998a; b). Data exist that relate teratogenesis, 

hatchability, and reproductive success to Se concentrations in food, avian eggs, and fish larvae 

(reviews in Heinz, 1996; Lemly, 1998b; Maier and Knight, 1994; Skorupa, 1998a; b). 

Ecological risk thresholds and a risk index based on Se concentrations in water, sediment, and 

tissue are currently under debate (Peterson and Nebeker, 1992; Engberg et al., 1998; Lemly, 

1995; Skorupa, 1998a; b; c). 

10. Uncertainty exists in the USEPA Se criteria for the protection of aquatic life, especially for 

criteria derived from water-only, short-term exposure of surrogate species. Uncertainty also 

8
exists for criteria derived using limited field data on food chain exposure, because few studies 

were available at the time of promulgation (USEPA, 1992; 1998). The toxicity-testing database 

does not consider bioaccumulation, although bioaccumulation from food determines the 

ecological effects of Se. A Se criterion derived primarily from food web exposure would be 

more relevant to field conditions in aquatic systems. 

11. Effects of Se on human health are of concern. State human health advisories have restricted 

consumption of edible fish and birds and eliminated consumption for children and pregnant 

women when Se concentrations exceed a certain criterion [California Department of Fish and 

Game (CDFG), 1985; 1986; 1988, all on-going; 1987; Fan et al., 1988; SJV Drainage Program, 

1989; 1990b]. 

12. No satisfactory chemical, physical or biological treatment technology yet exists to remove Se 

contamination from irrigation drainage waters (Hanna et al., 1990; Hansen et al., 1998; SJV 

Drainage Implementation Program, 1999a; b; c; d). Treatment technologies that work on small 

effluent streams are inefficient and expensive to employ on large volumes of contaminated 

water (SJV Drainage Program, 1990a; SJV Drainage Implementation Program, 1998; National 

Irrigation Drainage Program, 2000). Treatment technologies still being tested are flow-through 

wetlands and biological precipitation (Hansen, et al., 1998; SJV Drainage Implementation 

Program, 1999a), 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 SJV 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 (SJV Drainage Program, 1990a). 

 

Selenium Issues in the Bay-Delta 

The surface and ground waters of the SJV are part of a complex, hydrologic system that extends 

from the riparian wetlands of the Sacramento River and SJR through the Bay-Delta to the Pacific 

Ocean (Presser and Piper, 1998) (Figures 3 and 4). This natural system provides the framework for the 

Central Valley Project (CVP) which is a massive engineered complex of dams, off-stream storage 

reservoirs, pumping facilities, irrigation and drinking water supply canals, and agricultural irrigation 

drainage canals [U.S. Bureau of Reclamation (USBR), 1984a]. Figure 5 presents a detailed schematic 

9
of the hydrologic connections of the SJV (Figure 3) to the Bay-Delta (Figure 4) including the 

Sacramento River and SJR. The sustainability of the balance and quality of water in this system are 

crucial to the welfare of California, especially to the arid SJV. 

Selenium issues are of special concern within the Bay-Delta ecosystem because: 

1. Selenium contamination exists under present conditions in the Bay-Delta from known sources 

of Se within the estuary and in watersheds draining to the estuary. Watershed sources are 

linked to SJV farmland activities where irrigation of salinized soils has led to proposed 

management alternatives to sustain agriculture by draining salts and Se collected as subsurface 

drainage to the Bay-Delta via the SJR or SLD [e.g., CSWRCB, 1985; SJV Drainage Program, 

1990a; Presser and Ohlendorf, 1987; Presser and Piper, 1998; Skorupa, 1998a; California 

Central Valley Regional Water Quality Control Board (CCVRWQCB), 1998a; b; USFWS and 

NMFS, 1998 and amended 2000). Proposals for construction of a collector drain and an 

extension of the existing SLD to remove salts and Se from the SJV have been under 

consideration for approximately 50 years (Table 1). Water quality in the SJR has degraded 

significantly since the 1940’s because of disposal of agricultural wastewater from the SJV 

(CCVRWQCB, 1995). Even though the SJR is a source water for the Bay-Delta, selenium

sources and contamination within the North Bay (i.e., Suisun Bay and San Pablo Bay) have 

been linked in the past mainly to oil refineries discharging waste from processing Se-enriched 

crude oil from the SJV and adjacent Coast Ranges (e.g., White et al., 1987; 1988; 1989; Cutter, 

1989; Johns, et al., 1988; Cutter and San Diego-McGlone, 1990; Urquhart and Regalado, 1991; 

San Francisco Estuary Project, 1991; 1992; Luoma, et al., 1992; Brown and Luoma, 1995a; 

Luoma and Linville, 1997; Linville and Luoma, in press; USFWS and NMFS, 1998 and 

amended, 2000). 

2. Selenium contamination documented from 1982 to the mid-1990’s was sufficient to threaten 

reproduction (> 10 μg Se/g in tissue) in key species within the Bay-Delta estuary ecosystems 

(Table 2) [White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991; San Francisco Estuary 

Project, 1991; 1992; Harvey et al., 1992; California San Francisco Bay Regional Water Quality 

Control Board (CSFBRWQCB), 1992a; b; 1993; Brown and Luoma, 1995a; Linville and 

Luoma, in press]. The most severely threatened species appear to include, but are not restricted 

to white sturgeon (Acipenser transmontaus), Sacramento splittail (Pogonichthys 

macrolepidotas), starry flounder (Platichthys stellatus), Dungeness crab (Cancer magister), 

10
surf scoter (Melanitta perspicillata), greater scaup (Aythya marilla), and lesser scaup (Aythya 

affinis) (Ohlendorf et al., 1986; White et al., 1987; 1988; 1989; Ohlendorf et al., 1989b; c; 

Urquhart and Regalado, 1991; Luoma et al., 1992; USFWS, 1995; Hothem et al., 1998). In 

1989-1990 in the North Bay, average Se concentrations in surf scoter liver samples exceeded 

the threshold level for avian reproductive toxicity (Heinz, 1996) by eight-fold and in sturgeon 

flesh samples exceeded the threshold for effects in fish (Lemly, 1998b) by two-fold. Currently, 

populations and catches per unit effort (where applicable) of all the 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 of the exceedance 

of Se thresholds for adverse effects in tissue of prey and predators, Se cannot be excluded as 

one. 

3. Some food webs in the Bay-Delta may be particularly vulnerable to moderate Se 

contamination. Analyses in 1982-1996 showed that the animals with the highest Se tissue 

concentrations from the North Bay (i.e., Suisun Bay, Carquinez Strait, and San Pablo 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-1990’s (Linville and Luoma, in 

press) than in 1977 through 1990 (White et al., 1987; 1988; 1989; Cutter, 1989; Johns et al., 

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 (bottom feeding fish, diving ducks, and 

Dungeness crab) may be the most important route of Se transfer to the upper trophic levels in 

the estuary. Levels in P. amurensis reached 20 μg Se/g dry weight (dw) in the North Bay in 

October 1996, exceeding two-fold the toxicity threshold in food for predators (> 10 μg Se/g 

dw) that result in adverse effects. 

4. Portions of the Bay-Delta and the SJR are currently listed by the state as being subjected to 

contamination from a suite of chemicals (e.g., mercury, diazinon, PCBs, dioxin, PAHs, and Se) 

(CCVRWQCB, 1994a; 1998b; CSWRCB, 1999b; c). State or federal criteria have been 

exceeded in these listed waterbodies, causing adverse aquatic life and human health impacts 

(e.g., Fairey et al., 1997; Davis et al., 1997; Dubrovsky et al., 1998). Portions of the SJR are 

11
designated as water-quality limited due to Se. Most recently, portions of the Bay-Delta have 

been listed as known toxic hotspots of high priority due to Se. 

5. The amount and quality of the wetlands in the Bay-Delta leaves in doubt the future status of 

many wildlife populations (Harvey et al., 1992; CALFED, 1998a; b; San Francisco Estuary 

Project, 1999); Se contamination affects the quality of the already limited acreage of wetlands 

and other crucial habitat (CALFED, 1998a; b and 1999a; b; c; d). A recovery plan was deemed 

necessary for Sacramento/San Joaquin Delta native fishes (USFWS, 1995). The plan includes 

designation of critical habitat (i.e., 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 threatened Sacramento splittail (Pogonichthys 

macrolepidotas) (64 Federal Register 5963) is not currently designated. 

6. Environmental safeguards were enacted after the ecological disaster at Kesterson National 

Wildlife Refuge, but many may be inadequate for the specific problems of the Bay-Delta. For 

example: 

a) The USEPA criterion for the protection of aquatic life (5 μg Se/L) is not in effect for 

upstream inflows to the Bay-Delta (i.e., the SJR and its tributary sloughs) due to state 

postponements of compliance until 2010 (USEPA, 1992; CCVRWQCB, 1996d). Selenium

concentrations in the river have exceeded USEPA criteria (50% of the time for the period 

1987 to 1997 at Crows Landing, Figures 3 and 5) since the discovery of Se effects at the 

Kesterson National Wildlife Refuge (CCVRWQCB, 1996a; b; 1998f). Load limits enacted 

by the state in 1996 were exceeded in 1996 through 1998. Impacts from Se on the SJR have 

not been directly evaluated partly because no program systematically collects biological, 

water quality, and flow data (Presser et al., 1996; Presser and Piper, 1998). An aquatic 

hazard assessment of a tributary slough receiving the greatest impact from agricultural 

drainage found the Se hazard as “high” (Lemly, 1995; 1996a; USBR et al., 1998; 1999). 

Replacement of native species of varying tolerance in the SJR has led to a rating of “poor” 

on the index of biological integrity (Moyle et al., 1986) for river sites above and below 

drainage discharges. Populations of fish in the SJR and adjacent sloughs are now 

dominated by introduced species having broad environmental tolerances (USBR et al., 

1998; 1999). The role of Se in these changes is not proven, but effects on native fish 

12
populations are documented elsewhere (e.g., Lemly, 1997b; Hamilton, 1998; 999; and 

Hamilton et al., 2000a). 

b) Refinery inputs to the Bay-Delta have declined since 1998. State waste discharge permits 

limit oil refinery effluents based on Se loads. Effluents, however, may reach a daily 

maximum of 50 μg/L Se, which is ten times above the promulgated USEPA criterion 

(CSFBRWQCB, 1992b; USEPA, 1987 and 1992). It is expected that food web 

contamination attributable to the refineries will decline; dilution of the effluent discharges 

by low Se inflows is critical. In 1995, deformed embryos were found in 30% of mallard 

(Anas platyrhynchos) nests and in 10% of American coot (Fulica americana) nests at a 

marsh used for Se remediation in the North Bay receiving a refinery effluent of 20 μg Se/L 

(without dilution) (Skorupa, 1998a). 

c) Selenium concentrations were below all promulgated water quality protection guidelines (2 

to 5 μg Se/L) in both the Delta and the Bay in all surveys of the Bay-Delta from 1982 to the 

mid-1990’s (Cutter, 1989; Cutter and San Diego-McGlone, 1990; Cutter et al., in 

preparation). Nevertheless, Se in the food web was sufficient to be a threat to some species 

and a concern to human health if those species were consumed (CDFG, 1988 and on-going; 

Fan et al., 1988; SJV Drainage Program, 1990b; CSFBRWQCB, 1992a; b). 

13

d) A biological opinion and formal consultation by the USFWS and NMFS (1998 and 

amended, 2000) on 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 Se jeopardizes several Bay-Delta or SJR fish [Delta smelt (Hypomesus 

transpacificus), Sacramento splittail (Pogonichthys macrolepidotus), steelhead trout 

(Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytsch], 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/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 Se/L chronic 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.
e) State permits for Se discharges to private evaporation ponds used for agricultural drainage 

disposal are limited only to a Se hazardous waste criterion of 1,000 μg Se/L (California 

Code of Regulations, 1979 and as amended). These ponds, in the Tulare basin of the 

southern SJV, are 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 (CDFG, 1987; SJV Drainage Program, 1989; 1990b). A 10-50% rate of 

embryo teratogenesis was documented during the period 1987 to 1990 (Skorupa, 1998a; b). 

An attempt to regulate evaporation ponds on the basis of field observations of bird impacts 

was not adopted in lieu of altering drainage evaporation ponds to limit bird-use (i.e., “birdfree” ponds) and provision of compensatory and alternative wetland habitat (CSWRCB, 

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%) was the highest ever reported (Skorupa, 1998a). 

f) Federal (40 CFR 131.12) and state (CCVRWQCB, 1994a; 1996a) anti-degradation policies 

may apply to the impaired water quality segment of the SJR or the groundwater aquifers of 

the SJV. In addition to the degradation of the SJR noted above, mobilization of Se by 

irrigation and contamination of ground water have resulted in concentrations of Se greater 

than 1,000 μg/L Se (a hazardous waste; California Code of Regulations, 1979 and as 

amended) in some aquifer locations of the SJV (Deverel et al., 1984). 

8. Human health advisories against consuming Se-contaminated edible tissue of fish [bluegill 

(Lepomis macrochirus) and largemouth bass (Micropterus salmodes)] and birds (ducks and 

coots) are presently posted for the SJV (CDFG, 1985 and on-going; 1986 and on-going; Fan et 

al., 1988; SJV Drainage Program, 1990b). Advisories also exist for eating birds (scoter and 

scaup) from the Bay-Delta (CDFG, 1988 and on-going). The advisories are issued when Se 

concentrations in flesh reach or exceed 2 μg/g wet weight [6-12 μg/g dw, assuming 65-85% 

moisture] (SJV Drainage Program, 1990b; Saiki et al., 1991) and restrict human consumption to 

not exceed 112 grams of flesh per one- or two-week period or 20 grams of fish or bird muscle 

per day in addition to the regular daily intake (Fan et al., 1988). Children and pregnant women 

are advised not to consume any game from the posted areas. 

9. Important gaps also occur in existing knowledge (Luoma and Fisher, 1997; Clements, 2000). 

Most Se studies have taken place in wetlands and in freshwater reservoirs. There is a deficit of 

14
knowledge about the fate and effects of Se in estuarine environments similar to the Bay-Delta, 

and important data gaps exist for specific regions of the Bay-Delta. Many of the processes and 

mechanisms that determine Se impacts may be known generically, but are less well known in 

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 Se than for many other contaminants. 

 In this paper we primarily: 

• describe Se issues and their history in the SJV, the SJR, and the Bay-Delta; 

• project potential loading of Se from the western SJV resulting from engineering solutions and 

management alternatives proposed historically; 

• detail the state of knowledge of the processes that determine the fate and effects of Se released 

to the Bay-Delta; 

• summarize existing knowledge concerning Se contamination in the Bay-Delta ecosystem; 

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

• forecast concentrations, form, bioaccumulation, trophic transfer, and effects of Se on predators 

for several load scenarios; and 

• define research needs and actions that might help narrow the uncertainties about proposed 

discharges of Se to aquatic ecosystems. 

 Selenium inputs to the Bay-Delta are changing, or could be changed, by activities expected to occur 

within the Bay-Delta and in the SJR/SJV 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 BayDelta. Scientific data and models are necessary to develop such forecasts. 

ISSUES ARE CHANGING 

 The probability is high that inputs of Se to the Bay-Delta via the SJR or an artificial conveyance 

such as the SLD will increase in the future. The SJR is the only current means (i.e., the only natural 

channel) by which Se and salts can be removed from the SJV. The SJR is hydrologically connected to 

the Bay-Delta, but recycling back to the SJV occurs via the Delta-Mendota Canal. Changes in Se 

15
discharges to the SJR will be manifested in these downstream receiving waters (i.e., 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. 

 Existing policies for the western SJV are probably not sustainable [Wanger, 1994; Stevens and 

Bensing, 1994; CSWRCB, 1997 and 1999a; d; Westlands Water District (WWD), 1996; 1998; U.S. 

House of Representatives, 1999; Hug et al., 2000]. Soil and ground water quality are deteriorating in 

un-drained lands (SJV Drainage Implementation Program, 1998); disposal sites of sufficient scale for 

collected drainage (e.g. at Kesterson National Wildlife Refuge and Tulare Basin evaporation ponds) 

have resulted in adverse ecological effects (Skorupa, 1998a). Effects of several disposal options for 

drainage have long been discussed, environmental impact reports prepared, and engineering studies of 

the problem made (Table 1) [e.g., USBR, 1962; California Department of Water Resources (CDWR), 

1965a; b; 1969, and 1974; USBR, 1978; SJV Interagency Drainage Program, 1979a; b; Brown and 

Caldwell, 1986; SJV Drainage Program, 1990a; SJV Drainage Implementation Program, 1998). As 

discussed later in more detail (also see Appendix A), many studies of Se contamination have provided 

insufficiently holistic evaluations of the problem. These studies do not adequately account for linked 

factors that determine effects of Se on the aquatic food web and higher trophic levels. 

 Salinization and Se contamination issues in the western SJV ultimately stem from the geologic 

setting, an imbalance in the hydrologic cycle, and clay layers impeding drainage (SJV Interagency 

Drainage Program, 1979a; CH2M HILL, 1988; SJV Drainage Program, 1989; 1990a). High 

evaporation rates in the semi-arid climate cause salinization of valley soils; the salts are rich in Se 

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 Se (Presser and Ohlendorf, 

1987). Where drainage has been halted, Se is accumulating in the internal reservoir of ground water in 

the SJV (SJV Drainage Program, 1990a; SJV Drainage Implementation Program, 1998; WWD, 1996; 

1998). The accumulation of salts and contaminants in ground water will, eventually, impede beneficial 

use of this resource (CSWRCB, 1985; 1987; 1994; 1999a; d; CCVRWQCB, 1988; 1996a; 1998b). 

Where drainage water is being collected, its disposal results in increases in Se contamination of surface 

water resources, with possible effects on ecological integrity (see mandated environmental reviews for 

proposed SLD in 1965, 1975, 1977, 1979, 1981, 1984, 1985, 1987, 1991, 1994, and 1999, Table 1). 

16
No feasible engineering solutions yet exist for treating irrigation drainage to remove Se from the watercolumn, at least not at the scale necessary to alleviate the problem of waste disposal (Hanna, et al., 

1990; SJV Drainage Program, 1990a; SJV Drainage Implementation Program, 1999a). 

 In August 1999, the California State Water Resources Control Board (CSWRCB, 1999d) held an 

agricultural drainage discharge workshop in which it was decided to go forward with a memorandum

of understanding that would begin permit applications and environmental documentation for a master 

drain (i.e., an extension of the SLD) to remove salts from the western SJV. As in earlier proposals, the 

final point of discharge of this drain was the Bay-Delta. This action was an effort to seek relief for 

California farmers. Environmental groups remain opposed to studying the drain as an alternative 

solution to source control implemented through a number of measures including water conservation, 

drainage reuse, and land retirement (i.e., cessation of irrigation in areas of elevated Se concentrations 

in shallow ground water). Nevertheless, during the next few years, federal and state agencies may be 

required to evaluate proposals and discharge permits that could significantly change Se inputs to the 

Bay-Delta. Particularly affected would be the SJR watershed, the south Delta, and the North Bay, 

which includes Suisun Bay and San Pablo Bay (Figures 3 through 5). 

The proposals could include the following: 

As stated above, a 100-mile extension of the existing SLD is being proposed to alleviate the 

build-up of salts in agricultural soils and the aquifers of the western SJV by removing salts 

from the valley. The SLD would convey subsurface agricultural drainage from the western SJV 

to a discharge point near Chipps Island in Suisun Bay (Figures 4 and 5). This extension of the 

SLD would result in increased Se loading to the Bay-Delta. 

• 

• Current projects allow discharge of agricultural drainage into the SJR. Renewals are underway 

of the federal agreement and state permit to allow an existing 28-mile section of the SLD to 

convey subsurface agricultural drainage to the SJR. Load targets and management alternatives 

are under negotiation. A net increase or an increase during some months (i.e., during high 

flows) in Se discharges to the SJR is possible in the future. These Se loads discharged from

this de facto drain could reach the Bay-Delta under some types of river discharge and 

management scenarios. 

• In response to state regulated salinity objectives and USEPA’s regulation of non-point source 

pollution through TMDLs (Total Maximum Daily Loads), real-time dilution of salt, Se, boron 

or dissolved oxygen could occur in portions of the SJR. This approach would change the 

17
amount and timing of Se loading to the Bay-Delta (CCVRWQCB, 1994b; 1996a; 1998a; 

CSWRCB, 1997; 1999a; USEPA, 2000) as loads are integrated with flows. 

• Linked to the above issue is proposed restoration of the SJR by increasing flows in the river to 

aid fish passage (National Resources Defense Council et al., 1988; CALFED, 1999a; URS 

Greiner Woodward Clyde, 2000). 

• Changes in Se inputs will also be influenced by decisions about drainage of salts from the SJV. 

A recent state water right decision requiring the USBR to meet salinity objectives at Vernalis 

on the SJR and at three locations in the interior of the southern Delta (CSWRCB, 1994; 1997; 

1999a; EA Engineering, Science and Technology, 1999) and a state program aimed at salt 

reduction (CCVRWQCB, 2000a) will affect management alternatives. Currently, the salinity 

objectives adopted in 1991 are violated most months of the year (67 to 78 % from 1986 to 

1998). 

• Physical changes in water management could result in greater inflows into the Bay-Delta from

the Se-laden SJR. The 1994 Bay-Delta Water Accord (CSWRCB, 1994) mandated greater 

inflows to the Bay-Delta from the SJR. Inflows of Se from the SJR have traditionally been 

small compared to other sources (Cutter, 1989; Cutter and San Diego-McGlone, 1990; Johns et 

al., 1988), because most of the flow of the SJR was recycled back through the Delta-Mendota 

Canal to the SJV before it reached the Bay-Delta (Figures 3 and 5). Changes in water 

management could reduce recycling and thus increase throughput to the Bay-Delta. 

• Construction of an isolated conveyance facility (a Peripheral-Canal-like water conveyance 

alternative) or modifications of current diversion and export channel dimensions could also 

result in an exchange of Sacramento River inflow for SJR inflow to the Bay-Delta (CALFED, 

1998a; b). Any activity that results in more SJR inflow entering the Delta or Bay will result in 

more Se input to areas that are part of the recently enacted Bay-Delta Ecosystem Restoration 

Plan (CALFED, 1998a; b and 1999a; b; c; d). 

• Refineries have reduced their Se discharges due to mass emissions reduction regulations (Table 

2) (CSFBRWQCB, 1992a; b; 1993). In July 1998 refineries were required to meet the goals set 

by the CSFBRWQCB (1996; 1997). This means that concentrations of at least some forms of 

Se (i.e., selenite) in the Bay-Delta are decreasing (Cutter et al., in preparation), and that the 

predominant cycling pathways could change. In Belews Lake, North Carolina, for example 

18
(Lemly, 1997a), exposures of fish to Se changed from water column-based pathways to 

sediment-detrital pathways after sources were eliminated. 

• Refinery Se was dominated by selenite; Se from the SJV is dominated by selenate, with some

apparent conversions to organo-Se in receiving waters (Cutter, 1989; Cutter and San DiegoMcGlone, 1990, CSFBRWQCB, 1992a; b; 1996; 1997). Thus the predominant biogeochemical 

transformation pathways and bioavailability of Se could change as the predominant sources to 

the Bay-Delta change. 

• 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 (another possible 

outcome of changes in water management) could result in increased residence times in the BayDelta 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 et al., 1985). Longer hydraulic residence times seem to be associated with greater Se 

contamination in the food web (Lemly, 1997a; Zhang and Moore, 1997a; Skorupa, 1998a). 

 Biological changes also are occurring in the ecosystem, and some of these appear to affect Se 

cycling. These changes include: 

• The dominant consumer organism in the Bay-Delta changed with the invasion of the Asian 

clam Potamocorbula amurensis in 1986 (Nichols et al., 1986; Carlton et al., 1990; Brown and 

Luoma, 1995b). It is possible that this species is especially efficient at bioaccumulating Se, 

although studies directly addressing the mechanisms of Se bioaccumulation by P. amurensis

are not yet complete (Brown and Luoma, 1995a; Luoma and Linville, 1997; Linville and 

Luoma, in press). 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 et al., 1989; Nichols et al., 1986). 

• One implicit goal of a successful restoration is to develop a more complex, native speciesdominated 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 raises 

the question of the compatibility of existing or greater levels of Se contamination with 

restoration goals. 

19
• The cause of the declines of some key species in the Bay-Delta (e.g. white sturgeon, 

Sacramento splittail, starry flounder, surf scoter) may include Se effects on reproduction and 

ultimately, survival of the population. Increased Se in the Bay-Delta could increase that threat. 

• Marsh restoration in the Bay-Delta, if accompanied by increased Se discharges, could result in 

trapping and recycling of increased quantities of Se in the system, with the possibility of greater 

Se contamination in some species. Under the worst scenarios, it is conceivable that 

management of concomitant issues—water and salt management—rather than Se contamination 

could create another ecological crisis in the Bay-Delta similar to that created at Kesterson 

National Wildlife Refuge. 

 Refinements of Se water quality criteria, especially for the Bay-Delta, also are likely. The current 

USEPA promulgated national Se chronic criterion for the protection of aquatic life (5 μg Se/L) is based 

upon bioaccumulation-related toxicity observed in Belews Lake and Hyco Reservoir (USEPA, 1987 

and 1992). The USFWS recommends a criterion of 2 μg Se/L, based upon a series of case studies of 

Se contamination and effects on birds in western wetlands (Skorupa, 1998a; USFWS and NMFS, 1998 

and amended 2000). The Canadian criterion for wildlife protection is 1 μg Se/L (Environment 

Canada/Health Canada, 1995; Outridge et al., 1999). The technical limitations of the basis for the 

existing water quality criteria raise questions about their suitability as the sole standard to assure 

protection of the Bay-Delta. As stated previously, Se concentrations were below all recommended 

guidelines in both the Delta and the Bay in the latest surveys in 1996. Nevertheless, Se in the food web 

was sufficient to be a threat to some species and a concern to human health if those species were 

consumed (Table 2) (Linville and Luoma, in press; CDFG, 1988 and on-going; Fan et al., 1988; 

CSFBRWQCB, 1992a; b). The Bay-Delta is probably best suited for site-specific Se guidelines, but 

the details of such guidelines have yet to be identified. 

APPROACH TO UNDERSTANDING CHANGING ISSUES 

In this evaluation of Se issues we systematically describe the linked factors that determine effects 

of Se on aquatic food webs and higher trophic levels (see conceptual model, Figure 2). This holistic 

approach to the issue differs from earlier attempts to skip links in tying waterborne Se to the effects of 

the element. We propose that the holistic approach offers opportunities to more accurately project 

20
ecological effects from loads and to identify resolutions of the difficult questions involved. The steps 

that are considered include: 

• Projecting loads from the potential sources of Se. Selenium loads projected from available data 

on concentration and drainage volume provide the basis for determining the upper and lower 

limits of Se discharge from the western SJV that can be expected to enter the Bay-Delta via 

either a proposed direct conveyance to the Bay-Delta or the SJR. Analyzing the annual, 

monthly, daily, and hourly variability of Se loading is necessary to address trends and patterns 

in discharges. The accuracy of Se load calculations on any time-scale is dependent on the 

number and frequency of the measurements taken to determine flow and Se concentration 

(Presser et. al., 1996). Large uncertainties are associated with data compiled for annual average 

loads of Se from agricultural and natural sources. Annualized, generalized averages of 

concentration, flow, and load hide infrequent samplings, sampling that does not reflect flowdependent concentration changes, or spatially dispersed samplings. Annual average data used 

here, although documented as to source and type (see Appendices A through D), should be used 

with caution and are applied here to obtain ranges of projected Se loads. 

• Identifying implications of the modes of conveyance that determine transport of those Se loads 

to the Bay-Delta. A SLD extension or the SJR are the most likely modes of conveyance 

(Figures 3 and 5). The SJR was mostly recycled during the period when studies of Se were 

conducted in 1986 to 1990, so little Se reached the Bay-Delta from this source. The passage of 

SJR inflows into and through the Delta is not well known at present, but hydrologic models 

exist that can be used as frameworks for future modeling (e.g. Cheng et al., 1993; Monsen, 

2000). Throughput of SJR inflows could be influenced by changes in water management to aid 

fish passage including construction of elaborate Delta barriers and scheduling of flushing flows. 

If a SLD extension is constructed to Chipps Island in the Delta (Figures 4 and 5), Se and salts 

from the soils of the SJV would be released directly into the Bay-Delta. 

• Identifying effects of projected loads on concentrations in receiving waters. Loads and 

seasonal variability in Sacramento River and SJR discharges are critical considerations in 

determining concentrations in the Bay-Delta. 

• Identifying changes in and implications of biogeochemical speciation of Se and biogeochemical 

transformations of Se between dissolved and particulate forms. Speciation of Se is critical in 

that it drives routes and efficiency of transformation of Se from dissolved to particulate forms. 

21
Understanding particulate Se and its speciation cycle is critical in determining biological 

effects. 

• Incorporating factors controlling the bioavailability and biotransfer of Se to macroinvertebrate 

primary consumers under the different concentration and speciation conditions. 

Bioaccumulation of Se is primarily determined by the form and concentration of particulate Se 

(food). 

• Determining exposure of sensitive predators from projected Se concentrations in invertebrate 

and vertebrate prey in the Bay-Delta ecosystem. Existing data from 1988 to 1999 for Se 

concentrations in bioindicator clams show elevated levels compared to uncontaminated 

reference areas (Johns et al., 1988; Brown and Luoma, 1995a; Luoma and Linville, 1997; 

Linville and Luoma, in press). Exposure of predators is determined by the level of 

bioaccumulated Se in these prey organisms (CSFBRWQCB, 1992a; b; 1993; 1996; 1997). 

• Estimating effects of Se 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 et al., 1985; Nichols et al., 1986; Davis 

et al., 1991; Harvey et al., 1992; Monroe et al., 1992; and USFWS, 1995). Many threatened 

species are not resident in the system all year. Through 1996, both Se concentrations in tissue 

of predators and in their food pointed to threats to the reproductive health of the predators 

(White et al., 1987; 1988; 1989; Cutter, 1989; Johns, et al., 1988; Cutter and San DiegoMcGlone, 1990; Urquhart and Regalado, 1991; San Francisco Estuary Project, 1991; 1992; 

CSFBRWQCB, 1992a; b; Luoma et al., 1992; Brown and Luoma, 1995a; Luoma and Linville, 

1997; Linville and Luoma, in press). However, such estimates of risk are derived from

laboratory and field studies conducted elsewhere (USEPA, 1998; Lemly, 1993a; 1995; 1996a;

1998a; Skorupa, 1998a; Engberg et al., 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 

The major sources of the Se in the Bay-Delta are (Figures 4 and 5): 

22
discharges of irrigation drainage conveyed from agricultural lands of the western SJV via the 

SJR or potentially from an extension of the SLD; 

• 

• 

• 

effluents from the North Bay refineries which refine crude oil from the western SJV along with 

crude oil from other sources; 

Sacramento River inflows which is the dominant freshwater inflows (high water volume) to the 

Bay-Delta; and 

Effluents from Bay-Delta wastewater treatment plants and industries other than refineries are minor 

sources of Se (Cutter and San Diego-McGlone, 1990) and will not be considered further. 

Inputs of Selenium from Agriculture in the Western San Joaquin Valley 

The problem

 The Coast Ranges, which border the SJV on the west, are composed of marine sedimentary rocks 

that are enriched in Se (Figures 3 and 5) (Presser and Ohlendorf, 1987; Presser et al., 1990). An 

internal reservoir of salt (and by inference Se) has accumulated through 1.0 to 1.2 million years within 

the SJV 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 et al., 1989; Presser et al., 1990; Presser 

et al., 1994; Presser, 1994b). The most Se-rich region of the SJV is the Panoche Creek alluvial fan 

which supports intensively irrigated land (Tidball et al., 1986; 1989). Salts and Se build-up on soils as 

a result of both the arid climate (i.e., less than 10 inches of precipitation and greater than 90 inches of 

evaporation) and poor drainage (i.e., clay layers impede downward movement of water causing waterlogging of the root zone). 

 The SJV has a net negative annual water budget (evaporation exceeds precipitation). Prior to 

development of the water management system, a permanent shallow groundwater table only occurred 

in groundwater discharge zones near the SJV 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. 

 Massive irrigation leaches salt and Se and moves them into aquifers and surface waters. Installation 

of subsurface drains increases the speed, volume, and control of the drainage of shallow groundwater 

that impedes agricultural production. Collection of drainage from irrigated soils in drainage canals 

23
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 SJV (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) (Figures 3 and 5). 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; CDWR, 1979). Simple water and mass balance observations explain the 

attractiveness of an engineering solution that would increase salt and water discharge from the SJV. 

 

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

 In planning for the 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; SJV 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 SJV. Planned volume of drainage discharge increased over the 100-year 

management 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 SLD, with a slowing in the rate 

of increase after 40 years (Appendix A, Figure A3). 

 The geohydrologic balance of Se (or salt) ultimately determines the degree of contamination buildup in the SJV (Appendix A, Tables A2 and A3). The primary geologic inventory of Se in the Coast 

Ranges is the ultimate source of influx. Drainage from the SJV is the source of efflux, whether natural 

or artificially accelerated by engineering means. The internal reservoir of labile Se in SJV is growing 

because the rate of removal of Se-enriched salts from the valley is naturally slow. In general, 

calculations of the amounts of Se in the reservoir within the Panoche Creek alluvial fan also confirm

the massive nature of Se accumulation in the SJV. Calculations based on two scenarios (Appendix A, 

24
Tables A2 and A3) show that no long-term reduction in Se discharge would be expected for 63 to 304 

years at the lower range of reservoir projections, even if influx of Se from the Coast Ranges could be 

curtailed. Drainage of wastewaters outside of the SJV may slow the degradation of SJV resources, but 

drainage alone cannot alleviate the salt and Se buildup in the SJV, at least within a century, even if no 

further inputs of Se from the Coast Ranges occur. On a current, specific scale: 1) the Panoche Creek 

upper watershed Se load is a small percentage of the total annual load except during infrequent large 

magnitude storms (Presser et al., 1990; Appendix B, Table B8); and 2) in 1998 (a wet year), 16% of 

the Panoche Creek load was in the dissolved fraction and 84% was in the suspended fraction 

(Appendix A, Table A3; U.S. Geological Survey, 1999; Kratzer, et al., in press). Selenium

concentrations in sediment samples, however, were relatively low historically and in 1998 (1-2 μg/g), 

depending on the large mass of sediment eroded during storms to accounts for the large loading of Se 

during runoff (Presser, et al., 1990; Presser, unpublished data). Dissolved Se 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, et al., in press). 

Selenium concentrations in source waters 

 The effect of the large reservoir of Se calculated above can be seen in the quality of the ground 

water in the western SJV (Table 3). Extensive measurement and study of the groundwater aquifers in 

the SJV have been made since 1917, but Se concentration analyses were not a part of water quality 

studies until the 1980’s (Mendenhall et al., 1916; Davis and Poland, 1957; Presser and Barnes, 1984; 

1985; Deverel et al., 1984; SJV Drainage Program, 1989; 1990a). Average Se concentrations in 

drainage sumps in the area of the Panoche Creek alluvial fan range from 140 to 4,200 μg Se/L (Presser 

and Barnes, 1985). These concentrations are reflective of shallow groundwater conditions as opposed 

to managed drainage, which may be blended. Studies in 1989 in the area of the Panoche Creek alluvial 

fan showed Se concentrations ranged from 96 to 7,300 μg/L Se in individual sump discharges or well 

samples at depths up to 50 feet below land surface in areas served by subsurface drains (Gilliom et al., 

1989) (Table 3). The Se concentrations depended, in part, on the number of years the fields were 

drained. The concentration of Se in subsurface drain water in the area of the wells ranged from 400 to 

1,000 μg/L Se. A more recent compilation used in the evidentiary process (Wanger, 1994; Stevens and 

Bensing, 1994; WWD, 1996) and in regulatory planning shows concentrations in shallow groundwater 

25
range from 75 to 277 μg/L Se (range of means) (SJV Drainage Program, 1990a; CCVRWQCB, 1996c; 

d) (Table 3). Data presented in testimony and by the state (Table 3) project an average concentration 

of Se in shallow ground water and hence, subsurface drainage, of at least 150 μg/L Se in the farming 

areas affected by the Panoche Creek alluvial fan. 

 Most Se concentrations in shallow ground water listed in Table 3 are above those concentrations of 

blended discharges presently regulated as oil refinery effluents (50 μg/L Se) and above the 

concentration estimated that is possible with treatment (50 μg/L Se) (WWD, 1996). Most Se 

concentrations in currently regulated discharges to evaporation ponds in the southern SJV (Tulare and 

Kern subareas, Figures 3 and 5) are above those associated with avian risk, and consequently 

dischargers are required to provide mitigation and alternative habitat (CSWRCB, 1996c). 

 The effect of the large reservoir of Se on recent subsurface drainage flow and quality is generalized 

from data collected during frequent sampling of drainage source water (i.e. current agricultural 

discharges to the SJR in WY 1997 and 1998 from the Grassland subarea, see Appendix B, Tables B9 

and B10; and Appendix D) (USBR et al., 1998; 1999). Selenium concentrations in drainage are not 

diluted when the volume of drainage increases, except in infrequent, extreme precipitation events 

(Figure 6). Generally, more input of water to western SJV soils results in more Se transport and 

increased Se load with increased hydraulic discharge. These observations from recently collected data 

confirm the effect of irrigation in creating increased Se loads from the SJV. When considering Se 

source waters as opposed to receiving waters, Se concentration in source waters will increase as more 

irrigation water is applied and more discharge occurs. Therefore, Se loads increase over those seen 

without irrigation. Testimony in the state water right hearing similarly confirm that the action of 

irrigation supply (mainly from the Central Valley Project) is the principal cause of the drainage 

discharge of salinity, and hence, the cause of violations of water quality objectives for salinity for the 

Bay-Delta (CSWRCB, 1999a). 

26

 Removal of salt (and Se) also is slowed by the recycling of the SJR (Figure 5). The SJR can be 

almost completely diverted back into the SJV before it enters 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). The recycled SJR water is then used again in irrigation. As noted above, the degree of 

recycling is determined by water management. Water management began changing toward less 

recycling in 1994 and direct throughput of the SJR may increase in the years ahead to help restore SJR 
fish and fish habitat. A reduction in recycling and an increase in drainage discharge during seasons of 

elevated flows are strategies for slowing the salinization of agricultural soils. However, management 

to meet all goals including meeting the salinity standard for the SJR at Vernalis is complex. Strategies 

may include the need for storage or holding ponds to optimize timed release of drainage and meet the 

salinity standards for the SJR at Vernalis. Agricultural drainage outputs are not, in general, 

coordinated with periods of high river flows (Appendix A, Figure A11). 

Drainage management

Management plans have discussed “in-valley” and “out-of-valley” drainage management 

alternatives. “In-valley” solutions imply local storage and treatment of Se-rich drainage. Satisfactory 

treatment technologies have not yet been demonstrated and storage does not seem sustainable (SJV 

Drainage Program, 1990a). “Out-of-valley” solutions mean export of the salt-laden drainage (and its Se 

load) to somewhere else. The most frequently mentioned of these solutions is an extension of the SLD 

with discharge to the Bay-Delta. 

 Planning for a drain to carry salt-laden irrigation return water (and the accompanying Se) from the 

SJV began in 1955 (Table 1). An 85-mile section of the SLD was completed in 1975, to collect 

irrigation drainage water from one section of the valley, the WWD (i.e., Figures 3 and 5, Westlands 

subarea). The SLD began discharging concentrated drainage water in 1981 to Kesterson National 

Wildlife Refuge (Figures 3 and 5), 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 twelve ponds, at the discharge 

point of the agricultural drainage. Subsequent monitoring revealed elevated levels of Se in the 

organisms within the ponds (Saiki and Lowe, 1987). Avian deformities were ultimately linked to Se 

exposure from food chain contamination (Ohlendorf et al., 1986; Presser and Ohlendorf, 1987). The 

SLD 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 Se concentrations persist in the remediated terrestrial ecosystem at 

Kesterson Reservoir (CH2M Hill, 1996; 1997; 1999a; 1999b; Presser and Piper, 1998). 

 Management of Se differed among regions (subareas) in the SJV in the 1990’s. The five subareas 

(i.e., Northern, Grassland, Westlands, Tulare, and Kern) of the western SJV were designated based on 

27
hydrologic and geologic features and on options for management of irrigation and agricultural 

wastewater discharge (SJV Drainage Program, 1990a) (Figures 3 and 5). Selenium-laden wastewater 

is stored as ground water in some areas of the valley. In others, drainage is collected in privately 

owned evaporation ponds located on farms, although reproductive impacts, including teratogenesis 

(deformation of young) and death of avian offspring, were observed in some of these ponds and 

associated wetlands (Skorupa, 1998a). Some drainage is discharged into collector canals, sloughs, and 

wetlands that eventually discharge into the SJR. The Grassland Bypass Channel Project was 

implemented in 1995 [i.e., water year 1996 (WY 1996); a water year begins in October] to again begin 

to collect drainage from one area of problem lands and transport drainage via the SLD to outside the 

SJV. Drainage from the SLD is currently discharged into Mud Slough, a tributary of the SJR (Figures 

3 and 5). The goal is to remove drainage inputs from wetland supply channels, a national wildlife 

refuge, and a state wildlife area by shifting drainage discharges further downstream into the SJR. 

Degradation is occurring in a smaller area of ecosystems while phased-in management activities 

potentially reduce loads from historic levels and thus attempt to comply with water quality standards 

(USBR, 1995; USBR et al., 1998; 1999). 

Forecasting loads of selenium: general consideratons

 The problem of progressive soil salinization and the build-up of ground water contamination could 

require collection of drainage from larger and larger areas of the SJV if agricultural activities continue 

and a drainage outlet is available. A realistic, long-term evaluation of the potential for Se discharge 

must fully consider both the present and the potential future extent of the problem (Appendix B). 

 Identification and classification of problem lands in the SJV took place as early as 1930 (Ogden, 

1988). Since the 1950’s, technical studies have estimated the extent of the acreage requiring drainage 

under varying conditions of water import, water export, salinity, and groundwater 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 CVP’s 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 SJV Drainage Program conducted “comprehensive studies to identify the 

magnitude and sources of the drainage problem, the toxic effects of selenium on wildlife, and what 

28
actions need to be taken to resolve these issues” (SJV Drainage Program, 1989). Between 1985 and 

1990, the joint federal/state program (SJV Drainage Program, 1990a) predicted areas of problem 

acreage (land characterized by water-logging and related water quality problems) and volumes of 

problem water (the annual drainage water volume that must be managed because of adverse impacts to 

agriculture or aquatic resources) (Appendix B). The program developed an “in-valley” management 

plan for agricultural subsurface drainage with specific management alternatives (SJV 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 SJV Drainage 

Program’s regional studies and data provide much of the information used in our assessment of loads 

from the subareas of the SJV (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 Se 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 SJV Drainage Program. Recommendations for treatment techniques were not included because 

success of technology on a large-scale was not proven as of 1990 (SJV Drainage Program, 1990a). 

Implementation of the management plan was only partial and systematic monitoring and data analysis 

has not occurred (SJV Drainage Implementation Program, 1998). 

 The SJV Drainage Program management plan (1990a) estimated a problem area of 444,000 acres 

would create 314,000 acre-feet (AF) 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-feet by year 2040. 

For these estimates of acreage, the SJV Drainage Program used a criterion of sufficiently elevated 

salinity and boron concentrations in ground water to limit use of the water and affect crop selection 

(i.e., lands with an actual drainage problem). The SJV 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 feet 

of land surface. Using this criterion, estimates ranges from 765,000 acres in 1990, to 918,000 acres in 

year 2000, to 1,057,000 acres in year 2040. Using the criterion of lands contributing the largest 

percentage of selenium to drainage discharge (i.e., lands overlying areas of shallow ground water with 

selenium concentrations of greater than 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 

29
2040 if the SJV Drainage Program management plan was not implemented. Land retirement 

recommended by the SJV Drainage Program by 2000 was 21,000 acres and by 2040, 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 (Table 1, 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 right hearings, the total acreage of lands impacted by rising water tables and increasing 

salinity is approximately 1,000,000 acres in the SJV (CSWRCB, 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 (U.S. Department of the Interior, 1999; 

SJV Drainage Implementation Program, 1999b). 

How to determine load

One approach to forecasting Se loads is to examine historic records and planning efforts for 

agricultural discharges with the goal of developing relations between acreage, drainage generated or 

discharged, Se concentration, and load of Se. Forecasts in this report were based on historical, 

annualized drainage volumes and assigned concentrations 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 Se distribution and 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 Se loads involves three factors (SJV Drainage Program, 1990a): 

• Acreage requiring drainage. Acreage is expressed as either the extent of problem acres or tiledrained acres. Problem acres generate a generic problem water as an expression of the extent 

of affected acres. In our context, 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 our 

analysis, the distinction made between problem water and subsurface drainage helps in 

forecasting 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). 

30
The average annual volume of problem water generated from problem lands under conditions 

in 1990 was estimated as 0.7 acre-feet per acre per year (SJV Drainage Program, 1990a). The 

SJV Drainage Program predicted that changes in on-farm drainage management practices could 

reduce the volume generated to approximately 0.4 acre-feet 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-feet per year (Appendix B, Table B8). An average annual pollution abatement objective of 

0.2 acre-feet per acre per year has been considered as necessary to meet Se load limits in the 

Grassland subarea (Environmental Defense Fund, 1994). 

• The concentration of Se in the irrigation drainage. Reconnaissance-level data on Se 

concentrations in shallow ground waters are available from all areas (Table 3) (Deverel et al., 

1984; SJV Drainage Program, 1989; 1990a). The concentration of Se in effluent drainage 

reflects a managed balance of input, output, and storage. Treatment technologies (mostly 

unspecified) or dilution with Se-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 Se (e.g., SJV 

Drainage Program, 1990a). 

 All three factors can vary greatly depending upon assumptions about management strategies. Two 

possible alternative management futures were defined by SJV Drainage Program: 1) no 

implementation of the SJV Drainage Program management plan, 0.60 to 0.75 acre-feet per acre per 

year generated drainage, namely, “without future” and 2) with implementation of the SJV Drainage 

Program management plan, 0.40 acre-feet per acre per year generated drainage, namely, “with future” 

(SJV Drainage Program 1989 and 1990a). A third condition defined for use in our projections is called 

“with targeted future”. The “targeted future” condition applies a factor of 0.20 acre-feet 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 SJV Drainage 

Program plan were implemented, the amount of drainage would be reduced to 0.4 acre-feet per acre per 

year, but the total land in production would be preserved. 

 We employ a mixture of metric and English units in the forecasts and the following discussion. 

This is unconventional for a scientific report, but is done here to aid communicating our study to the 

31
widest audience in the most recognizable terms. The agricultural discharges of Se are expressed as 

loads of Se in pounds (lbs); area is described in acres and volume of discharge is expressed in acre-feet 

(AF) or million acre-feet (MAF); Se concentrations are expressed as μg Se/L (equivalent to the 

regulatory term ppb), or μg Se/g (equivalent to the regulatory term ppm). Conversion between these 

units and scientific units, which are used in the analysis of Se ecological effects, can be found in Table 

4. Selenium load (in pounds) is calculated using the equation: 

[Se concentration (μg Se/L or ppb) X volume of drainage (acre-feet)] X 0.00272 = load of Se (lbs), 

or 

[Se concentration (μg/L) X [(acres) X (acre-feet per acre)] X 0.00272 = load of Se (lbs), 

where 0.00272 lbs Se per acre-foot is equal to a concentration of one part per billion (μg/L) Se in an 

acre-foot of water. 

 

Characteristics of agricultural subareas 

 The links between demands for drainage and estimates of potential loadings of Se require 

consideration of specific agricultural subareas in the SJV (i.e., Northern, Grassland, Westland, Tulare, 

and Kern subareas, Figures 3, 5 and Appendix B). Evaluation of issues requires understanding the 

history, agricultural activity, and geohydrologic characteristics of these subareas. A brief summary is 

given below for each subarea designated by the SJV Drainage Program (1989 and 1990a). Data given 

in bold in parentheses is from the SJV Drainage Program (1989). 

• Westlands Water District (WWD) and Subarea (770,000 total acres; 576,000 irrigated acres; 

5,000 acres with subsurface drains, relieving salinization in 42,000 acres). 

The Westland subarea (Figures 3 and 5) was the first to discharge irrigation drainage to the SLD, as 

noted above. This drainage was released into Kesterson National Wildlife Refuge from 1981 to 1986. 

As a result of the ecological crisis associated with the Kesterson National Wildlife Refuge, Westlands 

subarea now has a "no discharge" policy. Drainage is recycled onto farmlands and/or “stored” in the 

underlying groundwater aquifers, where irrigation and aquifer supplies are used for dilution. 

Currently, as a result of a U.S. Court of Appeals decision (Hug et al., 2000), the USBR is ordered to 

initiate the process to provide drainage service to the San Luis Unit. The specifics of such drainage 

service have not been provided. 

32
 The data record from the Westland subarea is particularly limited with no specific monitoring for Se 

since closure of the SLD in 1986. Only data on groundwater elevations are available in the area most 

impacted by geologic sources of Se (WWD, 1998). This area is potentially the greatest generator of Se 

load in the SJV because it, more than any other subarea, encompasses the Panoche Creek alluvial fan 

area (Presser et al., 1990). This fan and interfan area receive the most seleniferous runoff and erosion 

from the Coast Ranges (Tidball et al., 1986; 1989; Presser, 1994b). Used here are the estimates of 

areas of shallow groundwater that impact farming presented in management plans, testimony, and a 

recent status report by WWD (1996; 1998). Westlands Water District contended (CSWRCB, 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 WWD 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-feet of drainage per year (e.g., 200,000 acres X 

0.3 acre-feet per acre = 60,000 acre-feet) (USBR, 1992; WWD, 1996) (Appendix B, Table B2). No 

formal long-term stipulations control the ultimate fate of the drainage water in the WWD, but pressure 

to discharge Westlands subarea drainage into a completed SLD extension to the Bay-Delta is 

increasing as lands become waterlogged, the quality of the soils declines, and ground water quality 

declines. 

 Because discharges from the Westlands subarea were discontinued in 1986, no current direct 

measurements of effluent quality are available. Historic discharges provide some guidance. Average 

Se concentrations that were discharged to Kesterson National Wildlife Refuge from the historic SLD 

ranged from 330-430 μg/L Se in 1983 and 1984 (CSWRCB, 1985; Presser and Barnes, 1984; 1985) 

and as quoted from regulatory documents, from 230-350 μg Se/L (Table 3) (WWD, 1996). This 

resulted in 4,776 lbs per year of Se discharge and a discharge of 17,400 lbs to Kesterson Reservoir over 

the period of discharge (USBR, 1986) (Appendix B, Table B1). We will term a cumulative 17,400 lbs 

load of Se as 1 kesterson (kst). The use of this unit provides perspective on the quantity of Se that was 

a hazard to wildlife when released directly to a wetland (Presser and Piper, 1998). 

 Testimony in recent legal proceedings summarized the data for Se in broader areas of shallow 

ground water in the WWD (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 Se concentration in shallow 

33
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; 311,000-329,000 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 SJV is to the north and downslope of the WWD (Figure 3; SJV Drainage Program, 1990a). 

The Grassland subarea contains 70,000 to 100,000 acres of land that have historically contributed the 

majority of subsurface drainage to the SJR (Appendix B, Table B3). The adjacent Grassland federal, 

state, and private riparian wetlands contain the largest tract of habitat remaining in the SJV. Varying 

lengths of the complex channel system within the wetlands have been and are currently utilized to 

convey agricultural drainage to the SJR. Mud and Salt Sloughs (Figures 3 and 5) are examples of 

tributaries that flow through the wetlands of the Grassland Resource Conservation District and the San 

Luis National Wildlife Refuge Complex. In 1995, the discharge from approximately 100,000 acres of 

farmland was consolidated into a 28-mile segment of the original SLD (renamed the Grassland Bypass 

Channel Project) in order to reduce contaminated wetland water supplies, but the inputs to the SJR 

remain unchanged (USBR, 1995). 

 The available historical record from the Grassland subarea includes data from discharges to the SJR 

that were collected mainly to compare Se concentrations in the river to water quality objectives (Table 

5; Appendix B, Tables B4 to B7; and Appendix C, Figure C1). Only recently have measurements or 

estimates of flow been conducted consistently, so limited data exists to determine Se loads (USBR et 

al., 1998; 1999). Historic data from the CCVRWQCB that document Se and salt loading to the SJR 

were recently reviewed (CCVRWQCB, 1998f). Limitations were described in measuring flow and 

concentration and in the methodology used to calculate loads and regulatory targets. 

 The effects of Se discharges on water quality are monitored for the SJR at Crows Landing (below 

Mud and Salt Sloughs and downstream of the Merced River), Patterson, and Vernalis (Figures 3 and 

5), where the SJR enters the Delta (Table 5). The monitoring shows that: 

o The load of Se is variable from year-to-year from 1986 to 1998. Loads vary at the upstream

source from 5,083 to 11,875 lbs per year among years; at Crow’s Landing they vary from 3,064 

to 14,291 lbs per year (Table 5). 

o The variability in load is at least partly driven by precipitation, with larger loads in wet years 

than in dry years (Appendix A, Figures A9 and A10). 

34
o Estimated Se loads in the source waters (i.e., agricultural drains or canals) differ from load 

estimates for the SJR monitoring sites. Some downstream estimates are higher and some are 

lower than the drainage source estimates. The difference among sites is usually small compared 

to the year-to-year variability in the initial load except for unusually wet years (e.g., 1995 and 

1998). Reductions in downstream loads may occur because of uptake by sediment and biota 

(Presser and Piper, 1998). 

o Besides biochemical reactions, some of the variability among sites undoubtedly occurs because 

the monitoring data have important deficiencies (Presser and Piper, 1998). As of 1999, the 

monitoring did not include determinations of particulate Se, Se speciation, Se in sediments, or 

sufficiently frequent analyses to accurately depict loading during variable flows. Discharge 

schemes that involve regulating concentrations or loads in the SJR will require more reliable 

monitoring. 

 Despite some deficiencies, Se concentrations in the drainage from the Grassland subarea are better 

documented than in other subareas. Monthly average total Se concentrations in blended drainage 

ranged from 40 to 105 μg Se/L in 1997 and 1998 (USBR et al., 1998; 1999) (Appendix B, Tables B9 

and B10). The daily range was 15 to 128 μg Se/L over this period (Appendix D, Figures D15 and 

D16). The annual average Se concentration observed in collected drainage from the Grassland area 

was 62 μg/L in WY 1997 and 67 μg/L in WY 1998 (Table 5 and Appendix A, Tables B9 and B10) 

(USBR et al., 1998; 1999). These averages are comparable to the historical average of 64 μg/L from

1986 to 1994 (Table 3) (CCVRWQCB, 1998 d; e; f; g; h). Modeled discharges from the Grassland 

subarea have estimated 80 to 150 μg/L Se (Table 3) (SJV Drainage Program, 1990a; CCVRWQCB, 

1996a; b). 

• Tulare subarea (883,000 total acres; 506,000-551,000 irrigated acres; 42,000 drained acres) and 

Kern Subarea (1,210,000 total acres; 686,000 irrigated acres; 11,000 drained acres) 

Tulare and Kern subareas are located in the southern SJV and discharge to privately owned 

evaporation ponds. Sixteen ponds (5,900 acres) were initially developed from approximately 1975 to 

1990 in the Tulare subarea and ponds covered 1,300 acres of ponds in the Kern subarea (SJV Drainage 

Program, 1989). Since that time, no new ponds have been built and many ponds have been closed, 

CCVRWQCB, 1997; 1998c) (Appendix B, Tables B19 to B21). The subareas are internally drained 

basins with relict lakebeds (i.e., Tulare, Goose, Buena Vista, and Kern) as dominant geologic features. 

35
The lakebeds are little influenced by the Panoche Creek alluvial fan but are surrounded by geologic 

sources of trace elements from both the Coast Ranges and Sierra Nevada. Water quality is 

characterized by elevated concentrations of Se, uranium, arsenic, molybdenum, and boron (Fujii and 

Swain, 1995). The geochemistry is controlled in part by oxidizing and reducing zones in the lakebeds 

and surrounding alluvial fan and basin zones. Geomorphological features affect the placement and 

number of subsurface drains installed in the subareas. Delineated water quality zones affect the 

chemical composition of the discharge to specific evaporation ponds. Currently, subsurface drains are 

mainly limited to lower elevations of the lakebeds (42,000 acres in Tulare subarea and 11,000 acres in 

Kern subarea) (SJV Drainage Program, 1989). 

 Current estimates of acreage adversely affected by shallow ground water are “gross estimates” due 

to sparse data and extrapolation over a 696,000-acre study-area selected for coverage by the CDWR

(1997). The study area boundaries differ from those given above as part of the SJV Drainage program

designation. The CDWR has historically studied an area called the Tulare Lake region. Estimates 

based on data collected by the CDWR after 1991 are considered of some worth and could be used in 

future comparisons, but historic baseline values are suspect. The current disposition of ground water 

within 0 to 15 feet is unclear from the reported CDWR “gross estimates”. Initial estimates made by the 

SJV Drainage Program (1989) show the Tulare subarea with 320,000 acres of land with ground-water 

levels within 5 feet of land surface. Estimates for the Kern subarea show 64,000 acres are affected. 

For year 2000, the SJV Drainage Program estimates of affected acres increase to 366,000 in Tulare and 

100,000 acres in Kern subarea. 

 The Se monitoring in Tulare and Kern subareas is limited to annual reporting by dischargers as 

required by the state as part of permit requirements for discharges to privately owned evaporation 

ponds (CCVRWQCB, 1993; 1997; 1998c; CSWRCB, 1996a; CCVRWQCB, Anthony Toto, personal 

communication, 1998) (Appendix B, Tables B19 to B21). Any discharges to evaporation ponds must 

be considered in estimates of valley-wide Se loads, although it is not clear, in view of the impacts to 

waterfowl populations (Skorupa, 1998a), whether these discharges will continue. Discharge from the 

Tulare subarea to private evaporation ponds is remarkable for being low in Se concentration when 

compared to the Se concentration in discharge from Westlands or Grassland subareas. The record is 

limited, but values measured in 1988, 1989 and 1993 through 1997 show most concentrations were 

below 10 μg/L Se, with the exception being the South Tulare Lake Drainage District discharge of up to 

30 μg/L Se. Some higher Se concentrations, ranging up to 760 μg/L Se, have been reported in some

36
discharges to smaller ponds (Table 3 and Appendix B, Tables B19 to B21). For the Kern subarea, 

limited data on inflows to evaporation ponds in 1988, 1989 and 1993 to 1997 show Se concentrations 

range from 83 to 671 μg/L, with the exception being the Lost Hills Ranch discharge of approximately 2 

μg/L (CCVRWQCB, 1990 a and b). In general, Se concentrations in discharges from the Tulare 

subarea are less than 50 μg/L and for the Kern subarea are greater than 180 μg/L. 

• Northern subarea (236,000 total acres; 157,000 irrigated acres; 26,000 drained acres).

The Northern subarea has been included here and in our forecasts for consistency with other regional 

evaluations. The Northern subarea presently drains to the SJR through both discharge and 

groundwater seepage. Estimates of acres demanding drainage have not been updated since 1990, nor 

are current records concerning Se available for compilation from this subarea. Most estimates suggest 

that drainage needs are relatively small compared to other areas (CH2M HILL, 1988; SJV Drainage 

Program, 1990a) and will remain so if access to the SJR for drainage remains available to the same

degree (i.e., the subarea remains in hydrologic balance). 

 

Development of forecasts

While most technical evaluations stop with estimates of problem acreage and problem water

volumes, understanding the range of possible Se concentrations in drainage is critical to evaluating 

potential loads. To bracket possible Se concentrations in our different scenarios of Se loads from the 

western SJV, we will employ three concentrations in conjunction with different estimates of problem

drainage volume and acreage (Appendix B). In general, a concentration of 50 μg/L Se 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 Se concentration to an overall 50 μg/L; then this 

product water would be disposed of in an extension of the SLD. Therefore, one scenario is that such 

treatment options will be available, and/or mixtures of drainage water will resemble those presently 

being released from the Grassland subarea (i.e., 62 to 66 μg/L Se). For this forecast we will use Se 

concentrations of 50 μg/L Se for treated or blended (i.e. diluted) drainage. Alternatively, another set of 

forecasts will assume a maximum case (300 μg/L Se), and one will assume the intermediate possibility 

[150 μg/L Se, an average for present day subsurface drainage waters in the Grassland subarea 

(CCVRWQCB, 1996c), near the mean (163 μg/L Se) presented for the 42,000 acres in WWD (Stevens 

and Bensing, 1994), and a conservative estimate (at least 150 μg/L Se) in WWD by USBR (Wanger, 

37
1994)]. Given the quality of the ground water noted in our previous analysis of reservoir conditions 

(Table 3) and the lack of adequate monitoring to trace groundwater movement and Se concentrations 

as a function of time, these estimates may be conservative. 

One further approach to forecasting potential total Se loads from the SJV and thus narrow the range of 

forecasts is to generate forecasts using a compilation of data on Se concentration and load that has 

become available from each subarea since the SJV Drainage Program (i.e., 1985 to 1990) (Appendix B, 

Tables B9, B10 and B19 to B21). It is recognized that this involves use of data which all have 

significant limitations. However, we stress the importance of collecting high quality hydro- and biogeo-chemical data in the future. Nevertheless, the existing area-specific data incorporates the 

geographical heterogeneity of drainage in establishing the boundaries of potential Se discharges. This 

approach is not as broad as that of the SJV Drainage Program in that an extensive database 

documenting the implementation of management actions and their effects is not available as part of 

public record. But, the scenarios may be more reflective of specific geologic and hydrologic 

conditions in each of the five subareas. 

 

Forecasting selenium loadings using the sum of data from all subareas

 The total out-of-valley drainage is the sum from all five subareas (Figures 3 and 5) (Table 6). 

Table 6 is specific to SJV Drainage Program management option (implementation, i.e., “with future”, 

no implementation, i.e., “without future”, and “with targeted future”) and projected year (1990, year 

2000, year 2040) and gives ranges of combined annual Se loads potentially discharged from all five 

subareas. A wide range of Se loadings in the future from the western SJV is possible given the ranges 

of acre-feet of drainage and drainage quality. These scenarios based on the broad SJV Drainage 

Program approach do consider, to some extent, addressing the longer-term problem of an accumulated 

imbalance of water, salt, and Se and the sustainability of agriculture in the SJV, rather than just 

managing an annual imbalance. 

One alternative is that the volume of drainage water will not increase beyond the volume of 

subsurface drainage that existed in 1990. If 100,000 acre-feet volume of subsurface drainage is 

discharged at an assigned concentration of 50 μg/L Se, then 3,600 lbs Se per year are projected. 

Assigned Se concentrations of 150 μg/L or 300 μg/L would yield loads of 40,800 or 81,600 lbs Se per 

year, respectively. 

38
 Total drainage can be projected using problem acreage across all subareas of the SJV (Table 6). 

Specifically, a forecast using an assigned concentration of 50 μg/L Se to represent blended generic 

drainage in conjunction with the most quoted estimate from the SJV Drainage Program of 314,000 

acre-feet of problem water (i.e., year 2000 without implementation of the specified management plan) 

yields a load of 42,704 lbs Se per year. For year 2040, the amount of problem water would increase to 

666,000 acre-feet, generating a load of 90,576 lbs Se per year at an assigned concentration of 50 μg/L 

Se. 

A forecast using an assigned concentration of 150 μg/L Se to represent generic subsurface drainage 

and the SJV Drainage Program estimate of subsurface drainage of 144,000 acre-feet (“with future”) in 

year 2000 yields a load of 58,751 lbs Se per year. For year 2040 under the condition of 

implementation of the SJV Drainage Program (303,600 acre-feet per year), the discharged load would 

be 41,290 lbs Se per year. 

Using an assigned concentration of 300 μg/L Se in year 2000 and the least amount of estimated 

drainage (72,000 acre-feet per year “with targeted future”), the load discharged would be 58,753 lbs Se 

per year. In year 2000, 163,000 acre-feet (without future) at 150 μg/L Se would produce a load of 

66,504 lbs Se per year. In year 2040, 223,000 acre-feet (without future) at 150 μg/L Se would produce 

a load of 90,984 lbs Se per year. 

Forecasting selenium loadings using data from individual subareas

Using the same approach as above, specific loadings can be projected from each of the five 

subareas based on the detailed data given by the SJV Drainage Program for year 2000 and assigned 

concentrations of 50, 150, and 300 μg/L Se (Appendix B, Table B18). Appendix B (Figure B2a, b, c) 

illustrates use of a graphical tool to enable a prediction or projection of an annual Se load for any of the 

three assigned concentrations given a specific drainage volume. Again, the ranges are due to varying 

estimates of predicted problem water and subsurface drainage under different management 

alternatives. 

In an effort to reduce the magnitude of the ranges given for each subarea, Table 7 gives the 

derivation and details of specific loads projected from each of the five subareas based on our 

compilation of currently available data on problem acreage, drainage volume, and Se concentration 

(Appendix B, Tables B9, B10 and B19 to B21). The values based on current data show only that 

39
amount discharged on the surface (e.g., to the SJR or to the evaporation ponds of Tulare and Kern 

subareas), and hence address only the present discharge being used to manage an annual imbalance of 

water, salt, or Se (Table 7). Depending on the type of data available from each subarea, projections 

were made concerning concentration or load. Because of the limited data and broad range of 

management alternatives across the subareas, maximum and minimum Se concentrations are given to 

bracket possible load scenarios at each specific volume of drainage. The projected concentration range 

is 5 to 10 μg/L Se for the Northern subarea , 68 to 152 μg/L Se for Grassland subarea, 49 to 150 μg/L 

Se for Westlands subarea (note, no current data, only testimony on acreage is available), 1.7 to 9.8 

μg/L Se for Tulare subarea, and 175 to 254 μg/L Se for Kern subarea. Current conditions for each 

subarea (Table 6) give projected ranges for annual Se loadings of: 

• Northern subarea 350 to 700 lbs Se per year 

• Grassland subarea 6,960 to 15,500 lbs Se per year 

• Westlands subarea 8,000 to 24,480 lbs Se per year 

• Tulare subarea 91 to 519 lbs Se per year 

• Kern subarea 1,089 to 1,586 lbs Se per year 

o Northern + Grassland + Westlands + Tulare + Kern subareas

TOTAL 16,490-42,785 lbs per year 

A graphical depiction of these projections for each subarea is given in Appendix B (Figures B4a 

through B4f). The high range and the low range of possible annual discharges are illustrated in Figures 

7 and 8. As noted above, the largest Se loads come from Westlands subarea and Grassland subarea 

because of their combination of high problem acreage, and thus problem water volume, and high Se 

concentration. 

Loading scenarios

 Table 8 illustrates the total Se load from various combinations of subareas that might be included in 

a drainage collection system. These projected loads of Se provide the basis for determining the upper 

and lower limits of Se discharge from the western SJV that can be expected to enter the Bay-Delta via 

either a proposed direct conveyance to the Bay-Delta or the SJR. Secondarily, the projections provide 

the basis for determining the magnitude of Se load reduction that may become necessary to achieve a 

specific load of Se. Estimates like those in Table 8 implicitly assume that Se loads will be primarily 

40
driven by the demand for drainage, with different degrees of management superimposed. Of course, 

different demand scenarios than those shown are also possible. 

 The first four scenarios in Table 8 show that the load of Se increases from a minimum of 6,960 lbs 

per year to 42,785 lbs per year as additional area is added to drainage collection and/or as drainage 

volume and quality is less managed. The scenarios are: 

• Only the existing discharges to the SLD from the Grassland subarea would be carried to the 

Bay-Delta. It seems unlikely that demand would remain at this level once an out-of-valley 

conveyance was available. Growing acreages of saline soils, rising ground water tables, and 

the availability of a conveyance facility are very likely to generate strong pressures from other 

areas to use the facility. 

• Discharge from the Grassland subarea via the SLD or SJR would be discontinued and only the 

Westlands subarea would use an extension of the SLD. 

• Grassland subarea discharges and Westlands subarea discharges would both be carried to the 

Bay-Delta; this seems a likely outcome if a conveyance is constructed. 

• Drainage is collected valley-wide from all five subareas. This would require extensions of the 

SLD into Kern and Tulare. 

A future that considered only agricultural needs might call for draining all 444,000 acres of 

problem lands. The fifth and sixth scenarios in Table 8 provide estimates of Se loads for a valley-wide 

drain that includes all potential problem lands estimated for the year 2000. The first of these 

calculations shows the range of Se loads expected if drainage management follows the plan submitted 

by the SJV Valley Drainage Program. If both quality (treating drainage to 50 μg/L) and quantity (e.g. 

reducing acre-feet per acre per year of drainage from 0.7 to 0.4) are managed, loads would calculate at 

19,584 lbs per year. If only quality is managed, total Se loadings for the problem lands would then 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, Se 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-feet per acre per 

year, and 150 μg/L Se drainage). 

41
 As a comparison, the final forecast in Table 8 lists the load targets set in recent management plans 

for discharge to the SJR from the Grassland subarea (USBR, 1995; CCVRWQCB, 1998a). The target 

Se loads range from 1,394 lbs per year to 6,547 lbs per year depending on flow (i.e., wet or dry year). 

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

 It is also feasible that exports of Se from the SJV could be determined by assigning a water quality 

goal to the drainage in a SLD extension and operating the drain at some pre-defined capacity (Table 9). 

The drain is presently designed to flow at 300 cubic feet per second (cfs) or carry approximately 

220,000 acre-feet per year. That capacity could be a factor limiting loads, if a water quality standard is 

employed. Forecasts are given for 1) 50 μg/L representing an overall average given in testimony that 

treatment technologies (so far unspecified) or blending could achieve and near present day discharge 

from Grassland to the SJR (i.e., 62-67 μg/L; 2); 150 μg/L Se representing an average for current 

subsurface drainage without blending in the Grassland subarea (CCVRWQCB, 1996c) and near the 

mean (163 μg/L) presented for shallow groundwater from 42,000 acres in the Westlands subarea 

(Wanger, 1994); and 3) 300 μg/L representing a concentration approaching that discharged from

WWD 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 loadings derived from the 50 

to 67 μg/L quality forecast and that from a drain managed at full capacity is 30,000 - 40,000 lbs (Table 

9), are within the probable forecast derived from drain demand to manage the current annual imbalance 

from specific subareas in Table 8. If the drainage conveyance discharges 150 μg/L Se, at full capacity, 

the loading forecast converges on that estimated from all problem lands with little management (Table 

9). 

 Despite the range of assumptions and range of possible outcomes considered in Tables 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 Se inputs to the Bay-Delta. Selenium loads based upon the 

demand for drainage converge on a mass discharge of 15,000 to 45,000 lbs of Se per year, if volumes 

and concentrations are carefully managed. Loads quickly grow beyond this level, if more land is 

drained and/or volumes or drainage quality are poorly managed or controlled. 

 

42
The San Joaquin River as a conveyance facility, a de facto drain

 The above estimates present Se loads primarily defined by demand from agriculture, and collection 

in an extension of the SLD. An alternative is to assume that water quality in the SJR would determine 

Se discharges, and no drain would be constructed. Two approaches have been discussed historically. 

Both approaches consider only the amount of dilution water available; no consideration is given to 

defining the assimilative capacity of the receiving water (i.e., the SJR) based on the bioaccumulative 

nature of Se. 

1. Total Maximum Daily Load or Total Maximum Monthly Load models. This alternative models 

load allocations based on historical flows in the SJR. A water quality standard is applied to 

design flows to calculate a Se load limit for dischargers (Environmental Defense Fund, 1994). 

This is the technique mandated by USEPA for discharges to impaired water bodies such as the 

SJR (Clean Water Act, as amended, 1987; USEPA, 2000). The SJR compliance site for the 

130-miles of impairment is the SJR at Crows Landing. This site is below the confluence with 

the Merced River, but above the SJR at Vernalis that is considered the entrance to the BayDelta (Figure 5). Between the Merced River confluence and Vernalis, the Tuolumne and 

Stanislaus Rivers flow into the SJR. Inherent in the TMDL model approach are an 

identification of sources and a program of load reduction to achieve compliance with water 

quality objectives. 

2. Real-time model. This alternative goes one step further than TMDL modeling in that discharges 

are allocated based on real-time updates of flow (i.e., instantaneous measurements). This 

means maintaining a constant Se concentration at or below the 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 

Se measurements, since technology is not available to assess Se on a real-time basis). Loads 

based on real-time dilution maximize disposal of Se 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 SJR to avoid violations of water quality objectives. This 

methodology 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. 

43
As such, it is of less value that the TMDL approach in regulating the SJR as a Se-source water 

for the Bay-Delta. 

 Appendix C details the historical record used for derivation of loads for the SJR at Crows Landing 

and the load allocations for the dischargers using the TMDL, TMML, and real-time models. These 

models encompass both quasi-static and dynamic modeling of flows. The quasi-static TMDL and 

TMDL derived loads range from 1,394 to 6,547 lbs Se 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 

upon flow regimes. 

 Our estimates of Se loads conveyed by the SJR to the Bay-Delta treats the SJR as a Se source water 

for the Bay-Delta using an annual static inflow for the SJR at Vernalis based on wet or dry year flows 

and consideration of recycling. The main consideration in our development of this type of scenario in 

which the SJR is used as a de facto drain from the SJV is that the starting point is the targeted load. 

This is a supply driven strategy, with consideration of environmental protection a priority, rather than a 

load driven by agricultural demand. The effects on the SJR itself, of managing the constant 

concentrations in view of bioaccumulation are not known and are not considered here. 

 To obtain these modeled loads we used several assumptions about flow conditions (Table 9): 

• little recycling of the SJR occurs in a wet year therefore 3.0 MAF enters the Bay-Delta annually 

• 1.1 MAF of SJR inflow is allowed to enter the Bay-Delta annually indicative of partial SJR 

inflows in a wet year or total SJR inflow in a dry year. 

• almost complete SJR recycling is 220,000 AF comparable to the capacity of the existing SLD 

A range of 60 to 2,992 lbs Se would actually reach the Bay-Delta under the latter condition (probably 

like the drought years between 1987 through 1994) (Table 9). Maintaining a criterion of 5 μg Se/L in 

the SJR allows a load of 14,960 lbs per year to 40,800 lbs Se per year to enter the Bay-Delta at the two 

higher hydraulic discharges. Maintaining the USFWS proposed criterion of 2 μg Se/L would result in 

a range of 5,980 to 16,320 lbs Se per year. 

 

Summary 

 Even though the full range of possible Se loadings 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 upon management strategy: 

44
• Supply-driven management (3,000 to 8,000 lbs Se per year): By this we mean management that 

puts priority on environmental protection and targets a load that cannot be exceeded. For 

example, the TMDL/TMML approach target loads for the SJR from Grassland subarea alone of 

1,400 to 6,500 lbs annually to stay below the 5 μg/L Se criterion depending upon flow regime

for the SJR. The present prohibition for discharge from the Grassland subarea or drainage 

basin targets a load of 8,000 lbs. 

• Demand-driven load with management of land and/or drainage quality (15,000 to 45,000 lbs 

Se per year): By this we mean Se loads are driven by the agricultural demands for draining 

saline or waterlogged soils. We assume the quality and quantity of the drainage are 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 SJV 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 Se (controlled concentration), yields a Se load 

range of 19,584 to 42,704 lbs Se 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 Se 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 SJV Drainage Program for year 2000 without 

implementation of the management plan (demand driven volume) in conjunction with a 

concentration of 150 μg/L Se (non-controlled concentration), yields a Se load range of 42,704 

to 128,112 lbs Se 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 Se per year or 

even more. 

Inputs of Selenium from Oil Refineries 

 The heavy crude oils that are produced in the SJV and refined in the Bay-Delta are especially 

enriched in Se (400 to 600 μg/L) (Cutter and San Diego-McGlone, 1990). So, refinery effluents have 

historically provided a quantitatively important load of Se to the Bay-Delta. Furthermore, the Se in 

these effluents is highly concentrated in a relatively small volume of wastewater, so inputs increase the 

45
ambient concentration of Se, especially around the Carquinez Strait (Cutter, 1989). In eight 

determinations of refinery effluents in 1987 and 1988, Cutter and San Diego-McGlone (1990) 

estimated that annual Se loadings could vary from 2,035 lbs per year to 4,641 lbs per year from all 

refineries combined. Annual loads from 1986 to 1992 ranged from 3,103 to 7,457 lbs Se per year as 

reported by the (Table 10) CSFBRWQCB (1993). In March 1988, refineries inputs accounted for 74% 

of the internal Se input to Bay-Delta; in May 1988, they accounted for 96%. Selenium inputs from

refineries are relatively constant through the year, so they have their greatest influence on Se 

concentrations during the low river inflow season. 

 As a result of regulations imposed by the CSFBRWQCB, refinery inputs to the Bay-Delta declined 

after July 1998. The annual Se loads allowed for the five major refineries by state permit 

(CSFBRWQCB, personal communication, Johnston Lam and Khalil Abu-Saba, 2000) are listed in 

Table 10 in comparison to the annual range reported by the CSFBRWQCB from 1986 to 1992 

(CSFBRWQCB, 1993). By this estimate, refinery inputs declined by about half (to approximately 

2,200 lbs Se per year), from the amount measured from 1986 to 1992 (Cutter, 1989; Johns et al., 1988). 

On the other hand, refinery effluents also are regulated to concentrations of 50 μg/L Se and to the 

volumes discharged in the late 1980’s. If volumes of effluent remain what they were in the late 1980’s, 

the resulting Se load would be 1,400 lbs Se per year. Treatment technologies in the refineries also 

remove only selenite. So the Se discharged was, presumably, mostly selenate in 1999; historic 

discharges were >50% selenite. No mass balance model has yet been constructed to evaluate whether 

1,400 lbs or 2,200 lbs Se per year best describe refinery discharges, but the difference is relatively 

small considering the variability within years and within refineries (Table 10). Preliminary data 

suggest the selenite concentration peak near the refineries disappeared after the treatment technologies 

were implemented (Cutter et al., in preparation). 

Inputs of Selenium from the Sacramento River 

Most of the river inflow to the Bay-Delta comes from the Sacramento River (Figure 5). The 

discharge ratio between the SJR (at Vernalis) and the Sacramento River (at Freeport) is typically 10 to 

15%. The dissolved Se concentrations in the Sacramento River at Freeport are consistently low, 

averaging 0.06 ± 0.02 μg/L (Cutter and San Diego-McGlone, 1990). Thus, the Sacramento River 

represents a low concentration, high volume source of Se. Using a concentration of 0.04 μg/L Se (a 

46
conservative estimate) and the inflows given below, the projected annual Se loads conveyed by the 

Sacramento River to the Bay-Delta are: 

• 32 MAF, wet year 3,482 lbs Se per year 

• 17 MAF, median year 1,850 lbs Se per year 

• 10 MAF, dry to critically dry year 1,088 lbs Se per year 

• 5 MAF, most critically dry year 544 lbs Se per year 

Selenium load increases with volume of inflow from the Sacramento River, because Se concentrations 

in the river are low but constant. The Sacramento River inflow therefore establishes the baseline flow 

and Se concentration entering the estuary. 

Summary 

 In our model, four inputs in different proportions determine the Se load to the Bay-Delta. The 

Sacramento River loadings vary purely as function of inflow volumes (1,859 lbs Se per year, median 

precipitation year). The potential loadings from an extension of the SLD vary quite widely. Supplydriven loadings are lowest; demand-driven loadings with management and treatment capabilities fall 

within the range of 15,000 to 45,000 lbs Se per year. Loading rates escalate steeply if treatment 

strategies are not applied. Loadings from regulated concentrations in the SJR vary with the quantity of

SJR water that reaches the Bay-Delta. The Se load from the SJR, at present, is 5,660 to 8,000 lbs Se 

per year, if considered separately and no recycling occurs. We assume oil refinery loadings will 

remain at post-1998 values reflecting regulation and treatment technology (approximately 1,400 to 

2,200 per year). The sums of combinations of these scenarios represent the loadings under different 

management and hydraulic conditions. We will consider a few specific, most likely, scenarios for the 

Bay-Delta in detail for forecasting Se concentrations in water, sediment, and the food web and 

evaluating the ecological effects on predators (birds and fish) in the Bay-Delta estuary. 

HYDRAULIC CONNECTIONS AND CONVEYANCE OF SELENIUM TO THE 

BAY-DELTA 

 

The loads from the SJV can be conveyed to the Bay-Delta either via the SJR or via a proposed 

extension of the SLD. As discussed earlier, the originally planned valley-wide drain or SLD was a 

47
proposed canal that would collect irrigation drainage valley-wide or from the San Luis Unit (i.e., 

Westlands subarea and parts of what is now the Grassland subrea) and deposit it directly into Suisun 

Bay (Table 1; Figures 4 and 5; and Appendix A). If extensions of the SLD are constructed, the drain 

could potentially collect drainage from all five subareas of the western SJV or, as configured, from

Westlands subarea and Grasslands subarea only and release it directly into the Bay-Delta. 

 The SJR is the only natural outlet from the SJV. A substantial proportion of the freshwater flowing 

toward Bay-Delta from its watershed is diverted (exported) for agricultural and urban uses. Before the 

1990’s, the inflows of the SJR were almost completely diverted and recycled. That meant little or none 

of the Se discharged into the SJR reached the Bay-Delta. After the 1994 Bay-Delta Water Accord 

(CSWRCB, 1994), water management changed; more Se will reach the Bay-Delta as less recycling of 

the SJR occurs. However, not all water that leaves the SJR at Vernalis enters the Delta or the Bay. 

The merging of the Sacramento River and SJR systems in the estuary and exports or water diversions 

add complexity (Figures 9 and 10). The amount of potentially Se-laden SJR inflow reaching specific 

locations in the Bay-Delta is influenced by (CSWRCB, 1999a; Monsen, 2000): 

• tidal cycles; 

• variable inflows of the Sacramento River and SJR due to seasons and upstream withdrawals; 

• quantity of water diverted from the Delta to the CVP, SWP and local water users; 

• discharge of agricultural drainage from the SJV and drainage inputs 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 

and 1999a; b; c; d). 

 Figures 9 and 10 show the balance for the Bay-Delta in a wet year (1996) and in a dry year (1994) 

among: 

• total river (Sacramento River and SJR) inflow; 

• SJR inflow; 

• water diversions [i.e., pumping at Tracy and Clifton Court Forebay (CCtF) south to the DeltaMendota Canal and the California Aqueduct]; and 

• total outflow of the Bay to the Pacific Ocean. 

48
Total inflows and SJR discharges are very 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, SJR discharge at Vernalis can be a large proportion of total inflows. During this time of 

year, if SJR 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 SJR inflow reaches the Bay-Delta 

during this time of year. Better understanding of water movement from the SJR thorough the BayDelta and processes within the estuary are critical to future evaluations of Se issues. Evaluations of the 

implications of water management decisions must consider effects on Se transport and residence time. 

A large range of residence times have been estimated for freshwater in various parts of the Bay-Delta 

(Walters et al., 1985). The estimated residence times (days) for high flow periods/low flow periods 

are: 

• Suisun Bay 0.5/35 

• San Pablo Bay 0.8/25 

• Northern reach 1.2/60 

• South Bay 120/160 

• South Bay (north of Dumbarton Bridge) 80/120 

• Extreme South Bay (south of Dumbarton Bridge) 40/70 

CONCENTRATIONS OF SELENIUM IN THE BAY-DELTA 

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

Interpretation of mass loadings from individual sources requires understanding how load and 

volume in different source waters combine to produce concentrations in receiving waters. It is 

concentration in receiving waters that determines biological impacts. So ultimately the interaction 

between source water loading and receiving water concentration must be understood. 

Load will increase with increased volumes of drainage, given the characteristics of Se 

concentrations in the drainage (Figure 6). Load also increases with volumes of inflow from the 

Sacramento River, because Se concentrations in the river are low but constant. On the other hand, 

concentrations in the mixture of waters where the sources combine will be dependent upon the sum of 

49
the volumes of the sources and the masses of Se in each of those sources. Dissolved Se comprises 80 

to 93% of the total Se (Cutter, 1989) in the Bay-Delta so loads based on total Se can be employed to 

derive concentrations of dissolved Se. 

The volume of water (or the rivers) input to 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 SJR. Monitoring of Se concentrations in the 

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 approximately June, 

followed by lower inflows through the last six months of the calendar year (Conomos, 1979; Conomos 

et al., 1985). In contrast to water volumes, the mass of Se in anthropogenic effluents such as oil 

refinery effluents is not highly variable because both volumes and concentrations are relatively 

constant (CSWRCB, 1992a; b). Monthly load targets for discharge to the SJR from the Grassland 

subarea vary from 348 lbs Se to 1,066 lbs Se, with the largest loads discharged during February. 

Volumes of agricultural drainage discharged from the Grassland subarea in 1997 varied from 1,274 to 

4,867 acre-feet per month with concentrations varying from 25 to 106 μg/L Se to enable a targeted 

load. The Westlands subarea during 1981 to 1985 discharged an average concentration of 330 to 430 

μg/L Se and the volume ranged from 304 to 772 acre-feet per month. In all these cases, the degree of 

variability in volume will be small compared to the variability in river inflows. 

 As a result of the mixing of variable inflows from the rivers (mostly with low Se concentrations) 

and relatively constant anthropogenic inflows (with high Se concentrations) a strong seasonal 

fluctuation and year-to-year fluctuations of Se concentrations would be expected. The protocol for 

linking load and concentration under the current hydraulic and Se inflow conditions in the Bay-Delta 

is: 

• Composite Input Load = Sum Se loads from each input (six month season or monthly) 

• Composite Input Volume = Sum volumes for each input (mainly inflows of Sacramento and SJR 

(six month season or monthly) 

• Composite Se Input Concentration = Composite Input Load / Composite Input Volume 

50

In wet years (high precipitation), reduced Se concentrations are expected in Bay-Delta receiving 

waters; in dry years and dry seasons, concentrations in receiving waters will increase. Therefore, 

evaluations of Se impacts must consider the time periods before, after, and during low flow periods, 
because this is when the highest concentrations of Se will occur. The dry years and dry seasons will be 

the ecological bottleneck (the times that will drive impacts) with regard to Se. Factors such as 

residence times and exchanges within the Bay and Delta are also important, but the models necessary 

to understand these smaller scale effects (e.g. elevated concentrations near sources of input; detailed 

distribution within the Delta or Suisun Bay) are not adequately developed. Further development of 

hydrodynamic models (Cheng et al., 1993; Monsen, 2000; Burau and Monismith in preparation), 

multiple media mass balance models, and kinetic geochemical models are very important to defining 

detailed ecological effects of Se and resolutions to future Se problems. 

Existing Concentrations in the Bay-Delta 

Regional baseline 

 Dissolved Se concentrations are low (0.06 ± 0.02 μg Se/L) in the Sacramento River (at Freeport) 

(Cutter and San Diego-McGlone, 1990) and in the seawater (0.02 to 0.08 μg Se/L) with which it mixes 

(Cutter and Bruland, 1984) in all seasons. The regional Se baseline in the Bay-Delta is defined by 

mixing the Se concentrations in these two endmembers, as determined by a salinity gradient through 

the estuary (Figure 11). A more complex case is one of a composite freshwater endmember comprised 

of the Sacramento River, the SJR, and the refineries effluents. The regional baseline can be compared 

to a theoretical mixing line for which the Se endmember concentration in the freshwater composite 

represents anthropogenic sources. In Figure 11, the example mixing profile gives a Se concentration of 

0.23 μg Se/L (Figure 11). The composite freshwater endmember concentration is calculated from

annual Se loads and volumes in the Sacramento River at 20 MAF plus a refinery input of 4,400 lbs Se 

per year (typical conditions in a wet year before refinery cleanup). The 1997 gradient shows Se 

concentrations through the estuary as the 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 Se 

concentrations in the Bay-Delta. This approach to modeling Bay-Delta Se inputs illustrates that 

variation in Se loads delivered by an endmember consisting only of the Sacramento River will not 

cause changes in average Se concentrations in the Bay-Delta. This is because average concentrations 

in the river are relatively constant (i.e., within the range of 0.04 to 0.08 μg/L Se). However, the sum of 

source input Se loads determines the Se concentration of the composite freshwater endmember. 

51
Therefore, adding a low volume/high concentration source of Se to obtain the composite freshwater 

endmember Se concentration will cause changes in the Se concentrations in the estuary system. 

 The spatial details of observed Se distributions can be compared to theoretical distributions to draw 

conclusions about internal sources or trapping of the property within the estuary. The projected Se 

concentration in the theoretical composite freshwater endmember used above (i.e., 0.23 μg/L Se) is 

similar to the Se concentration observed in surveys of the estuary (see discussion below and Cutter et 

al., in preparation). 

Concentrations observed in the Bay-Delta

 Five studies have been conducted that have employed reliable analyses of dissolved Se 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 et al. (in preparation; unpublished data quoted in Luoma and 

Fisher, 1997) sampled the salinity gradient again in May 1995 and October 1996. The San Francisco 

Estuary Regional Monitoring Program since its inception in 1993 has also analyzed Se 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 Se concentrations less than the 1 μg Se/L level 

designated as the Canadian wildlife hazard level (Environment Canada/Health Canada, 1995; Outridge 

et al., 1999); the 2 μg/L USFWS proposed 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 Se/L USEPA chronic criterion for protection of aquatic life (derived from

freshwater studies) (USEPA, 1992). The maximum concentrations of dissolved Se in most surveys are 

less than those observed in the adjacent watersheds (Cutter, 1989; Cutter and San Diego-McGlone, 

1990; CCVRWQCB, 1992a; b; 1993) (Tables 2 and 5). Slightly higher concentrations are sometimes 

observed near the Golden Gate, but these appear to originate from the South Bay (Cutter, 1989). The 

highest dissolved Se concentration observed in any North Bay survey was 0.44 μg Se/L in August 

1993 (San Francisco Estuary Institute, 1994). The lowest concentrations were observed in the 

Sacramento River in September 1986 and June 1995 (0.048 to 0.052 μg Se/L). No analyses have been 

52
conducted of Se concentrations in the Delta, although a recent CALFED supported study has begun 

some data collection in this area (Cutter et al., in preparation). 

 The spatial features of the Se gradient in the North Bay (Figure 12) were initially described by 

Cutter (1989). Surveys conducted between 1986 and 1996 show that Se concentrations are 1) highest 

in Suisun Bay, in the mid-salinity ranges near Carquinez Strait; and 2) lowest in the river and oceanic 

endmembers. This suggests a source of Se exists in the middle of the estuary. Cutter (1989) 

determined that the oil refineries were that source, an observation consistent with the distribution of 

biologically available Se reported by Johns et al., (1988). 

 Seasonal and year-to-year variations in the inflows from the rivers influence dissolved Se 

concentrations. Higher concentrations appear to occur during periods of low inflow than during 

periods of high inflows (Figure 12). Distributions also change with inflows from the rivers. In April 

1986, after a very large flood in February, dissolved Se declined linearly from freshwater to seawater, 

correlating with salinity. Estimates of fluxes indicated that the export of Se from the Bay-Delta to the 

ocean was controlled by riverine sources during this month. During low flow seasons, dissolved Se 

concentrations increase and the peak in Suisun Bay becomes more distinct. Cutter (1989) and Cutter 

and San Diego-McGlone (1990) showed that in September 1986, total Se inputs from the rivers was 

2.45 lbs per day (or extrapolated, 894 lbs Se per year) and total Se from internal sources was 17.9 lbs 

per day (or extrapolated, 6,534 lbs Se per year). Flux calculations from different sources indicated that 

the Se input from refineries were 2- to 8-times inputs from the rivers in this month, and were the cause 

of the shape of the gradient. In March of 1987, during a drought, refineries were 74% of the Se flux; in 

May 1987 they were 96%. Presumably, this has changed since July 1998; but only preliminary data 

are available. 

Thus, while estuarine waters in the Bay-Delta are enriched in Se compared to the regional baseline, 

the Se concentrations in the estuarine waters are low compared to many contaminated freshwater 

environments. The concentration of dissolved Se 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 μg Se/L to 0.39 μg Se/L. Presumably some of these sites were anthropogenically 

contaminated like the Bay-Delta. This range 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 Se concentrations result in the 

degree of food web contamination described next. 

53
CHEMICAL FORMS OF SELENIUM (SPECIATION) 

 Concentrations of waterborne Se are not sufficient to predict the biological implications of Se 

contamination. The geochemical speciation of Se is a critical consideration. Speciation of dissolved 

Se ultimately controls transformation reactions between dissolved and particulate forms (i.e. the 

reactions with sediments, detrital particles, and primary producers). Transformations and particulate 

concentrations are important factors determining the biological effects of Se; 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 

Although dissolved Se in aerobic waters can sometimes occur predominantly as an organic form

(Takayanagi and Wong, 1984; Cutter and Bruland, 1984), selenate and selenite are the most common 

forms in most waters. Selenate is the thermodynamically-predicted stable form of Se in oxic waters, 

but due to its slow oxidation rate in natural waters, selenite can be an important species (Cutter, 1982). 

Selenite is the most bioavailable of the dissolved phase inorganic species (Maier et al., 1993; Skorupa, 

1998b). Comparative toxicity laboratory studies demonstrate that some forms of organo-Se are also 

very bioavailable and hence toxic to tested algae, invertebrates, and fish (Maier et al., 1993). 

 Examples exist in nature where each of the three major species of Se 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); and 3) organo-Se can predominate where Se is strongly recycled (Takayanagi 

and Wong 1984). In the Bay-Delta, speciation differed among the source waters in 1980’s (Cutter and 

Diego-McGlone, 1990): 

Sacramento River inflow was 30 to 70% selenate, depending upon season; organo-Se was the 

other main component. 

SJR inflow was 70% selenate and 22% organo-Se. 

54
• refinery wastewaters averaged 62% selenite.

• 

• 

during low flow in Carquinez Strait, as much as 50% of the Se was selenite in the late 1980’s, 

reflecting the predominance of refinery inputs.

preliminary studies in Suisun Bay in the late 1990’s showed less selenite, but selenite plus 

organo-Se could comprise 60% of the mass of Se. 

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 Se is the partitioning reactions that determine the distribution between dissolved and particulate 

phases, where particulate phases include primary producers (e.g. phytoplankton), bacteria, detritus, 

suspended inorganic material and sediments. There are several reasons these reactions are important: 

• The pathway for nearly all Se transfer to the second trophic level in the system is via particulate 

forms (i.e., animals bioaccumulate Se from their food to a much greater extent than they take up 

Se from water, at the distributions typical of nature, Luoma et al., 1992). 

• The transformation efficiency from dissolved to particulate Se ultimately determines food web 

concentrations of the element (i.e., higher Se concentrations on particulate material means 

greater contamination in the food web, although the form of the Se in the particulate can also be 

important); 

• Concentrations of Se on particulates can differ by as much as 100-fold, at the same dissolved 

concentration, depending upon the biogeochemical transformation reactions governing the 

dissolved particulate interaction. Thus, forecasts of effects depend upon understanding what 

transformations will occur. 

 The largest inventory of Se in a contaminated ecosystem usually occurs in sediments. For example, 

90% of the inventory of Se in Kesterson National Wildlife Refuge was deposited in sediments 

(Tokunaga et al., 1996). However, the proportion of Se on suspended particles, at any one time, may 

be only a small fraction of the total quantity of Se in the water column. For example, in April 1986, 

55
Cutter (1989) found that only 7% of total Se in the water column of the North Bay was particulate; in 

September 1986, only 13 ± 7% was particulate. The large inventory of Se in sediments results either 

because suspended particulate Se is progressively deposited in sediments over time and/or because 

reactions within the sediments progressively strip Se from solution. 

 The concentration per unit mass on the particulate material is more critical than the mass in 

suspension (per unit volume of water). In fact, the most important measure of Se in any environment 

may be the concentration of Se per unit mass of suspended particulate material. This concentration 

determines the exposure of the many species that feed on such material. Each species' exposure to Se 

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 μg Se/g food or particulate material, 

along with the efficiency with which that concentration is assimilated (Luoma et al., 1992). 

Assimilation efficiency (AE) is the proportion of ingested Se that is taken up into tissues; and AE 

varies with the type of food or the form of particulate Se. 

 Direct determinations are rare of Se concentrations per unit mass on suspended sediments. This is 

at least partly a result of the difficult challenge of collecting a sufficient mass of suspended material for 

direct analysis. 

Transformation

Several different primary reactions can transform (or affect transformation of) dissolved species of 

Se to particulate Se. Transformation reactions include biological, redox, 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) via uptake by plants or, perhaps microorganisms. Microbes, 

plants, and microflora (phytoplankton) reduce the Se they concentrate to Se(-II). Most 

biochemically transformed Se is found within the cell solution, at least in phytoplankton 

(Reinfelder and Fisher, 1991), and is highly bioavailable to animals that consume the 

microorganisms for food. When cells die and breakdown the plants release both Se(IV) and 

56
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 Se in water contacts reduced 

particles (little oxygen) 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 et al., 1989). Dissimilatory reduction of either Se(IV) or 

Se(VI) generates predominantly elemental Se [Se(0)] in sediments; but it may also generate 

some operationally defined organo-Se [Schlekat et al., in press (b)]. Elemental Se 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. The particulate Se generated by the transformation reactions can occur in 

different oxidation states depending upon the transformation reaction and subsequent exposure 

to geochemical conditions. Understanding the form of particulate Se is critical to evaluating 

impacts of Se contamination, because each form has a different biological availability (Luoma 

et al., 1992). Reduction/oxidation status, determined by the balance of redox couples, is 

especially important in determining particulate form. Possible particulate forms include: 

adsorbed/coprecipitated selenite (SeIV) and selenate (SeVI), organic selenides, either in the 

form of intracellular Se(-II) or detrital Se(-II), or elemental Se (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 et al., 1997; 1998; Myneni et al., 1997). 

• Volatilization. Biogeochemical volatilization of Se is well documented in wetland soils 

(Cooke and Bruland, 1987; Thompson-Eagle and Frankenburger, 1992) and in evaporation 

ponds (Fan and Higashi, 1998). Volatilization rates depend upon physical/chemical 

conditions, vegetation, water management or other rate limiting factors (Flury et al., 1997; 

Zhang and Moore, 1997a; c; Hansen et al., 1998). The influence of volatilization on Se 

concentrations in sediments (the relevance to this discussion) is determined by the mass of Se 

volatilized, compared to that in sediments. A careful mass balance including determination of

Se inputs, outputs and internal inventories is the only way to verify effects of volatilization on 

57
Se inventories. 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 approximately 30% of the incoming Se was volatilized at 

Kesterson Reservoir. Zhang and Moore (1997d) and Hansen et al. (1998) reported results 

consistent with that figure for other wetland systems. If this value of 30% is typical, it is 

possible to calculate the effect of volatilization on Se concentrations in a wetland that receives 

a continuous input of Se. If 90% of incoming dissolved Se is trapped in the sediments, and if 

30% of that is volatilized, then the net effect of volatilization is to reduce the progressive 

accumulation of Se in particulate material to: 0.90 trapped X 0.30 volatilized = 0.63 trapped X 

100 = 63% of incoming Se retained. Thus volatilization could slow Se accumulation to a rate 

less than would otherwise be achieved. However, in no known case has volatilization 

eliminated Se contamination or alleviated water quality problems. Wetland trapping can 

remove Se from contaminated waters, but most of the Se remains in the sediments; efforts to 

completely volatilize Se to the atmosphere have not proven successful. If Se 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 Se load (e.g., 

Flury et al., 1997). 

Range of distribution coefficients (Kd’s)

The distribution coefficient (Kd) is a way to quantitatively describe the partitioning of total Se 

between dissolved and particulate states. The Kd is the ratio of Se per unit mass particulate material 

versus Se per unit volume water, in equivalent units. An example of a calculated Kd for the Bay-Delta 

from typical 1986 data (Cutter, 1989) is: 

(700 μg particulate Se/kg particulate)/(0.315 μg dissolved Se/L) = 2.2 X 103 L/kg. 

Speciation of dissolved Se and transformation reactions have a combined influence on the distribution 

coefficient of Se. The Kd oversimplifies both with the result that Kd’s based upon 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 employs the data most widely available from a variety of systems. Table 

11 lists Kd’s typical of the variety of ecosystem from which reliable geochemical data are available. 

The Kd’s in various field studies have ranged from 0.3 X 103 to 2 X 104

, reflecting the complicated 

transformation reactions and processes described above. Skorupa (1998a) also summarized the range 

58
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. The range of Kd’s allows understanding of the 

potential range of particulate Se 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 

 The general sources of particulate Se in the Bay-Delta include: 

• Autochthonous (internal) sources in the SJR or the Delta (external to the Bay-Delta): 

Selenium could be transformed to particulate forms in the marshes of the SJR and the 

wetland/lakes of the Delta by either dissimilatory reduction to Se(0) or biotransformation to 

Se(-II). Very little is yet known about Se trapping or transformation within the Delta itself. 

• Allochthonous (external) sources: It is possible that Se contaminated particles produced in the 

SJR could be transported to and trapped in the Delta. Particulate Se 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 irrigation return water to the Bay-Delta 

will contain externally and internally produced particulate Se. 

• Autochthonous 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 Se in the sediments of wetlands or shallow waters (Zhang 

and Moore, 1997a; b). Thus the time 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 Se are wetlands and shallows with long residence times. Restoration activities could affect 

Se contamination in the SJR-Bay-Delta system if they change hydraulic residence times or generate a 

larger area of the kinds of systems that trap Se, without remediating Se inflows. 

 

Particulate selenium in the San Joaquin River

Direct inputs of irrigation drainage to the SJR have long occurred, via canals and wetlands. Since 

1996, the SLD has also directly discharged drainage from the Grassland subarea to the river. 

59
Difficulties arise in drawing generalizations about temporal trends or spatial distributions of particulate 

Se in the SJR, 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, concentrations of suspended material, Se concentrations on suspended material in different 

seasons or bed sediment characteristics like particle size and differences in organic carbon 

concentrations. A detailed, systematic and carefully designed study of particulate Se occurrence and 

trends would be relatively easy to implement and is badly needed. The existing data (Appendix E, 

Tables E1 and E2) show the following: 

• Upstream of SLD: Concentrations of Se were 0.01 to <0.18 μg Se/g dw in sediments from

upstream of the SLD discharge, in the SJR at Lander Avenue in 1987 - 1989. These are 

probably baseline concentrations of Se for the system. In 1993-1996 and 1997, concentrations 

upstream of the SLD discharge, in Mud Slough, were within the range: 0.10 to 0.44 μg Se/g 

dw; the higher values probably reflect contamination from historic Se inputs to the slough. 

• Downstream of SLD, before 1996 discharges: The range of concentrations, among several ad 

hoc studies, in sediments of the SJR downstream of the inactive discharge site (pre-1996) was 

0.3 to 1.9 μg Se/g dw. One value of 5.2 μg Se/g dw was reported from the SJR near Vernalis. 

• Downstream after current operations began: In September 1996, after operation of the SLD 

began, Se concentrations of 0.1 to 0.76 μg Se/g dw 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 Se/g dw. Recent data show Se increasing to 4.8 μg/g dw in sediments in a 

seasonal backwater tributary of Mud Slough where residence time increases (USBR et al., 

1999). 

• Suspended sediments. Several surveys also have analyzed suspended sediments in the SJR or 

adjacent marshes or sloughs. In all cases, concentrations in suspended sediments exceeded 

concentrations in bed sediments. In a backwater where stagnant conditions would be expected 

(high hydraulic residence time), a concentration of 4.4 μg Se/g dw was determined. The range 

of concentrations in suspended sediments was 0.91 to 6.7 μg Se/g dw. Systematic studies of 

seasonality, relationships to hydrology or forms of Se could be instructive with regard to 

sources and causes of the large range of variability. 

 

60
Particulate selenium in the Delta

 Little is known about Se concentrations in the Delta. In 1986-88, Johns et al. (1988) sampled 

Corbicula and sediments near-monthly at a station in the Old River channel near Clifton Court 

Forebay. At that time and location, Se concentrations in both indicators (Corbicula sp., mean 3.1 μg 

Se/g dw and particulates grand mean, 0.19 ± 0.03 μg Se/g, dw) were significantly lower than found 

within Suisun Bay (Corbicula sp., range of means, 3.9 to 5.2 μg Se/g dw and particulates range of 

grand means 0.23 to 0.53 μg Se/g dw); and similar to concentrations found in the un-enriched 

Tuolumne River, which drains the Se-poor geology of the eastern San Joaquin Valley. No systematic 

Se studies were conducted in the Delta after SJR inflows to the Delta increased in the mid-1990's. The 

lack of study in Delta wetlands or shallow waters leaves open the question of whether Se can be 

sequestered there, at least in some locations. 

Particulate selenium in existing portion of the San Luis Drain

Transport, re-suspension and re-oxidation of the particulate material in the existing SLD, if 

extended, might also be a source of bioavailable particulate Se to the Bay-Delta. Transformation of 

dissolved Se(VI) into particulate Se has been demonstrated within the existing SLD. Early surveys 

conducted when the SLD was carrying Westlands subarea drainage to the Kesterson National Wildlife 

Refuge observed a maximum sediment concentration of 210 μg Se/g dw and an average of 84 μg Se/g 

dw in the SLD (Presser et al., 1996; Appendix E, Table E1). A compilation of 1994 surveys, after the 

Grassland Bypass Channel Project had begun, showed a maximum of 146 μg Se/g dw and an average 

of 44 μg Se/g dw in SLD sediment samples (Appendix E, Table E1). In whole core samples collected 

in 1997 from the SLD, the range of concentrations was 3.8 to 100 μg Se/g and the mean was 30 μg 

Se/g dw (USBR et al., 1998). The elevated Se concentrations and the wide range of concentrations 

documented in bed sediment of the SLD are consistent with observations from wetlands (including 

Kesterson Reservoir) where microbial dissimilatory reduction and biotransformation by primary 

producers stripped dissolved Se from the water and converted it to particulate Se(0) and particulate 

Se(-II). Martens and Suarez (1997) showed that Se in SLD sediment was probably approximately 90% 

elemental Se, 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 

61
in sediments, which is apparently sufficient to transform a significant quantity of incoming Se to 

particulate form (Presser et al., 1996; Presser and Piper, 1998). Re-suspension and transport of 

sediments from the SLD, therefore, must be considered as a source of Se for the SJR, deserving of 

further study. Similarly, re-suspension of sediments in a SLD extension to the Bay-Delta could 

provide a similar direct source of highly contaminated particulate Se to the Bay-Delta. The hydraulic 

residence time of the North Bay at low flows is about 60 days (Walters et al., 1985). Substantial 

oxidation of Se(0) could occur if fine particles or plant detritus generated in the SLD were transported 

to the Bay-Delta. Elemental Se 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 any discharge from a SLD extension or within sediments deposited within the SLD 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 SLD into Kesterson 

National Wildlife Refuge showed that Se 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 Se 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 et al., 1996) 

Sedimentary selenium in Suisun Bay and San Pablo Bay

Wetland transformation of Se in the Bay-Delta has not been well studied, nor have surveys of marsh 

sediments been conducted systematically. Zawislanski and McGrath (1997) reported concentrations of 

1.0 to 1.25 μg Se/g in the sediments of a marsh on Carquinez Strait. Concentrations were similar in 

core samples collected down to 15 cm depth in the sediment. Compared to dissolved concentrations in 

Carquinez Strait (0.1 to 0.3 μg Se/L), the Kd for the marsh sediments varied from 3.33 X 103

 to 1.25 X 

104

. Zawislanski and McGrath (1997) also reported pore water concentrations of 2 to 10 μg Se/L, but 

further verification of such high values is necessary. 

Bed sediments that have been studied to date in shallow water habitats of the Bay-Delta are not 

heavily contaminated with Se. For example, Se concentrations were determined in fine-grained 

sediments from a core collected in Richardson Bay, near the mouth of the estuary (Hornberger et al., 

62
1999). Concentrations of Se (0.2 to 0.4 μg Se/g dw) were similar throughout the length of the core, 

with no clear anthropogenic signal accumulating in recent sediments. 

 Zawislanski and McGrath (1997) reported concentrations of 0.5 to 1.0 μg Se/g in mudflat sediments 

adjacent to a marsh in Carquinez Strait. Johns et al. (1988) found mean concentrations of 0.31 μg Se/g 

in repeated analyses of sediments from four locations in Suisun Bay in the late 1984 to 1986. 

Concentrations in New York Slough, where the SJR enters Suisun Bay, were the highest in the region 

(0.53 ± 0.28 μg Se/g dw) and varied, the most widely of any station, from 0.2 to 1.0 μg Se/g dw. 

Recent studies by Cutter et al. (in preparation) show results across a range similar to those reported by 

Johns et al (1988). In summary, concentrations of Se in fine-grained Suisun Bay sediments are 

approximately 0.3 to 0.5 μg Se/g dw and median concentrations of dissolved Se are 0.2 μg Se/L. 

These data show that the sediment water distribution coefficient is approximately 1.5 to 2.5 X 103

, 

within the range reported for other ecosystems. 

Suspended particulate selenium in Suisun Bay and San Pablo Bay

 Water column biogenic transformation of dissolved to particulate Se is well known and is especially 

important in determining exposures of filter-feeding consumer organisms. Selenium concentrations 

per unit mass suspended material exceed concentrations in bed sediments, based upon several analyses 

conducted in 1986 (Cutter, 1989), June 1995 and October 1996. The concentrations on suspended 

material can vary widely. 

• In April 1986, after an episode of extremely high river inflows, the maximum concentration of Se 

on particulate material near Carquinez Strait was 0.64 μg Se/g dw particulate and an average 

concentration throughout the North Bay was 0.33 μg Se/g dw particulate. 

• In September 1986, during low inflows, the concentration of particulate Se averaged 0.75 μg/g 

dw, with a maximum of approximately 1.25 μg/g dw. The particulate Se concentrations were 

approximately 5 X 103

 to 1 X104 greater than the concentration per unit mass dissolved in the 

water column. 

• In June 1995, during a prolonged period of very high inflows, particulate Se concentrations 

ranged from 0.53 to 0.99 μg Se/g dw with an average concentration among six samples of 0.68 

μg Se/g dw. The Kd for median concentrations in this sampling was: 

 [0.075 μg Se/L] / [0.75 μg Se/g dw] = 1 X 104

. 

63
• In October 1996, during low flows, particulate Se concentrations were more than twice the 

concentrations in September 1986 (Figure 13). Concentrations of approximately 7.70 μg Se/g 

dw were observed in suspended material in the Sacramento River channel at Rio Vista and 3.57 

μg Se/g dw was found in the SJR channel. The two are interconnected at this time of year, so 

the SJR was the likely source of this material. Concentrations declined down the estuary, 

further suggesting a delta/riverine source. Elsewhere in the Bay-Delta, Se concentrations on 

suspended material were approximately 1.54 to 2.51 μg Se/g dw, with an average concentration 

in eight bay samples of 1.98 μg Se/g dw [i.e., more than two times higher than the mean (0.75 

μg Se/g dw) in September 1986]. The Kd’s for the median Suisun Bay concentrations for the 

October 1996 survey were therefore: 

 [0.18 μg Se/L] / [2.1 μg Se/g dw] = 1.17 X 104 

• For the landward site at the head of the estuary with highly elevated concentrations, the Kd was: 

 [0.18 μg Se/L] / [5.6 μg Se/g dw] = 3.1 X 104. 

Summary

 Concentrations > 1 μg Se/g dw in suspended materials are common and concentrations as high as 8 

μg Se/g dw 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 X 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 suspended and sedimentary Se and the differences in Kd’s between 

these two reservoirs of Se. Time-intensive studies and continued assessment of the sources of the 

highest Se concentrations transported in suspended material to the Bay-Delta are also needed. 

BIOACCUMULATION OF SELENIUM BY INVERTEBRATES 

Processes 

Bioaccumulation by lower trophic level invertebrates (e.g., zooplankton and bivalves) is a critical 

step in determining effects of Se. These are the animals that provide the vector (food) that is the source 

of Se exposure to higher trophic level predators such as fish and birds. Estuarine invertebrates are 

exposed to Se via: 

• direct uptake of dissolved Se; 

64
• primary producers taking up Se and they themselves being consumed by animals: and/or 

• direct uptake of detrital or sedimentary Se-enriched particles via filter-feeding or deposit 

feeding. 

In laboratory studies of the muscle Mytilus edulis, dissolved selenite [Se(IV)] is the most 

bioavailable form of inorganic Se taken up from solution, but the uptake rate is slow compared to many 

trace elements (Wang et al., 1996). Luoma et al. (1992) showed that the uptake rate of dissolved 

selenite explained less than 5% of the tissue burden of Se accumulated by the clam Macoma balthica at 

concentrations typical of the Bay-Delta. The role of dissolved organic selenides in Se bioaccumulation 

is not as well understood as availability of inorganic Se, 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 Se (dissolved selenite plus dissolved organo-Se) by 

invertebrates is not as important as uptake from diet (Luoma et al., 1992; Lemly, 1993 a). Dissolved 

Se speciation strongly influences uptake by primary producers (e.g. 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 approximately 10 4 or 10 5 (e.g., 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), which are then transferred to the next trophic level with great 

efficiency. Assimilation efficiencies for phytoplankton-associated Se vary from 55 to 90% among 

different invertebrates (e.g., Reinfelder et al., 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 et 

al., 1996; Luoma et al., 1992). For example, Luoma et al. (1992) studied uptake of particulate 

elemental Se produced from the microbial reduction of 75Se-selenate. The particulate Se(0) was 

formed by simulating the biogeochemical transformation process thought to be predominant in 

wetlands. The assimilation efficiency of elemental Se was 22%. 

Selenium in Invertebrates from the Bay-Delta 

 Fish and birds are the wildlife of greatest concern with regard to Se contamination. However, fish 

and birds are mobile, impractical to sample in large numbers, and difficult to monitor routinely. On 

65
the other hand, consumption of prey, comprised of primary and secondary consumer species, is the 

route by which these predators are exposed to Se. Consumer species like bivalves, polychaetes, 

amphipods or zooplankton can be practical to employ as resident bioindicators of Se exposure (Phillips 

and Rainbow, 1993; Brown and Luoma, 1995b). As discussed below, the predators with the highest 

tissue concentrations of Se in the Bay-Delta are benthivores that consume bivalves in their diet. 

Therefore, the most relevant bioindicators to these sensitive predator species are bivalves. 

Interpretations are least ambiguous when Se 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 geology are not Se-enriched, if no anthropogenic sources of Se are known, and if 

the concentrations in the indicator organism are in the lowest quartile of all available data. 

Concentrations of 1.70 μg Se/g to 2.66 μg Se/g dw were reported by the San Francisco Estuary 

Regional Monitoring Program for Trace Substances 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 et al. (1988) found a mean reference concentration and 95% confidence limits of 

3.08 ± 0.28 μg Se/g dw in C. fluminea from apparently uncontaminated sites near Clifton Court 

Forebay and in the Tuolomne River (Figure 14a). 

 Bivalves from the Bay-Delta have elevated Se concentrations compared to these references 

(Risebrough et al., 1977; Johns et al., 1988; Urquhart and Regalado, 1991) (Figure 14a). Risebrough et 

al. (1977) reported concentrations of 10.0 to 11.4 μg Se/g dw in a single deployment of transplanted 

mussels (Mytilus sp.) in Carquinez Strait, and concentrations of 5.0 to 7.4 μg Se/g dw near Mare Island 

in Suisun Bay. Anderlini et al. (1975) reported concentrations of 4.5 to 6.7 μg Se/g dw in the clam M. 

balthica near Mare Island in 1974. Although conducted more than 20 years ago, both these studies 

analyzed their samples by neutron activation, which is a relatively insensitive but reliable analytical 

technique. Johns et al. (1988) collected C. fluminea from resident populations at six locations in 

Suisun Bay, between January 1985 and October 1986. Figure 14a 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 et al. (1988). The mean concentration 

and 95% confidence limits among the Suisun Bay data was 5.08 ± 0.17 μg/g dw, significantly different 

than the reference values (p<0.001). These historic data show that the habitat in Carquinez Strait was 

66
contaminated two-fold or more with Se compared to reasonable reference locations, and that 

contamination was present since at least 1974. 

 In 1986, the bivalve Potamocorbula 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 et al., 1990). Figure 14b adds to the C. fluminea

distribution, the frequency distribution of Se among 62 composite samples of P. amurensis, collected 

between May 1995 and June 1997, from Carquinez Strait (Linville and Luoma, in press). The mean 

concentration and 95% confidence limits among all data for P. amurensis was 12.94 ± 0.75 μg/g dw. 

A wide distribution of concentrations was also observed, reflecting substantial temporal variability. 

 Thus, the mean concentration of Se in the dominant resident bivalve in Suisun Bay (C. fluminea in 

1985-86 compared to P. amurensis in 1996) has more than doubled since 1985-86. It is therefore 

likely that the total amount of Se experienced by birds and fish that feed on bivalves has similarly 

doubled. The 1995-1997 mean concentration in P. amurensis exceeds the dietary threshold (10 μg 

Se/g dw) for predators that has a high certainty of producing adverse effects in predators. During 1995 

- 1997, 32% of P. amurensis samples from Carquinez Strait contained greater than 15 μg Se/g dw. 

Lemly (1997a; b; c) cites case studies that indicate that concentrations of Se in prey species of 5 to 20 

μg Se/g dw initiate teratogenic deformities in fish and load the eggs of some bird species beyond 

teratogenic thresholds (see discussion below). 

 Se concentrations in P. amurensis from Carquinez Strait vary seasonally. Concentrations varied 

approximately three-fold with time during 1995 to 1997. The highest concentrations were observed in 

October 1996 (20 ± 1 μg/g dw) and the lowest concentrations were observed in May 1995 (7.13 ± 0.34 

μg Se/g) and May 1997 (6.2 ± 0.2 μg/g) (Figure 15). The changes in concentrations coincided with 

seasonal changes in mean monthly river inflows to the North Bay. The lowest concentrations occurred 

after the two episodes of highest river inflows. The greatest increase in Se occurred after prolonged 

periods of low flow. Inflows from the SJR and/or inflow-driven differences in residence times of local 

waters could also be important, because the highest ratios of SJR/total Delta outflow occur in fall 

(Figures 9 and 10). 

 An extensive spatial survey was conducted in October 1996 to determine how concentrations of Se 

in P. amurensis compare among different locations in the North Bay. Se concentrations were 

67
determined in replicate composite samples of P. amurensis at 22 locations (Figure 16) (Brown and 

Luoma, 1995a; Linville and Luoma, in press). The October 1996 sampling included an extensive 

investigation of the 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 et al. (1988). Among the stations, the 

greatest elevation of Se was found in resident P. amurensis from Carquinez Strait and from the deeper, 

westward channel of Suisun Bay and toward the mouth of the SJR. 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 concentrations were found in 

Grizzly Bay, in particular in association with inflows of Sacramento River water through a location 

called Suisun Cutoff.

Summary of Selenium in Invertebrates from the Bay-Delta 

 In summary, Se bioaccumulation data from invertebrates show the following: 

• Selenium enrichment in primary consumer species (bivalves) has been evident in Suisun Bay 

since the 1970's. 

• The spatial pattern of historic contamination was consistent with an origin from refinery 

effluents (as shown by water column analyses), which have been discharged to the Bay-Delta 

since approximately 1900. 

• The highest Se concentrations reported in the Bay-Delta in consumer organisms 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 Luoma (in press). No systematic studies of Se concentrations in clams 

are available since that time. 

• Selenium enrichment was apparently spread through all of Suisun Bay and all of San Pablo Bay 

in 1996. 

• Temporal variability was not significant in monthly samples of C. fluminea in 1985-86; but 

three-fold seasonal variability in Se 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 

68
• In the most recent survey, Se concentrations in P. amurensis near Carquinez Strait exceed 10 

μg/g dw in most months of the year (all months of some years), and 32% of values measured 

between October 1995 and June 1997, exceed 15 μg/g dw. Thus, thresholds for chronic Se 

toxicity in the food of birds and fish (> 10 μg/g, Skorupa, 1998a) are exceeded regularly. 

• It is not yet clear whether the high Se contamination in P. amurensis is unique to this species, 

represents greater Se inputs (probably from the Delta and SJV via the SJR) than occurred 

historically, or both. 

Modeling Selenium Bioaccumulation in the Bay-Delta: DynBaM 

 Bioavailability of Se 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 (i.e., include consideration of geochemical form), biologically specific, and 

flexible for a variety of environmental circumstances. Predictions from the model should be verifiable 

in nature. The USEPA approach (Peterson and Nebeker, 1992) uses the following simple ratio: 

Bioaccumulation = [concentration in organism]/[concentration in environment], 

where environmental concentrations are either those in water (the BAF, bioaccumulation factor) or 

sediment (the BSAF, biota to sediment accumulation factor). 

 The flaw of this approach is that it does not allow consideration of effects of speciation in water or 

of particulate material on bioaccumulation. Thus BAF’s 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 Model or DynBaM uses different 

experimentally established uptake rates for different forms of dissolved and particulate Se, along with 

environmental concentrations of these forms, to determine bioaccumulation in tissues (Luoma et al.,

1992). The advantages of this approach have been discussed extensively by Luoma and Fisher (1997) 

and Schlekat et al. [in press (a)]. One advantage for the Bay-Delta evaluation is that bioaccumulation 

can be derived for different speciation regimes. The speciation consideration is very important because 

speciation will change as sources change, and relations with total Se or individual species of Se will 

also change (e.g., CSFBRWQCB, 1992a). Another substantial advantage of the approach is that model 

predictions can be verified by comparison to analyses of Se in tissues of resident species. We will 

employ DynBaM in all predictions of Se effects on predators from forecasts of Se loadings. 

69
 The mathematics of the simplest kinetic model with food and water pathways illustrates the 

necessary data: 

 dCm/dt = (If + Iw) - C(ke + g) (1) 

 

Cm,t = [If + Iw/(ke + g)] [1 - e-(kt + g)t] (2) 

Cm,ss = If/ke (3)

where, Cm is concentration in animal, t is time, If is gross influx rate from food, Iw is gross influx rate 

from water, ke is rate constant of loss (slowest compartment), and g is growth. For Cm,ss or 

concentration at steady state 

Cm,ss = If + Iw/ke (4) 

if we assume that growth is not important. Mechanistically, the mathematics state that 

bioaccumulation 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 

(Equation 1, 2). Gross influx can come from water or from food and is a species-specific function of 

the concentration of bioavailable element. 

For influx rate from food alone, in μg Se/g tissue per day: 

If = FR X Cf X AE (5) 

where FR is feeding rate in g food/g tissue per day, Cf is concentration in food (particulate material) in 

g Se/g dw, and AE is assimilation efficiency. Influx rate from water can be broken into its components 

similarly (Wang et al, 1996), but because the influx rate from water was determined experimentally for 

specific species of Se by Fowler and Benayoun (1976), Wang et al. (1996) and Luoma et al. (1992), the 

rate will be employed directly here as μg Se/g tissue per day. 

 From Reinfelder et al. (1997), the ultimate concentration of Se that a bivalve would bioaccumulate 

under each environmental condition can be calculated from: 

Css = [Iw + (FR X Cf X AE)]/ke (6) 

70
BIOACCUMULATION OF SELENIUM BY PREDATORS 

 Numerous studies have demonstrated that a small increase in waterborne Se will result in a 

disproportionately large elevation of Se concentrations in fish and wildlife (Skorupa, 1998a). Several 

attributes affect Se uptake by these organisms: 

Processes that affect Se retention and inter-organ distribution are important considerations for 

fish and birds that range and feed widely over areas with varying Se exposure pathways. 

• 

• 

• 

Dietary exposure and, in most cases, progressive biomagnification through the food web is the 

pathway that leads to the disproportionately large bioaccumulation of Se in upper trophic 

levels. 

Some implications of dietary uptake are: 

o waterborne Se concentrations are poorly linked to predator bioaccumulation because 

environmental factors affect transformation of Se and uptake by invertebrates; 

o where data on predators is difficult to obtain directly, invertebrates may be the best 

indicator for monitoring predator exposures; 

o a predator’s choice of food, which varies widely among species, could result in some

trophic pathways being more efficient accumulators of Se than others. For example, longterm studies of the terrestrial environment created by burial of the contaminated evaporation 

ponds at Kesterson Reservoir show that invertebrate carnivorous and scavenger species tend 

to be higher than herbivorous species as a route to vertebrate exposure (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 Se in fish. This study was at a reservoir (Belews Lake, North Carolina) 

contaminated by the wastes of a coal-fired power plant (Cumbie and Van Horn, 1978). He compared 

concentrations of Se in bluegill and largemouth bass collected from the lake, with concentrations of Se 

in those species when exposed to sublethal concentrations of Se in water alone in a laboratory study. 

He found a lower concentration factor from water alone than from bioaccumulation via dietary plus 

waterborne sources. This finding was corroborated by the observation that piscivorous fish, at the 

highest trophic level, accumulated the most Se in the lake. All piscivores and omnivores eventually 

71
succumbed to the poisoning, while a few lower trophic level fish survived. Other studies have since 

verified directly and indirectly the overwhelming importance of Se bioaccumulation from food, as 

compared to direct uptake from water. 

 If the primary source of Se to wildlife is dietary, then it should not be surprising that waterborne or 

dissolved Se is an imprecise predictor of the Se exposure of birds and fish (Skorupa and Ohlendorf, 

1991). Differences in speciation, transformation to particulate form(s), speciation on particulates and 

invertebrate bioaccumulation all influence how waterborne Se is transferred to a predator. These 

processes are affected by the nature of the source and the environmental conditions in receiving waters 

(e.g. Se in agricultural drainage water can be a different form than the Se in industrial sources; Se 

discharged to a wetland is transformed differently than Se discharged to an estuarine water column). 

Physical processes like hydraulic residence time are also important. Particulate transformation of Se in 

a river (e.g. the SJR) may occur far downstream from the source of input; while transformations in a 

wetland or an estuary with a long residence time may occur near the input. Biological processes that 

affect exposure of the predator include differences among predator species in feeding, behavior, and 

physiology. 

 An example of the influence of confounding processes on this linkage can be found in data from the 

Bay-Delta watershed. Black-necked stilt, a wading bird, averaged about the same exposure to Se (20 

to 30 μg Se/g dw found in eggs) at Chevron Marsh in the Bay-Delta as at Kesterson Reservoir (25 to 

37 μg Se/g dw in eggs), but the source water in Chevron Marsh contained about 10% the concentration 

of Se found at Kesterson (maximums: 20 vs. 300 μg Se/L) (Skorupa, 1998a). The reason for the 

difference was that the transfer of Se from water to aquatic invertebrates was greatly enhanced at 

Chevron, compared to Kesterson, because the original form of the element was selenite. 

 Because of the above complexities, the strongest correlative predictor of Se concentrations in 

predator tissue that reflects Se exposures is probably Se concentrations in invertebrates (prey). 

Invertebrates may be the optimal indicator to use in monitoring Se in an ecosystem because they are 

practical to sample and are most closely linked to predator exposure (prey are the primary source of Se 

for the predators). Few authors have fully explored feeding relationships and resultant correlations 

with Se bioaccumulation in food webs. 

 One repeated observation in contaminated ecosystems is that predator species differ in their 

bioaccumulation of Se. 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) > 

72
omnivores > planktivores. These feeding guilds were probably too broad, however. In Lake 

Oltertjarn, Sweden, after treating the lake with selenite for two years, Se tissue concentrations in 

northern pike (Esox lucius) averaged 4.6 μg Se/g, whereas in perch (Perca fluviatilis) the average was 

23 μg Se/g (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 Se 

concentrations, whereas the pike ate water-column-feeding fish with low Se concentrations. 

Differences in Se exposure among predators also seem to be the case in the Bay-Delta. Fish (e.g. white 

sturgeon, starry flounder, and probably Sacramento splittail) that ingest benthos, and especially 

bivalves, have higher Se concentrations (e.g., 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 Se contamination. It is likely that the species experiencing the 

highest exposure of Se are at the greatest risk of extinction or to suffer population damage. It also 

should be remembered that biomagnification is sufficient to eliminate species at the top of the trophic 

structure, even when waterborne Se concentrations are in the 2 to 5 μg/L range (Lemly, 1985; 1997b; 

d). So some Se contaminated systems may already have lost vulnerable food web linkages. Study of 

systems with less extreme contamination may be one way to understand where those vulnerable 

linkages occur. 

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

 The CDFG conducted extensive sampling of a variety of bird and fish species in the Bay-Delta 

between 1986 and 1990 in a Selenium Verification Study for the CSWRCB (White et al., 1987; 1988; 

1989; Urquhart and Regalado, 1991). The Selenium Verification Study was one of the most extensive 

surveys of Se 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 Se. The greatest 

differences between the two ecosystems occurred in bottom-feeding fish [e.g. English sole (Parophrys 

vetulus) with 3.05 ± 0.2 vs 1.78 ± 0.2 μg Se /g in flesh, respectively; and starry flounder with 9.2 ± 2 vs 

3.6 μg Se/g in liver, respectively]. Although the sampling was limited in number, Dungeness crab 

from Suisun Bay contained a mean concentration of 14 μg Se/g dw tissue, compared to a mean 

concentration of 5 μg Se/g dw tissue in Humboldt Bay. Selenium concentrations in Pacific herring 

73
(Clupea pallasi), speckled sandabs (citharichthys stigmaeus) and longfin smelt (Spirinchus 

thaleichthys) were not different between the two ecosystems. Uptake of Se by striped bass in the North 

Bay also did not appear problematic in samplings in 1986 (average, 1.3 to 1.9 μg Se/g dw) (Saiki and 

Palawski, 1990). Thus, some bottom-feeding fish bioaccumulated Se in excess of the reference area, 

but fish (e.g., herring, striped bass) that were primarily herbivorous, or fed from the water column, 

showed little difference in Se tissue concentrations between the two ecosystems. 

 The highest concentrations of Se were found in white sturgeon in the Bay-Delta (Figure 17). 

However, white sturgeon were not found for comparison in Humboldt Bay. White sturgeon is a longlived benthic predator, that spends its life in the Bay-Delta, the Sacramento River, and to a small 

extent, the SJR (Kohlhorst et al., 1991). White sturgeon are voracious consumers of P. amurensis. 

This raises the possibility that Se trophic transfer via bivalves is a critical pathway of Se exposure in 

the Bay-Delta. If so, it would be expected that Se concentrations in white sturgeon should have 

increased after P. amurensis invaded the estuary in 1986. Average concentration of Se in the livers of 

ten white sturgeon sampled in 1986 were 9.2 ± 2.9 μg Se/g (White et al., 1987; 1988; 1989; Urquhart 

and Regalado, 1991). In 1989-90, 42 white sturgeon livers were sampled; the average concentration of 

Se was 30 ± 21 μg/g in liver. Although variability was high (as expected for animals that move over 

large areas), the average Se 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 et al., 1997; Fairey et al., 1997; San Francisco Estuary 

Institute, 1999). The number of white sturgeon analyzed were many fewer than determined for 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 Se contamination of white sturgeon in the late 1990’s. 

 It is interesting to contrast the Se concentrations in white sturgeon to those in striped bass, another 

major resource species in the system. Striped bass are also anadromous fish, like white sturgeon, 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 SJR downstream through San Pablo Bay. Some of their observations about 

Se concentrations in whole-body samples of striped bass included: 

74
• The highest Se concentrations were found in the main channel of Mud Slough and in the SJR, 

immediately downstream from Mud Slough. 

• The mean Se concentration among the six most contaminated sites was 5.3 μg Se/g dw. 

• Se concentrations were low above Mud Slough and also downstream in the SJR, as tributary 

dilution increased (range of 1.03 to 2.9 μg Se/g in the lower SJR, below the Merced River). So 

bioaccumulation was responsive to expected inputs of contamination. 

• Mean Se concentrations in the North Bay were 1.3 to 1.9 μg Se/g dw. These values are at least 

five-fold lower than the average concentration in white sturgeon from the Bay-Delta, at that 

time (Table 12, when Se in flesh is converted to Se in whole-body samples). 

 In summary, striped bass do bioaccumulate more Se in environments where more Se is present. 

However, these animals are not exposed to as much Se 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 Se than are white sturgeon. The latter suggests links between bioaccumulation and adverse 

effects need to be studied, perhaps comparatively, in these species. 

 Eleven species of waterfowl were also analyzed in the Selenium Verification Study (White et al., 

1987; 1988; 1989; Urquhart and Regalado, 1991) (Figure 18). 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, Grays Lodge Wildlife Area, 

and the Sacramento National Wildlife Refuge) showed the following average Se concentrations in liver 

tissue: dabbling ducks, 3 to 8 μg Se/g; shorebirds, 4 to 12 μg Se/g dw, and cormorants 18 μg Se/g dw 

(White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). Average concentrations in greater and 

lesser scaup liver were 9 μg Se/g dw and in surf scoter liver were 17 μg Se/g dw. These values are 

typical of uncontaminated areas elsewhere in the world, as well (Goede, 1994). Concentrations of Se 

in mallard (Anas platyrhynchos), American bittern (Botaurus lentiginosus), northern shoveler (Anas 

clypeata), and double-crested cormorant (Phalacrocorax auritus) were not different between the BayDelta and the reference areas. Mean concentrations in two species of shorebird—willet 

(Catoptrophorus semipalmatus) and American avocet (Recurvirostra americana)—were about 20% 

higher in Bay-Delta than in reference areas. Mean Se concentrations in livers of American coot and 

scaup from Suisun Bay and San Pablo Bay were 2-4 times those in samples from reference areas. The 

highest concentrations of Se in aquatic birds in the Bay-Delta were found in surf scoter (range 13 to 

75
368; average 134 μg Se/g range in liver) from Suisun Bay and San Pablo Bay. Annual averages from

Suisun Bay ranges from 80 to 240 μg Se/g 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 Se/g). These concentrations also exceeded concentrations found 

in surf scoter from Morro Bay, the Central Bay and the South Bay (White et al., 1987; 1988; 1989; 

Urquhart and Regalado, 1991). Concentrations in surf scoter livers from the North Bay were also two 

to three-fold higher in 1988, 1989 and 1990, than in 1986. 

 Concentrations of Se varied remarkably among bird species with different food preferences in San 

Pablo and Suisun Bay. The most contaminated birds (surf scoters) had Se concentrations in their livers 

that were up to two orders of magnitude higher than the Se concentrations in mallards and American 

bittern. Because of feeding habits, it seems that vegetarians exhibited some of the lowest Se 

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 et al., 1995; Hoffman et al., 1998). In general, scaup 

obtain approximately 40% of their diet from animal food sources versus scoter who obtain 

approximately 95% of their diet from animal food sources. 

 In 74 samples from an array of studies, Skorupa and Ohlendorf (1991) reported mean 

concentrations in bird eggs from reference sites as 1 to 3 μg Se/g. More than 90% of values were 

below 3 μg Se/g. The authors concluded that concentrations above 3 μg Se/g in eggs represent 

contamination (Skorupa and Ohlendorf, 1991). Thus, data exist to compare Se concentrations in bird 

eggs in the Bay-Delta. However, only limited studies in the broader Bay-Delta ecosystem are available 

(e.g., Lonzarich et al., 1992; Ohlendorf and Marois, 1990). 

 

EFFECTS OF SELENIUM ON WILDLIFE 

 Selenium is an essential element necessary for the formation and proper functioning of glutathione 

peroxidase, an important antioxidant enzyme. The window between required concentrations and toxic 

concentrations of this element is narrow compared to other toxins (e.g., National Research Council, 

1976; Wilbur, 1983; Hodson and Hilton, 1983; Presser and Ohlendorf, 1987; SJV Drainage Program, 

1990b). In excessive amounts, Se is erroneously substituted for sulfur in enzymes and the structure of 

76
the proteins is disrupted. The result is dysfunctional enzymes and proteins. Reproductive failure 

and/or teratogenesis (deformities in developing young) are the earliest manifestations in the organism. 

When eggs hatch, the developing soft tissues and hard tissues of the young are deformed, because of 

disrupted protein structure. In fish, teratogenesis is induced when larval fish are relying on their 

attached yolk sac for nourishment and development. Once external feeding begins Se will not cause 

further deformities in the juvenile fish. Thus the vulnerable pathway is mother to egg to developing 

larvae and fry. 

 Deformities may not always be lethal themselves, but they lower the probability that the 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 it is important to 

focus on newly emerging larvae and fry. 

 Community simplification (including local extinction of some species) is ultimately the result of

excessive Se contamination. Sixteen of the twenty fish species that originally inhabited Belews Lake 

disappeared when Se contamination increased. Kesterson Reservoir was thought to contain a multispecies assemblage of warm water fish before discharges of irrigation drainage waters began (Skorupa, 

1998a). Only mosquitofish (Gambusia affinis) persisted after Se contamination was introduced (Saiki, 

1986; Saiki and Lowe, 1987; Saiki et al., 1991; Skorupa, 1998a). Hamilton (1999) recently presented 

the hypothesis that Se 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 continues to inhibit their recovery. Hamilton 

(1999) cites four lines of evidence linking Se 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 inputs, which began in the 1890’s; 

• 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 (e.g., dam building) other than substantial input of irrigation drainage; 

and 

77
• absence of young razorback suckers in historic collections suggest reproductive failure (lack of 

recruitment) was the cause of the population collapse. 

Hamilton (1999) concludes that reservoir construction and introduction of exotic species have 

undoubtedly contributed to the decline of endangered fish species in the Colorado River, but that Se 

must also be included as an important contributing factor. 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 Se cannot be ignored as an issue 

that can inhibit accomplishment of that goal. 

 Selenium concentrations in food and concentrations in tissues have both been employed to evaluate 

how the exposure of Se experienced by an animal is linked to effects on reproduction or teratogenesis. 

Linkages 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, Se 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. 

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

Fish

 Concentrations of Se greater than 3 μg/g in the diet of fish result in deposition of elevated 

concentrations in developing eggs, particularly in the yolk. Dietary Se concentrations of 5 to 20 μg/g 

load eggs beyond the teratogenic threshold (Table 13 and Lemly, 1998a). Extinctions of fish species 

occurred in Belews Lake, when Se concentrations in invertebrates were in the concentration range of 

20 to 80 μg/g dw. Concentrations in invertebrates in Kesterson National Wildlife Refuge were greater 

than 100 μg Se/g dw in the presence of Se-induced bird deformities and disappearance of most species 

of fish. 

Birds

 Laboratory studies have evaluated dietary concentrations of different forms of Se that affect 

reproduction in birds. Concentrations of 20 μg Se/g causes food avoidance, weight loss and mortality 

78
in adult males (Heinz and Fitzgerald, 1993). Effects were enhanced during cold winter weather. 

Selenomethionine in food at concentrations of 16 μg Se/g causes complete reproductive failure in 

mallards (Heinz et al., 1989). A diet of 8 μg Se/g selenomethionine compared to 1 μg Se/g fed to 

mallards caused a 33% reduction in hatching success and a 17% reduction in survival of ducklings; 

approximately 7% of the unhatched eggs had deformities (Heinz et al, 1989; Stanley et al., 1996). 

According to Heinz et al. (1989) the 8 ppm diet resulted in a mean decrease of 43% in the number of 6-

day-old ducklings compared to controls. Most recently, Heinz (1996) concluded that the dietary 

threshold that results in teratogenic effects was between 4 and 8 μg Se/g dw; above 8 μg Se/g the 

percentage of deformities rose rapidly. 

 Ohlendorf (1989) reported that bird eggs generally contain 1 to 3 times the dietary Se of breeding 

females. Heinz et al. (1989) showed that Se in eggs of mallards (experimental exposure) was closely 

related to hen’s dietary exposure to Se (fed selenomethionine). Average egg concentrations were 2.5 

to 4.0 times dietary concentrations. However, diets supplemented with inorganic Se result in Se 

concentrations in eggs that are only 0.1 to 0.18 times dietary concentrations. Skorupa and Ohlendorf 

(1991) concluded that, if assimilation of Se in the wild is similar to Se-methionine in the laboratory, 

then dietary Se of 5 μg Se/g dw would yield 15 μg Se/g dw in eggs. This level in eggs was the lowest 

mean concentration associated with embryo teratogenesis at Kesterson Reservoir. Ohlendorf (1989) 

concludes that hatchability of eggs is reduced when dietary concentrationa are 6 to 9 μg Se/g. So, 

similar to fish, 5 to 9 μg Se/g dw in food encompasses the critical dietary thresholds in birds. 

 Thus, both field and laboratory studies suggest that the Se concentrations typical of bivalves in 

Suisun Bay and San Pablo Bay (6 to 20 μg Se/g, Table 13 and Figures 14 to 16) are beyond the 

threshold of Se concentrations in food that are likely to cause 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 Se in fish to teratogenic or reproductive 

effects (Table 14). Reproduction has the advantage of being a very sensitive endpoint to study. But, 

environmental factors as well as Se can affect reductions in reproductive success in nature. Short-term

79
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 pollutant caused changes are more likely to be uni-directional with 

exposure to the pollutant. No long-term studies are available from the Bay-Delta, however. 

Teratogenesis is perhaps a less sensitive measure of Se effects, but has the very attractive advantage of

being a more Se-specific outcome (i.e., many fewer factors cause teratogenesis than affect reproductive 

success). From a review of the literature, Lemly (1998b) recommended the following toxic effects 

thresholds from Table 14: 

• whole body, 5 to 7 μg Se/g dw; 

• 

• 

• 

• 

skeletal muscle, 6 to 8 μg Se/g dw; 

liver, 15 to 20 μg Se/g dw; 

ovary and egg, 5 to 10 μg Se/g dw, 

larvae/fry, 8 to 12 μg Se/g dw. 

 Deformities increase rapidly in prevalence once Se in fish eggs exceeds 10 μg/g dw. High 

proportions of some fish populations showed deformities above 20 μg Se/g dw whole-body tissue. 

Reviews of field and lab studies (Table 14) show that the lower whole-body tissue threshold for effects 

may be between 4 and 6 μg Se/g; and it seems quite certain that teratogenesis and reproductive failure 

consistently begin to appear at tissue concentrations in excess of 15 μg/g dw. 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 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 Se concentration found in 62 samples of white 

sturgeon muscle was 15 μg/g dw and in 42 samples of liver was 32 μg/g dw (Table 12 and Figure 17). 

Both means are above the levels at which deformities are likely to occur (Table 14) and some levels in 

individual fish (range 6 to 80 μg Se/g, liver; 2 to 50 μg Se/g, muscle) far exceed tissue thresholds for 

reproductive effects. However, the relation of reproduction and Se-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 Se concentrations in ovaries and egg yolk components above thresholds for 

effects (Table 14) (Kroll and Doroshov, 1991). 

80
Birds

 Tissue thresholds in birds are not too different from those in fish. Heinz (1996) stated that the 

embryo is the avian life stage most sensitive to Se poisoning. Skorupa (1998 a; b; c) has concluded 

that Se concentrations in eggs are a good choice for a risk metric to determine avian embryonic 

exposure and response. Skorupa and Ohlendorf (1991) originally suggested that teratogenesis 

thresholds were between 13 and 24 μg Se/g dw mean egg Se. This range remains consistent with later 

studies (Table 15), if dry weight is assumed to be 4 to 5 times wet weight. Hatchability is more 

sensitive 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, Ohlendorf et al. (1986) showed a strong correlation between embryonic Se exposure and 

embryonic viability (hatchability). Hatching failure started increasing rapidly above 10 μg Se/g dw 

egg. Skorupa (1998a) suggests the critical exposure concentration causing reduced hatchability, for 

sensitive birds, is 6 to 7 μg Se/g dw in eggs. He bases this conclusion 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 predicted embryo deformity threshold for ducks is 15 to 20 μg Se/g 

(Skorupa, 1998 a; b; c). In black-necked stilts the critical concentration in eggs for embryo deformity 

is 18 to 25 μg Se/g dw, and in avocets it is 38 to 60 μg Se/g dw. In Martin Reservoir, Texas (Skorupa, 

1998a), Se at 11 μg Se/g in red-winged blackbird (Agelaius phoeniceus) eggs was associated with 50% 

depression in egg hatchability, although patterns of contaminations were not as clear as in other field 

cases. Hepatic (liver) concentrations may be a less precise indicator of pathological conditions 

than are egg concentrations (Table 15). Heinz (1996) concluded that concentrations in liver greater 

than 10 μg Se/g wet wt (40 μg Se/g dw based on 75% moisture content) should be considered possibly 

harmful to the health of young and adult birds. A very high risk of embryo deformity exists when the 

mean Se concentration (wet weight) in the liver of a population of birds exceeds about 9 μg Se/g (36 

μg Se/g dw). Reproductive impairment occurred at 3.5 μg Se/g on a wet wt basis (14 μg Se/g dw) and 

at 4.7 μg Se/g on a wet wt basis (18.8 μg Se/g dw) (Heinz et al., 1989; Heinz, 1996). 

O’Toole and Raisbeck (1998) 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). 

81
Loss rates of Se are another important consideration for migratory waterfowl or fish. Surf scoter, 

greater and lesser scaup, and white sturgeon may experience high Se exposures during their residence 

time in the Bay-Delta, but Se concentrations 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 thresholds for adverse effects (Figure 18 

and Table 15). From 1986 to 1990, individual and mean annual average Se concentrations in liver of 

surf scoter far exceed thresholds during their residence in Bay-Delta (Table 15). Concentrations in 

liver of surf scoter in the North Bay are in the range of Se concentrations in livers of ducks, coots, 

grebes, and stilts sampled at Kesterson Reservoir in 1983-1984 (Table 15). Hoffman et al. (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 Se/g dw in greater scaup and 119 μg Se/g dw in surf scoter. Surf scoter populations are also 

rapidly declining in North America, and they remain one of the least understood of the migratory 

waterfowl species (Henny et al., 1995). Selenium concentrations seem to rise extraordinarily in scoter 

in response to Se exposures. Henny et al. (1995) have suggested that caution should be exercised in 

linking tissue concentrations to effects in animals with strong bioaccumulative capabililties. For 

example, in other ecosystems bottle-nosed dolphins (Tursiops truncates), Risso’s dolphins (Grampus 

griseus), and cormorants seem to bioaccumulate high concentrations of Se compared to other species. 

Mineral granules rich in Se are common in these species (Nigro and Leonzio, 1996). It could be 

speculated that some species concentrate Se 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 Se exposure and effects of Se across a range 

of species. Those species exposed to elevated Se concentrations as a result of their dietary choices 

should be of special interest in such studies. 

 There is currently no data proving that white sturgeon, surf scoter, or greater and lesser scaup are 

suffering from Se toxicity in the Bay-Delta because of the difficulties associated with studies of 

migratory fauna. Data from both 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 Se on reproduction, population biology, 

and life histories of migratory waterfowl and anadromous fish that are such important components of 

the Bay-Delta ecosystem. 

82
Comparison to Selenium Hazard Index 

 Lemly (1995; 1996a; b) defined hazard as a toxic threat to birds and fish that can be characterized by 

Se concentrations in the environment (water, sediment) and exposure of fish and birds to that hazard 

(tissues). His systematic approach can be applied to data compiled for the Bay-Delta from 1986 to 

1996. 

 Lemly 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. 

• 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 Se are slightly elevated as 

compared to uncontaminated reference sites. 

• No hazard: Se concentrations are not elevated in any ecosystem component compared to 

reference sites (Lemly, 1995; 1996a). 

Lemly developed a scoring method which assigned points to define Se hazard in specific systems: no 

hazard = 5; minimal hazard = 6 to 8; low hazard = 9 to 11; moderate hazard = 12 to15; high hazard = 

16 to 25 (Lemly, 1995; 1996a). The scores represented summation for the lines of evidence (i.e., 

samplings 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 route, alone, can cause toxicity. 

We can further define three levels of certainty of the 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 are 

available.

• Low certainty is chosen if the hazard evaluation is based upon one line of evidence. 

83
 Table 16 shows the results of the hazard analysis from several ecosystems (Lemly, 1985; 1995; 

1996a; 1997c; Kroll and Doroshov, 1991) compared to conditions in the Bay-Delta using data gathered 

in from 1986 to 1996. This table comparing hazard ratings from different ecosystems illustrates the 

diversity of conditions that can occur in ecosystems receiving Se discharges. Most notably, high 

dissolved Se concentrations in some rivers (e.g., LaPlata, Mancos, Animas Rivers in Colorado, New 

Mexico, and Utah, 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, Se cycling, Se 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 Se hazard. In all the reservoirs and pond environments 

surveyed by Lemly (1995; 1996a;b; 1997a; b; c), elevated dissolved Se concentrations are 

accompanied by Se 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 the high hazard. He suggested that as residence 

times increased, the potential increased for Se to be bioaccumulated, to be deposited in and recycled 

from sediment, and to adversely affect fish and birds. For hazard evaluations Lemly (1995; 1996a) 

suggested that sampled nesting birds should be those feeding locally. He suggested coots, grebes and 

dabbling ducks as good choices. Suggested choices of fish for hazard evaluation included minnows, 

sunfish (centrarchids), suckers, catfish, and trout. Our studies of Bay-Delta suggest these species are 

not the most sensitive because their exposure to Se 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 time subjected to Se contamination. 

Using data from the above analysis, a ranking of Suisun Bay under the conditions of 1990-96 is 

possible using Lemly’s scheme. The results of the aquatic hazard assessment and hazard rating for the 

Bay-Delta for the period 1990 to 1996 (Table 16) are: 

Total score = 17 Hazard = 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). Further, toxicity threshold/extinction 

84
information, in general, can be related to the Se 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 site-specific ratings. 

 If an out-of-valley solution to the Se problem results in carefully managed discharges of Se to the 

Bay-Delta via the SJR (for example at 7,000 lbs per year), the forecast suggest the resulting hazard 

could be high. Selenium from the SJV replaces, in terms of food web exposure and effects, the Se 

removed in refinery cleanup. If an SLD is constructed and it discharges during low flow seasons, a 

high hazard seems a certainty, and the risk of loss of fish and bird species will be substantial. 

Alternative engineering solutions (in-valley and out-of-valley) will undoubtedly be proposed. Each 

should be analyzed using the scheme above at its appropriate time scale in relevant detail. 

FORECASTS 

A major goal of this report is to illustrate a systematic approach or mechanism for conducting 

forecasts of Se effects on prey (food) and predators. Several feasible future conditions are used to 

develop examples of forecasts. The choices of conditions are not nearly as important as the process of 

evaluating those choices. However, the results of the chosen forecasts themselves provide guidance to 

help narrow the range of possible management alternatives. 

 The approach can be used with any set of explicitly stated conditions. From each set of assumed 

conditions we: 

• calculate or forecast loads, volumes, and concentrations; 

• define speciation and transformation; 

• model bioaccumulation in generic bivalves and 

• predict tissue residue-based effects on predators. 

 

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

 As noted previously, the protocol for linking Se load and Se concentration under assigned hydraulic 

conditions and time duration is: 

composite freshwater endmember concentration = composite input load/composite input volume 

Four major inputs make up a composite input load: agricultural drainage via direct discharge to the 

Bay-Delta, effluents from the North Bay refineries, SJR inflows, and Sacramento River inflows. The 

85
composite input volume in the Bay-Delta is most affected by inflows from the Sacramento River and 

SJR (Figures 9 and 10). We will constrain each of the inputs and volumes to a given set of conditions 

as we construct feasible forecasts for Se loads to the Bay-Delta. 

 The projections or outputs of the model are presented by season, where a season is defined as six 

months of predominantly high river inflows (December through May) or six months of predominantly 

low river inflows (June through November). Seasonal presentation (high flow season versus low flow 

season) is the least complicated approach to account for riverine influences which are very different in 

different seasons. Flows are also 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 for Se 

concentrations were determined from monthly loadings. Riverine influences also depend upon water 

year type. In combination with flow seasons, we forecast for a critically dry year and a wet year. 

 A wide range of agricultural Se input loads are possible, depending upon which management 

strategies are chosen, as described earlier (also see Appendices A and B). Several factors influence 

agricultural loads of Se that would be delivered directly to Bay-Delta: 

• choice of drainage conveyance, either the SJR or an extension of the SLD; 

• demand for drainage from agriculture or the Se load targeted by environmental safeguards; 

• hydraulic discharge in the SJR or the SLD; 

• selenium concentration in the SJR or the SLD or the load conveyed by the SJR or SLD; and 

• proportion of the conveyance discharge that reaches the Bay-Delta. 

Potential ranges of annual input loads were derived earlier (Tables 6 and 7) assuming Se discharge was 

continuous and are presented here as discharged load per six months (i.e. one-half the annual load 

under a constant rate of loading). We will constrain our forecasts to selected scenarios within the three 

general ranges of SJV loadings described earlier (Tables 8 and 9). 

1. Pre-targeted loads conveyed by the SJR (3,400 or 3,590 lbs Se discharged in six months). The 

value we will use for the targeted loads will be toward the maximum projected by the 

TMDL/TMML process: 6,547 lbs per year or 3,274 lbs in six months. We will assume this 

load is delivered via the SJR with full conveyance to the Bay-Delta (no recycling of the SJR). 

A SJR inflow of 0.5 MAF is assumed during the low flow season of both wet and dry years. 

During the high flow season of a wet year, we assume 1.1 MAF is allowed to enter the BayDelta. 

86
2. SJR as a de facto drain (range of 381 to 15,300 lbs in six months). If the TMDL/TMML 

process resulted in management of a constant concentration of Se in the SJR year-around, a 

different load would result than if management is based upon load. The Se load delivered to 

the Bay would also depend upon 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 

(i.e., percent of SJR that reaches the Bay-Delta) is necessary but it should be recognized as 

hypothetical. Effects of Se on the SJR ecosystem are not included in our analysis. Examples of 

Se loads that could be transported via the SJR are given below (also see examples in Table 9). 

Load is managed at the USEPA criterion of 5 μg Se/L in a wet year. If an annual 

discharge of 3 MAF for the SJR at Vernalis is assumed and it is assumed that 75% of 

that reaches the Bay-Delta, then an annual Se load of 30,600 lbs is expected (15,300 lbs 

Se in six months). 

• 

• Load is managed at the USFWS proposed criterion of 2 μg Se/L in a wet year. In this 

case an annual load of 12,240 lbs of Se is released to the Bay if annual flow is 3 MAF 

and 75% of it passes through the Delta (6,120 lbs in six months). 

• Dry years. If annual discharge from the SJR is 1.1 MAF and 25% reaches the BayDelta, as might be expected in below normal precipitation, then the annual Se loading 

would be 9,262 lbs from the SJR at the 5 μg Se/L criterion and 3,705 lbs at the 2 μg 

Se/L criterion (1,852 or 4,631 lbs Se in six months). 

• Restored ecosystem. Load is managed at a constant 0.5 μg Se/L with 75% of the annual 

SJR flow and load delivered to the Bay-Delta during the high flow season and 25% 

allowed to enter in the low flow season. A concentration of 0.5 μg/L is lower than both 

the USEPA criterion (5 μg Se/L) and the USFWS proposed criterion (2 μg Se/L). In 

this case an annual load of 4,080 lbs is conveyed by the SJR assuming a flow of 3 MAF 

in a wet year. In a dry year, annual SJR flow of 1.1 MAF, the annual load is 1,496 lbs 

Se. This type of forecast will be typified in a scenario that considers restoration of the 

SJR during proposed increases in flow of the river to aid fish passage. (381, 1,020, 

1,115, or 3,060 lbs in six months). 

3. Demand-driven loads with management of drainage quantity and quality in an extension of the 

SLD. For our specific calculations of SLD effects, we will assume that a) demand for drainage 

87
is met by construction of an extension of the SLD which discharges directly to the Bay-Delta; 

b) the SLD extension delivers either 0.05 MAF each six months (half design flow capacity of 

existing SLD, 150 cfs) or 0.11 MAF each six months (full design flow capacity of SLD, 300 

cfs); and c) Se concentrations in the SLD 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 Se discharged in six months). We will calculate one forecast using a 

condition of 150 cfs in the SLD (0.05 MAF of drainage or half capacity) with a Se 

concentration of 50 μg/L. Under this condition, 6,800 lbs Se would be discharged in six 

months. We assume, in a second forecast, that 62.5 μg Se/L drainage is discharged at 

full capacity (0.11 MAF); the loading would be 18,700 lbs Se discharged in six months. 

These two loads bracket the lowest end of the range of cumulative potential loadings 

from the different subareas (or combinations of subareas) of the SJV (Tables 5 through 

7). 

• Demand-driven loads with low priority given to management of quality and quantity 

(44,880 and 89,760 lbs Se in six months). We will calculate two forecasts 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 

employs 150 μg/L Se concentrations in the SLD with the drain running at full capacity 

(0.11 MAF in six months) (44,880 lbs Se discharged in six months). The second case 

will assume 300 μg Se/L and 0.11 MAF of discharge in six months (89,760 lbs Se 

discharged in six months), assuming little regional management (as described earlier). 

These two loads bracket potential loadings from a valley-wide system draining most 

potential problem lands, with minimal management (Tables 6 through 8). 

 In order to calculate the total Se load to the Bay-Delta, and the resulting Se concentrations, 

climate, oil refinery loads, SJR recycling, and Sacramento River condition are included in the forecasts 

as follows: 

1. As noted previously, the magnitude and fate of the Se loads are highly dependent upon climatic 

regime. Climate scenarios are derived from existing data. 

88
• Critically dry year. Eight critically dry years have occurred in the Bay-Delta watershed 

between 1978 and 1998, so this is an important condition to consider. The data for this 

calculation were taken from 1994. 

• Wet year. We used data from 1997, a wet year by the California DWR definition. 

2. We will assume in all forecasts that oil refineries meet the 1998 permit requirements of 

approximately 1,360 lbs Se per year or 680 lbs per six months (Table 10). 

3. In demand-driven load forecasts during dry years, we assume that Se loadings from the SJR are 

very low. The forecasts implicitly assume that use of the SLD could relieve the pressure for 

discharge of drainage in the SJR. The forecasts also assume continued substantial recycling of 

the SJR, so only 500 to 1,000 AF of SJR water with a concentration of 1 to 2 μg Se/L reaches 

the Bay-Delta in dry years during high or low flow seasons (3-5 lbs Se in six months). 

4. During wet years in periods of high flow, less recycling of the SJR occurs, with substantially 

more SJR throughput to the Bay-Delta. To accurately reflect this condition in demand-driven 

load forecasts, we assume 2 MAF of SJR inflow reaches the Bay-Delta. We assign a 

concentration of 1 μg Se/L for this inflow (5,440 lbs Se in six months). 

5. Loadings from the Sacramento River will be determined at 0.04 μg/L Se times the hydraulic 

discharge. 

 Table 17 shows the inputs to the Bay-Delta, the climatic scenarios (water year and season), and the 

range of Se loadings that will result from the above conditions. The loadings in Table 17 will be 

employed in the modeling of bioaccumulation and prediction of effects on predators. Specific cases 

will be highlighted in summary tables that follow. The examples are not exhaustive in their coverage 

of all conditions; but the choices bracket the wide range of loads possible in the future from SJV 

acreage that is in need of drainage (Tables 8 and 9, and Appendix B). 

 

 Forecasts of Waterborne Selenium Concentrations 

Calculating composite selenium input (or freshwater endmember) concentrations

89

 Ultimately, Se concentrations in the Bay-Delta will be determined by the sum of all Se loads from

different sources, the choice of conveyance to the Bay-Delta, and the sum of all freshwater inflows as 

influenced by climate and management. To forecast concentration ranges for Se in the estuary under 

different scenarios, the model assumes all Se inputs are confined to a single location at the head of the 
estuary. Then it is assumed that the composite Se input is diluted through the estuary, as freshwaters 

move toward the sea (Figure 11). We will represent Se concentrations by values for composite 

freshwater concentrations expected at the head of the estuary (i.e., landward value) and by the 

concentration expected at half the value of seawater [approximately 17.5 psu (practical-salinity units)] 

(i.e., seaward value) based on the salinity gradient. The chosen seaward location is similar to salinities 

that occur at Carquinez Strait (i.e., the narrow waterway between Suisun Bay and San Pablo Bay in the 

North Bay) during low flow seasons. It should be remembered that hydrodynamic models (e.g., Cheng 

et al., 1993; Monsen, 2000; Burau and Monismith, in preparation) are necessary to forecast the spatial 

detail under simulated physical SLD discharge conditions. Development of such models for Se is 

feasible and should be a high priority in future evaluations of effects of a SLD extension directly 

discharging to the Bay-Delta. In lieu of regionally specific models, a simple mixing model approach 

provides a useful first order estimate of mean regional Se concentrations. 

 

Comparing forecasted selenium concentrations to observed conditions prior to refinery cleanup

 To initially test the validity of the approach, an average composite freshwater endmember Se 

concentration was calculated for conditions resembling those that were documented in Suisun Bay 

prior to refinery cleanup (Tables 2 and 18). Forecasts are for a high flow season during a wet year; and 

for a low flow season during both a wet and dry year, similar to conditions selected for projections of 

future conditions. The Sacramento River flow for six months of high flow was taken from 1997 data 

(17 MAF). The Sacramento River inflow during six months of low flow in 1997 and 1994, 

respectively, provide two other cases (i.e., 2.3 MAF and 1.62 MAF). SJR inflows were 3 MAF for 

high flow inputs in 1997 and 0.1 MAF in the latter two low flow cases. Refinery discharges are in the 

range (2,040 lbs in six months) measured before refinery cleanup (average 1986-1992, 2,505 lbs per 

six months) (CSFBRWQCB, 1992a; b; 1993; Cutter and San Diego-McGlone, 1990) and no SLD 

discharge is included. 

 The calculated average composite freshwater concentration of Se during six months of high flow 

in a wet year is shown in Table 18. The forecast concentration is 0.22 μg Se/L, using a mean 

concentration of Se in the Sacramento River of 0.04 μg/L Se and in the SJR of 1 μg Se/L. This is 

comparable to the Se concentration of 0.16 μg Se/L determined after high flows in April 1986 (Cutter, 

1989). The contrasting influences of the SJR and the Sacramento River are interesting to note in this 

example. Concentrations of Se in the SJR are much higher than concentrations in the Sacramento 

90
River (1 μg Se/L vs. 0.04 μg Se/L, respectively). The load of Se from the SJR is also substantial 

compared to the load from the Sacramento River (2,992 lbs vs. 925 lbs Se per six months, 

respectively). Concentrations of Se are as low as 0.22 μg Se/L at the head of the estuary because of 

dilution by the high volume of low-Se water from the Sacramento River. A Se concentration of 0.11 

μg/L is projected at our selected seaward location of Carquinez Strait. 

 The concentration of Se at 17.5 psu (i.e., approximate location of Carquinez Strait) during the six 

months of low flow in a wet year is projected as 0.20 μg Se/L; in a critically dry year it is 0.27 μg Se/L 

(Table 18). Selenium concentration is highest during periods of low flows, because dilution from the 

Sacramento River is reduced in years of low rainfall. The concentration forecasts are remarkably close 

to the range of values found within the estuary by Cutter (1989) (0.15 to 0.44 μg/L Se). The 

correspondence of these calculations with observed data confirms that the basic foundation of the 

forecasts is reasonable. 

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

 Five specific forecasts were constructed to evaluate impacts on the Bay-Delta from direct 

discharge of an extension of the SLD (Tables 19 through 21). Those forecasts are calculated for the 

three different climatic conditions and feasible loadings described earlier. 

1. 6,800 lbs Se discharged in six months if management of drainage quality and quantity were a 

high priority (half-capacity or 150 cfs of drain water with a Se concentration of 50 μg/L). In 

the three different climate regimes (Tables 19 through 21), the six-month average Se 

concentration at the head of the estuary during the low flow season would range from 1.21 μg 

Se/L in a wet year (Table 20) to 2.07 μg Se/L during a critically dry year (Table 21). In the 

high flow season of a wet year, six months at this load would result in an average composite 

freshwater concentration of 0.28 μg Se/L (Table 19). 

2. 18,700 lbs Se discharged in six months if the SLD operated at full capacity, carrying drain 

water with a Se concentration similar to that in the Grassland Bypass Channel Project (i.e., 62.5 

μg/L). This forecast is one of the more likely demand-driven loadings in the long-term if 

successful treatment technology is applied to drainage and the amount of problem land is that 

considered by the SJV Drainage Program (Table 6). In the three different climate regimes, 

concentrations at the head of the estuary during the low flow season of a wet year would 

91
average 2.99 μg Se/L and would average 5.07 μg Se/L over six months of low flow in a 

critically dry. Concentrations would average 0.51 μg Se/L at the head of the estuary during the 

six months of high flow in a wet year. 

3. 44,880 lbs Se discharged in six months if drainage contained 150 μg/L Se, and the drain 

operated at full capacity. This loading would provide for drainage from problem lands without 

investment in management of the drainage (e.g., direct discharge of shallow ground water). 

Even during high flow, Se concentrations would exceed 1 μg Se/L (i.e., 1.02 μg Se/L) at the 

head of the estuary under these conditions. During low flow six-month average concentrations 

would always exceed the USEPA criterion no matter what the rainfall (6.97 to 11.87 μg Se/L). 

4. 89,760 lbs Se discharged in six months if the most severely salinated soils supplied a drain at 

full capacity and no treatment technology was available. This scenario is not highly likely 

given expected emphasis on source control and treatment. However, if it should occur, 

extremely high Se concentrations would be found in the estuary under low flow conditions 

(13.8 to 23.5 μg Se/L) (Tables 19 through 21). Average concentration at the estuary (1.9 μg 

Se/g) would approximately equal the USFWS recommended criterion (2 μg Se/L), even during 

the high flow season (Table 21). 

 

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

concentrations 

1. Regulating load. This scenario assumes Se load is targeted for regulatory or environmental 

purposes at 7,000 lb Se per year load limit and 3,500 lbs Se discharged in six months. 

Conveyance is fully via the SJR. The projected range of Se concentrations in the freshwater 

endmember for the Bay-Delta during the low flow season scenarios is 0.57 to 0.86 μg/L Se; 

concentrations would be 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 Se at the head of the estuary and 0.20 to 0.27 μg/L at Carquinez Strait) (Table 18). 

So, in terms of total Se concentrations, this load of Se from the SJV would replace the Se 

removed by investment in refinery waste treatment. During a six-month high flow season 

during a wet year if 3,500 lbs of Se were discharged (Table 19), concentrations would be twofold lower (0.12 μg Se/L at the head of the estuary and 0.06 μg Se/L at Carquinez Strait) than 

92
conditions prior to refinery cleanup (0.22 μg Se/L at the head of the estuary and 0.11 μg Se/L at 

Carquinez Strait, Table 18). 

2. Regulating concentrations in the SJR: a restoration forecast. Environmental restoration is 

often vaguely defined. A specific “restoration” scenario for the SJR might place explicit limits 

on Se concentrations in the river and emphasize increasing SJR inflows (less recycling of the 

SJR) 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 SJR contrasts to previous scenarios in which Se load was managed. In 

calculating the effect of such “restoration” on Se concentrations in the Bay-Delta, the 

concentration assigned in the “restoration” scenario is 0.5 μg/L for the SJR at Vernalis. It 

should be noted that this concentration has not been achieved in the recent past (Table 5), and 

we are not suggesting that the technology is available to achieve it or that it would be easy to 

achieve by management decree. This is a specific condition, done for illustrative purposes. 

Conditions and Se loads for the restoration scenario include: 

• no SLD input; 

• constrain concentrations in the SJR at Vernalis to 0.5 μg Se/L; 

• convey 75% of the annual SJR flow and load to the Bay-Delta in the high flow season and 

25% in the low flow season; 

• assume the SJR inflow for a wet year is 3 MAF annual flow and a dry year is 1.1 MAF; 

• control industrial inputs to meet the July 1998 mandate of approximately 1,400 lbs Se per 

year; 

• vary Sacramento River inputs with flows as they do now (i.e., 0.04 μg Se/L at 19.3 MAF 

annual inflow in a wet year and 0.04 μg Se/L at 6.6 MAF annual inflow in a dry year). 

Under the “restoration” scenario in the high flow season of wet or dry years, the composite 

freshwater Se concentration is 0.11 to 0.15 μg Se/L for a wet year and a dry year, respectively. 

In the low flow season of a wet year, the composite freshwater Se concentration is 0.23 μg 

Se/L. In the low flow season of a dry year, the composite freshwater Se concentration is a 

similar 0.24 μg Se/L. These Se concentrations would be 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, 21, and 22). Conditions would be most 

93
improved, compared to before refinery cleanup, during the “bottleneck” period of low flow 

seasons in both wet and dry years. Less increase in concentration occurs in the Bay-Delta 

during low flow seasons in the “restoration” scenario because inputs of Se decline as flows 

decline. In high flow seasons inputs of Se increase, but the increase in dilution due to the 

higher inflows of the Sacramento River offsets the higher loads from the SJR and 

concentrations in the Bay-Delta decline. 

3. Regulating selenium concentrations in the SJR: effect of high flows and consequent high loads 

as a result of expanded selenium objectives. The advantage of discharging an increased Se load 

during high flows under the concentration management scenario does have some limits in the 

low flow season and if Se concentrations in the SJR increase. The concentration objective at 

which the SJR is held constant by implementation of a management plan is increased in a series 

of scenarios illustrated in Figure 19. If the Se concentration in the SJR 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 Se/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 Se during a dry year in the low flow season. In this case, 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 the higher Se load during the wet year is not offset as 

much by increased flows as occurs seasonally. 

Monthly waterborne selenium concentrations

 The six-month scenarios described above represent average seasonal Se concentrations (i.e., low 

flow season versus high flow season). Six-month averaged forecasts 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, Se concentrations were forecast that would result 

from monthly loadings. The forecasts are based on wet year flows (1997). The results of the monthly 

forecasts are presented graphically in Figures 20 and 21 and supplemental data are given in Appendix 

F, Tables F1 and F2. The forecast conditions are: 

94
1. Operation of the SLD at full capacity (0.2 MAF) conveying drainage at quality levels typical of 

the present re-use of the drain by Grassland subarea (62.5 μg Se/L). The annual load of Se 

from the SLD would be 36,720 lbs (or approximately 18,700 X 2 = 37,400 lbs, Table 17). 

Although SLD monthly inputs are constant (3,060 lbs per month) in this scenario, Se 

concentrations at the head of the estuary increase progressively from 0.24 μg Se/L in January to 

4.5 μg Se/L in October (Figure 20). 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 Se concentrations as long as a constant 

load is released from the drain throughout the year (Figure 20). The vulnerability of the estuary 

to adverse effects is generally greatest during the seasons 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 (Figures 9 and 10). Figure 20 expresses 

this scenario as a function of both input load and composite freshwater endmember Se 

concentration. Figure 21 shows the composite freshwater endmember concentration at both the 

head of the estuary and at Carquinez Strait for comparison. 

95

2. Management of the SJR at 2 μg Se/L with full conveyance to the Bay-Delta during a wet year 

(6.06 MAF). It is also instructive to evaluate the variation in monthly concentrations that might 

develop at the head of the estuary as a result of managing a constant SJR input concentration. 

The annual load of Se discharged to the Bay-Delta from the SJR in this forecast is very similar 

to that discharged by the SLD in the above scenario (32,936 lbs vs. 36,720 lbs for the SLD 

scenario above, Table 17). The highest loads (approximately 10,400 lbs each month) are 

discharged in January and February. The highest Se 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 (Figure 20). The latter period of elevated 

concentration coincides with that under constant discharge from the SLD (Figure 20). 

Concentrations in the Bay-Delta are much lower from April through December if the SJR is the 

conveyance vehicle than if the SLD is the conveyance. This disparity in loading is because 

monthly loads from the SJR 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 Se concentration illustrates an important problem with releasing Se via an artificial 
conveyance facility. Additional limitations also exist when high loads are released during high 

flows (see Figure 19 and later discussion). 

3. Management of the SJR at 1 μg Se/L with full conveyance to the Bay-Delta during a wet year. 

The annual load discharged in this condition would be 16,468 lbs in a high flow year. The 

monthly trends are the same as those under the 2 μg/L Se scenario, but the amplitude of the fall 

peak is reduced (Figure 20). The highest concentrations in the landward reach of the estuary 

are 0.60 and 0.68 μg Se/L in September and October (Appendix F, Table F2), respectively 

(about 1.5 times the maximum observed before refinery cleanup, Table 18). Concentrations 

near Carquinez Strait in October (Figure 21) are about equal to the highest concentrations (0.30 

to 0.34 μg Se/L) observed prior to refinery cleanup based on as seasonal analysis (Table 18), 

although speciation would probably be different (see later discussion). 

Summary of forecasts

 In general, a summary of the forecasts for the SLD conveyance and SJR targeted load scenarios 

(Table 23; Figures 22 and 23) shows that the most vulnerable years are critically dry years. The low 

flow season is the critical period of each year for the Bay-Delta. However, if concentration in the SJR 

is regulated under a constant concentration management plan and SJR inflows are increased, wet years 

are more vulnerable than dry years, but only during the low flow season (Figure 19). 

 Specifically, Figure 23 is a graphical tool that forecasts waterborne Se concentrations that would 

result from a wide range of six-month hydraulic discharges (emphasizing lower flow regimes), and a 

wide range of Se loads. Each line illustrates a Se concentration that would result from the different 

combinations of these variables. From this figure, the composite freshwater endmember concentration 

of Se (i.e. that concentration at the head of the estuary) can be estimated from any combination of 

climate (as indicated by differing total river inflows) and Se load. The strong dependence of Se 

contamination on weather and water demand (which, together, determine discharge to the estuary) is 

evident. Figure 23 illustrates the extreme vulnerability of the estuary to Se inputs during low flow 

seasons (cumulative discharges of 1 to 2 MAF over six months). For example, for total input loads of 

approximately 7,700, 20,000 and 46,000 lbs Se at defined cumulative volumes of 1.3 and 2.3 MAF 

during low flow seasons, the range of estuary Se concentrations would be from 1.2 to 12 μg Se/L. 

96

Using the range of loading forecasts employed previously, selenium concentrations in the BayDelta will increase under all scenarios that include a SLD extension, and especially as the flow 
capacity of the SLD is achieved and/or if concentrations of Se increase in the discharge (Table 23 and 

Figure 22). A minimum estimate of loads from a SLD extension is 6,800 lbs in six months (or 13,600 

lbs annually). This scenario can only be achieved if the drain is managed at a flow of 150 cfs and the 

most optimistic treatment technologies are invoked. Even under this scenario, composite freshwater 

endmember Se concentrations would increase two to four-fold over concentrations typical prior to 

refinery cleanup (see also Table 18). Freshwater endmember Se concentrations in the driest of years 

could exceed the 2 μg Se/L toward the head of the estuary. 

If a SLD 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 the SLD may approach the level of 18,700 

lbs in six months (37,400 lbs per year). Under this load scenario, average Se concentrations in the 

Bay-Delta at the head of the estuary for the six-month low flow season of a wet or dry year are forecast 

to exceed the USFWS recommended criterion of 2 μg Se/L through all of Suisun Bay (Table 23 and 

Figure 22). This exceedance would also occur at Carquinez Stait during the low flow period of 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. If, on average, drainage quality 

becomes similar to that of subsurface drainage (>150 μg Se/L) rather than blended drainage in the 

western SJV, and that is combined with full flow in the SLD, then extreme concentrations would occur 

in the Bay-Delta. Under a forecast load of 44,880 lbs Se in six months, Se concentrations of >6.97 μg 

Se/L at Carquinez Strait are projected during the low flow season of both wet and dry years. 

 A concentration of 1 μg Se/L is three times higher than presently found in the Bay-Delta in a 

normal rainfall year (Cutter 1989; Cutter and San Diego-McGlone, 1990; and CSWRCB, 1992a; b; 

also see Table 18) and represents the Canadian quality guideline (Environment Canada/Health Canada, 

1995; Outridge et al., 1999). This Se concentration cannot be achieved near the Carquinez Strait in the 

low flow season by any scenario that includes an extension of the SLD, except a load of 6,800 lbs per 

six months (Figure 22). In the high flow season of a wet year, concentrations forecasts at the 

Carquinez Strait are 0.14 to 0.94 μg Se/L. 

An important component of the monthly analysis (not evident in the six month analyses) is the very 

high Se concentrations that result each year in the fall. The strong dependence of Se contamination on 

weather and water demand, which, together, determine discharge to the estuary, is also evident. 

97
Concentrations in excess of 2 μg Se/L would extend through much of Suisun Bay and San Pablo Bay 

in the SLD forecast. It is possible that the dilution assumptions employed here might understate the 

geographic extent of Se distributions in projections for October. Sophisticated physical models are 

being developed for Suisun Bay and could be very helpful in describing such important details 

(Monsen, 2000; Burau and Monismith, in preparation). 

Forecasts of Speciation and Transformation 

 Speciation of Se in the Bay-Delta is controlled by physicochemical processes and speciation in the 

sources of input (Cutter, 1989). Speciation will change as sources change in importance. Prior to 

1998, refinery inputs of selenite were a principal influence on speciation and bioavailability. Refinery 

inputs declined in July 1998. A lower proportion of the total Se was selenite in the late 1990’s than in 

the 1980’s (Cutter et al., in preparation). It is likely that the proportion of selenate in inputs would 

increase if a SLD extension were used to convey irrigation drainage to the Bay-Delta or if/when SJR 

inflows to the Bay-Delta increase. As we forecast, biotransformation to Se(-II) and/or sediment 

accumulation and recycling of Se(-II) in the Bay-Delta are highly likely under increased SJR loading if 

the transformation conditions prevalent at present in the Bay-Delta are operable on the SJR discharge. 

This influx of Se(-II) could be accentuated if marshes are restored in areas subjected to inflows from

the SJR or a SLD extension. 

As discussed previously, speciation is a critical consideration in estimating ecological effects of Se. 

Speciation drives the transformation reactions that determine particulate Se concentrations and forms. 

Bioaccumulation from particulates is the primary route by which Se enters the food web, so the 

reactions that determine particulate concentrations are critical to eventual trophic transfer. Trophic 

transfer determines food web exposures and effects on predators. 

Ultimately, forecasts of Se speciation should be derived from biogeochemical, kinetic speciation 

models (Bowie et al., 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 our analysis by forecasting based upon mixes of species that have been 

observed in nature under circumstances possible for the Bay-Delta. We will then forecast how each 

mix of species would affect transformations of dissolved Se to particulate Se (i.e. speciation is implicit 

in our choice of transformation reactions). 

98
Transformation will be quantitatively expressed by the distribution of Se between particulate and 

dissolved forms, the Kd (see previous discussion). The effect of speciation and transformation will be 

incorporated by using Kd’s observed in previous studies (Table 11) to project a ratio to total Se typical 

of a given speciation regime. For each combination of Kd and speciation, we will also incorporate the 

form of particulate Se observed under those circumstances at other locations (Table 11) to enable a 

projection of overall bioavailability. 

Defining speciation, transformation, and bioavailability

Three sets of speciation regimes and Kd’s in which we assume a specific distribution of Se among 

particulate forms are presented below. These speciation and biochemical behavior patterns will be 

used throughout the forecasting of concentrations of Se in particulates, bivalves, and predators. 

• High Bioavailability 

Speciation: high proportion of selenite plus organo-Se (> 60%) 

Kd: 1 X 10 4 (C1) 

Precedent: estuarine suspended material in the Bay-Delta 

Particulate bioavailability: 60% high and 40% moderate 

To bound a high bioavailability scenario, we assume that Se(IV) and at least part of the Se(-II) 

contribute to biotransformation to organo-Se. Preliminary studies in the late 1990’s showed 

that as much as 60% of dissolved Se was Se(IV) plus Se(-II) in Suisun Bay. Selenite has 

declined since the refineries reduced their inputs, but organo-Se has become a larger proportion 

of the dissolved Se (Cutter et al., in preparation). 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 X 10 3 to 2.1 X 

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. For bioavailability calculations, we will assumed 

the form of the particulate Se under these conditions is 60% biotransformed Se and 40% 

oxidized material of moderate bioavailability. Biologically, this Kd is most relevant to water 

column-feeding species of consumer organisms, like filter-feeders. 

• Moderate Bioavailability 

Speciation: low proportion of biotransformable (Se(IV) or bioavailable Se(-II)) (< 30%)

99
Kd: 3 X 103 (C2) 

Precedent: typical of shallow water estuarine sediments or marine waters

Particulate bioavailability: 60% moderate and 40% high 

If sources of Se change, it is possible that the proportion of Se as Se(IV) + Se(-II) in the BayDelta will decline to less than 60%. Even if the proportion of Se(IV) and Se(-II) remains high, 

it is possible that the bioavailability of Se(-II) is less than Se(IV). To account for either of these 

possibilities we will assume 30% of total Se contributes to biotransformation at the rate of

Se(IV). A speciation regime of 30% biotransformable Se and 70% less reactive Se 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 X 103 to 1 X 104

(Table 9, Velinsky and Cutter, 1991; Cutter et al., in preparation). Again, this Kd coincides 

with a mixed speciation regime [60% Se(VI) and 40% Se(IV) plus Se(-II)]. We will also 

assume that this speciation and Kd combination results in particulate Se that is 60% in a form

of moderate bioavailability [detrital Se(-II) or particulate Se(IV) + (VI)]; and 40% in a form of

high bioavailability (biotransformed organo-Se). Biologically, this scenario applies to biota 

that predominantly ingest sediments with concentrations diluted by non-transformed load. 

• Low Bioavailability

Speciation: predominantly Se(VI)

Kd: 1 X 103 (C3) 

Precedent: Systems like the area of a wetland near the input site of selenate-dominated 

irrigation drainage waters 

Particulate bioavailability: 50% low, 40% moderate, and 10% high 

This scenario assumes that most of the Se 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 

inflows of Benton Lake, Montana, where Kd’s are approximately 103 (Zhang and Moore, 

1996). This value is also at the lowest end of the partitioning constant range characterizing 

Bay-Delta sediments and is probably the most optimistic scenario that can be hoped for, in 

terms of generating particulate Se and ultimately biological effects. For forecasting 

bioavailability, we will assume this material is 50% slurry-generated Se(0) of relatively low 

bioavailability, 40% oxidized material of moderate bioavailability, and 10% organo-Se of high 

100
bioavailability. This scenario would apply most readily to deposit feeding benthos, especially 

those feeding within sediments. 

In general, we recognize that the Kd-concept used above has limitations and that there are 

uncertainties about future speciation should a SLD extension begin discharging Se loads to the BayDelta. Nevertheless, the three speciation/transformation regimes described above are quite likely to 

fully bound the possibilities. Using them we can forecast at least the ranges of particulate Se 

concentrations and particulate forms.

Comparison to Bay-Delta conditions prior to refinery cleanup

 It is instructive to visually compare projections from the Kd’s to existing data for the Bay-Delta. In 

Figure 24, suspended particulate Se concentrations (Cutter et al., in preparation) are plotted against 

dissolved concentrations. Lines describing predicted particulate concentrations using Kd’s of 1 X 103

and 1 X 104 are superimposed on the plots. A Kd of 1 X 103 (C3) is too low to describe any of the 

existing suspended sediment data making it a low probability forecast. The October 1996 data (the 

highest concentrations observed in any survey) exceed 1 X 104 (C1) and the September 1996 data fall 

between the two values. In Figure 25, similar data are presented in a different way. Particulate 

concentrations are forecast from dissolved concentrations that occurred landward to seaward in the 

Bay-Delta in October 1996. The different Kd’s described above forecast three different trend lines for 

particulate concentrations through the estuary. The October 1996 particulate data is superimposed 

upon these projections. The superimposed data illustrate that a Kd of 1 X 104 (C1) is the best choice 

for this data set. A Kd between 3 X 103 (C2) and 1 X 104 (C1) would best fit the September 1996 data 

if it were plotted similarly. The three Kd’s used for the forecasts were, of course, developed based 

upon 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 

Sediment quality guidelines 

 As discussed previously, the principal risk of sediment to fish and birds is via the aquatic food 

chain. Sediment guidelines are based on sediment concentrations as predictors of adverse effects 

101
through the food chain. Proposed sediment quality guidelines for Se (μg Se/g in particulate material or 

sediment) provide a context to evaluate forecast particulate Se concentrations: 

• no effect concentration: <1 to 2.0 μg Se/g. Concentrations lower than this value produce no 

discernible adverse effects on fish and wildlife and are typical of background concentrations in 

uncontaminated environments (Skorupa, 1998b). 

• threshold for effects and the level of concern for Se in sediment: 2 to 4 μg Se/g. Concentrations 

in this range are elevated 10 to 20 times above typical background concentrations (Engberg et 

al., 1998; Skorupa, 1998b). 

• site-specific for Suisun Bay, potential for increase in adverse effects: >1.5 μg Se/g. 

Concentrations in this range may produce discernible adverse effects in some circumstances 

(Luoma et al., 1992), whereas Engberg et al. (1998) and Skorupa (1998b) suggest such levels 

rarely produce discernable adverse effects in freshwater environments. 

• observed effect concentration: 4.0 μg Se/g (Canton and Van Derveer (1997). 

• toxicity threshold of > 4 μg Se/g. Concentrations in excess of this value have a high certainty 

of producing toxicologic and reproductive effects (Engberg et al., 1998). 

Skorupa (1998b) provided a compilation of background and biotic effects levels as part of the U.S. 

Department of the Interior’s National Irrigation Water Quality Program. Canton and Van Derveer’s 

(1997) conclusions about sediment-based criteria are based upon less data and a relatively insensitive 

community analysis (Hamilton and Lemly, 1999).

 

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

 Tables F3 to F5 in Appendix F show detailed data for four load scenarios under three different 

climate regimes should Se be released directly to Suisun Bay via a SLD extension (also see Tables 19 

through 21 for composite freshwater endmember concentrations). Transformation constants typical of 

suspended sediments (C1), shallow water bed-sediments (C2), and low reactivity conditions (C3) are 

employed in each set of calculations. Table 24 summarizes particulate Se concentrations under these 

four load forecasts using a proposed SLD extension, a targeted load scenario using the SJR, and under 

a “restoration” scenario for the SJR. Forecasts are compared to data reflective of conditions prior to 

refinery cleanup. Sediment quality guidelines for Se are also shown. 

102
 The forecasts using the SLD for conveyance show that during a low flow season in a critically dry 

year (Table 24): 

• all releases to the Bay-Delta via a SLD extension under the three assumed Kds (C1, C2, and 

C3) result in particulate concentrations >2.0 μg Se/g at the head of the estuary. 

• only under the lowest SLD extension discharge assumption (6,800 lbs in six months) combined 

with the lowest Kd (least likely, C3), would a particulate Se value be observed (2.07 μg Se/g) 

below the observed effects concentration of 4.0 μg Se/g. In all other cases the certainty of 

effects would be elevated. 

• if the Kd of suspended material were that observed in all existing studies of the Bay-Delta (C2), 

projected loads of Se from a SLD extension would result in particulate Se concentrations in 

upper Suisun Bay of 6.2 to 35.6 μg Se/g. The certainty of effects would be high to very high. 

Under all but the most optimistic transformation scenarios, forecast loads with management of quantity 

and quality of 6,800 to 18,700 lbs per six months would yield particulate Se concentrations in the 

upper estuary that would exceed 4.0 μg Se/g. Selenium concentrations of 5 to 119 μg Se/g are possible 

if management is not a priority. 

 A low flow season in a wet year would yield particulate Se concentrations that are approximately 

60% of those forecast for a dry year (Table 24): 

• if a load of 6,800 lbs were discharged in six months via a SLD extension, the forecast range of 

most likely concentrations (C1 – C2) is 4 to12 μg Se/g (rounded off). 

• if the SLD was managed at full flow capacity and with Se concentrations like those in the 

Grassland Bypass Channel Project (18,700 lbs in six months), particulate concentrations of 9 to 

30 μg Se/g are forecast under C1 and C2 conditions. The latter concentration is >7X higher 

than the level at which toxicologic and reproductive effects are highly likely (Engberg et al, 

1998). 

• Under a C3 transformation, only SLD loads in the range of the lowest loading scenario for the 

SLD (6,800 lbs in six months) would result in particulate Se 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 Se data trends presented on a monthly basis (Figures 20 

and 21; Appendix F, Tables F1 and F2)]. 

103
 Releases of a SLD discharge in the Bay-Delta during the high flow season of a wet year result in 

exceedances of the observed effects level under all assumed SLD discharges only if Kd’s of 1 X 104

(C1, typical of suspended sediment) characterize transformations (Table 24). However, it should be 

recognized that the forecast concentrations are averages over the six-month high flow period. Flows 

are very 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 SLD extension are 

most likely to add to the Se load in the estuary. 

 The forecast for the targeted load (3,500 lbs per six months) using the SJR for conveyance shows 

that (Table 24): 

• During a low flow season, the targeted load approach could result in particulate concentrations 

in excess of 4.0 μg Se/g if transformations are typical of suspended sediment (C1), but not if 

shallow sediment-type transformations prevailed (C2). 

• During the high flow season of a wet year, particulate Se concentrations remain below 1.5 μg 

Se/g for all three transformations considered. 

The forecast for the “restoration” scenario in the SJR shows that (Table 24): 

• During the high flow season of a wet year, particulate Se concentrations for the “restoration” 

scenario are similar to those that would occur during the targeted load scenario (i.e., below 1.5 

μg Se/g). 

• During the low flow season in a critically dry year or a wet year, particulate Se concentrations 

are less than those that would occur during a targeted load scenario and remain below 2.5 μg/g. 

All SLD discharge scenarios predict particulate Se concentrations greater than those forecast for prior 

to refinery cleanup (Table 24). Particulate Se concentrations lower than those modeled prior to 

refinery cleanup are predicted to occur: 

• in the “restoration” scenario for the SJR in all modeled water year types and seasons; and 

• in the SJR targeted load scenario during the high flow season of a wet year. 

Cumulative summary

 A cumulative summary of Se loads and concentrations is given in Table 25. Composite freshwater 

endmember and particulate Se concentrations at the head of the estuary are shown for an agricultural 

load input of 18,700 lbs released during six months via a SLD extension or of approximately 3,500 lbs 

104
released during six months via the SJR (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 

reactivity in determining particulate concentrations. Clearly, benefit would come from knowing these 

dissolved/particulate transformations with more certainty for the Bay-Delta. For each composite 

freshwater endmember Se input, we illustrate three assumed alternative particulate transformations 

[low reactivity (C3), shallow sediment (C2), and suspended sediment (C1)]. 

 For the SLD scenario of 18,700 lbs per six months (Table 25), it is notable that exceedance of the 

USEPA waterborne criterion of 5 μg Se/L (low flow season of a dry year) is always accompanied by 

exceedance of the proposed observed effect particulate criterion (4.0 μg Se/g), no matter what the 

reactivity of the Se. Also under this load scenario, the USFWS proposed waterborne criterion of 2.0 

μg Se/L is exceeded in the composite freshwater endmember concentration for the low flow season of 

a wet year. At a composite freshwater endmember Se concentration of 2.0 μg Se/L, particulate Se 

concentrations might exceed the lowest proposed no effect concentration (1.5 μg Se/g), but not the 

observed effect level. However, a typical estuarine Kd (C2) would result in particulate Se 

concentrations of >4 μg Se/g. Even during high inflows, the observed effect guideline is exceeded if a 

Kd typical of October 1996 occurs (C1). 

 For the SJR targeted load scenario of 3,500 lbs per six months (Table 25), composite freshwater 

endmember Se concentrations remain below 1 μg Se/L. However, particulate Se concentrations only 

remain below 1.5 μg/g at low reactivities (C3) or during the high flow season of a wet year. During 

low flow seasons of both wet and dry years, particulate Se concentrations exceed 1.5 μg/g, and in cases 

of high reactivity (C1) could exceed 4 μg Se/g. 

 In summary, loadings, inflows, and biogeochemical transformation rates are critical to determining 

particulate Se concentrations and thus important determinants of the ecological effects of a discharge 

conveyed directly to the Bay-Delta. Most feasible SLD discharges result in concentrations of 

particulate Se during low inflow periods that are above the threshold of toxicity based upon the only 

available estimates of no effect and observed effect particulate Se guidelines. This is especially true if 

the transformation conditions prevalent at present in the Bay-Delta (C1 and C2) are operable on a 

proposed discharge from an extension of the SLD. All forecast particulate Se concentrations exceed 

those forecast for conditions prior to refinery cleanup, except under the targeted load SJR scenario 

during the high flow period of a wet year. The “restoration” scenario for the SJR results in forecast 

105
particulate Se concentrations that are lower than those forecast for the Bay-Delta prior to refinery 

cleanup. 

Other possible scenarios

• No reaction of Se(VI). If inputs of Se from 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) will not be reactive in the Bay-Delta ecosystem. This 

minimal reactivity would require that dissimilatory reduction to sedimentary Se(0) not occur in 

sediments or wetlands, no adsorption because of competition with sulfate, and no selenate 

uptake by primary producers. Biotransformation of Se is, indeed, minimized in at least some

flowing water (lentic or river/stream) systems, compared to wetlands. However, there is no 

precedent in nature for a complete absence of Se biotransformation to particulate 

concentrations. At least a Kd of 0.5 X 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 shallow water environments of the 

system. 

• Direct SLD discharge of suspended particulate Se from an extension of the SLD. Input of 

suspended particulate material containing elevated concentrations of Se is likely from a SLD 

extension directly into the Bay-Delta. The SLD during its operation from 1981 to 1985 acted 

as a partial treatment facility by removing Se 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 Se have accumulated in the SLD to date 

and are likely to continue to accumulate during its renewed use by the Grassland subarea to 

convey drainage to the SJR (Appendix E, Tables E1 and E2). Selenium concentrations in SLD 

sediment have exceeded the hazardous Se waste criterion for solids (100 μg Se/g, wet weight) 

at times in the past and almost all concentrations are above that designated as a toxic threshold 

in sediment for biotic effects (> 4 μg/g) (Engberg et al., 1998). Re-suspension and at least 

some transport of those sediments during elevated flows seems a reasonable forecast should the 

SLD be extended to the Bay-Delta. For example, the SLD was briefly re-opened in early 1995 

to relieve flooding in the western SJV and acted as a conduit for discharges into Mud Slough 

and the SJR (Presser and Piper, 1998). Transport and dilution of such particles probably cannot 

106
be estimated with any reasonable certainty. The discharged particulate Se would probably 

originate as primarily Se(0), but oxidation would also occur with longer residence times in 

suspension or in the water column. Source material also may include algal mat that may 

contain organic-Se [i.e., bioavailable Se(-II)]. The following forecast of direct discharge of 

suspended particulate Se from a SLD extension is instructive, but speculative. It illustrates how 

even small inputs of the existing contaminated SLD sediments could affect the Bay-Delta. 

o If the SLD inflow is 5% of the flow of river inputs to the Bay-Delta and suspended material 

concentrations are similar in both the Sacramento River and the SLD (based on relative 

flows in a wet year at low flow). 

o If average particulate Se concentration in the SLD particles is 100 μg Se/g and particulate 

Se in the Sacramento inflows is 0.2 μg Se/g. 

o Then 5% of the particles in the Bay-Delta at the confluence of the two will be SLD particles 

and the Se concentrations in the particle mixture will be: 

[(0.05 X 100 μg Se/g) + (0.95 X 0.2 μg Se/g)] = 5.19 μg Se/g from direct particulate input. 

o During a critically dry year particulate Se concentrations would be twice this value. 

o Particulate Se transformed from the dissolved inputs from the SLD would add to these 

concentrations, therefore our estimate is conservative in this respect. 

• Local hotspots. The Se concentration estimates 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 (Burau and Monismith, in preparation). However, hotspots of particulate 

Se contamination could develop in an ecosystem subjected to direct SLD discharges. Most 

notably, wetlands close to a SLD-extension discharge would be likely to accumulate high 

concentrations of Se. 

Forecasts of Bioaccumulation in Consumer Organisms 

Calculating bioaccumulation in a generic bivalve (modeling)

107

 Table 26 shows the range of biological values employed in the DynBaM model for bivalves in the 

Bay-Delta. The model is for a generic bivalve (i.e., physiological constants are averages over a small 

range from several bivalve species, Reinfelder et al., 1997; Lee et al., in preparation). Calculations 
specific to P. amurensis and C. fluminea also could be conducted. Some data for these species are 

recently available. The common parameters for a generic bivalve used in the model are as follows: 

1. Ingestion rate (or feeding rate) of 0.25 gram food/gram tissue dw per day (estimate for many 

bivalves based on review of literature in Luoma et al., 1992). 

2. Efflux rates (or rate constant of loss) of 0.02 per day (average of 0.01 - 0.03 per day). 

3. Assimilation efficiencies (AE) approximately 20% (low bioavailability) to 80% (high 

bioavailability) as a function of particle type (see below). 

Combining the above factors and the range of particle transformations that affect bioavailability (Table 

26), bivalve bioaccumualtion will be cast in terms of assimilation efficiencies (AE in percent): 

• Inefficient transformation: Kd = 1 X 103

. The particulate forms are 50% Se(0) of relatively low 

bioavailability, 40% oxidized material of moderate bioavailability, and 10% organo-Se of high 

bioavailability. The AE derived from this mixture is 35%: 

AE1 (0.23 X 50%) + (0.4 X 40%) + (0.79 X 10%) = 35%

• Shallow water estuarine sediments: Kd = 3 X 103

. The particulate form are 60% of moderate 

bioavailability [detrital Se(-II) or particulate Se(IV) + (VI)]; and 40% in a form of high 

bioavailability (biotransformed organo-Se). The AE derived from this mixture is 56%: 

AE2 (0.40 X 60%) + (0.79 X 40%) = 56% 

• Estuarine suspended material: Kd = 1 X 104. The particulate forms include 60% 

biotransformed Se of high bioavailability and 40% oxidized material of moderate 

bioavailability. The AE from this material (presumably by an estuarine filter-feeder, Table 26) 

would be 63%, derived as: 

AE3 (0.79 X 60%) + (0.40 X 40%) = 63%. 

• Estuarine suspended material – purely biogenic: A fourth AE (79%) is also included to take 

into account the possibility that all suspended particulate Se in the estuary would derive from

biogenic transformation to Se(-II). 

AE4 (0.79 X 100%) = 79%.

• To complete the range of considered AEs, a fifth AE is derived for all particulate material being 

of a form of low bioavailability, Se(0). The AE derived is 23%: 

For range (0.23 X 100%) = 23% 

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

Generic bivalve data (Table 26) were employed to forecast bioaccumulation of Se for a range of 

concentrations using two extremes of AE, 80% (all biotransformed) and 20% (all elemental Se) (Table 

27). The purpose of this calculation was to verify that the model bracketed reasonable predictions of 

Se bioaccumulation. The range of particulate Se concentrations used in the calculation spanned the 

concentrations of Se determined in surveys of the brackish Bay-Delta (0.5 to 3.0 μg Se/g dw) and at 

the head of the Bay-Delta (0.5 to 8.0 μg Se/g dw). Three observations from the forecasts of Bay-Delta 

conditions prior to refinery cleanup are of interest: 

• The forecast concentrations of bioaccumulated Se span the exact range of Se concentrations 

found in bivalves in this system (Figures 15 and 16; Tables 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 et al., 1992 and Wang et al., 1996). 

• A four-fold difference in bioaccumulation would be expected if the particulate form of Se 

changed. At the same concentration of particulate Se, bivalves would bioaccumulate four-times 

more Se from the biotransformed particulate Se than from elemental Se. Although this 

bioaccumulation is significant, the effect is relatively small compared to the effects of changing 

the mass of Se in the load. 

• The field validation results verify that the model will be useful in forecasting the range of

consumer organism bioaccumulation under different input scenarios for Se. 

 

Bivalves as food for predators

The most sensitive response of ecosystems to Se occurs in higher trophic level predators (e.g., birds 

and fish) (Ohlendorf, 1989; Hamilton et al., 1990; Lemly, 1996b; c; Skorupa, 1998a; Hamilton et al., 

2000a; b). Effects on predators (see reviews in Lemly, 1998b; Skorupa, 1998a; Hamilton et al., 2000b) 

have been defined based on: 

• Se concentrations in their food 

• effects on predators themselves expressed as Se residues in tissue. 

 Bivalves (clams) are an important food source for the predators of interest in the present evaluation 

(Luoma et al., 1992). So one type of guideline for bivalve tissues should be based upon their use as a 

109
food source for fish and birds. Guidelines for predators based on food are (see also Tables 13 through 

15): 

• 10 μg Se/g in food = Threshold of effects on predators. Concentrations in predator food 

(invertebrate tissues) above 10 μg Se/g dw have been conclusively implicated in adverse effects 

on reproduction in predators (Saiki, 1986; Hodson and Hilton, 1983; Johns et al., 1988; Coyle, 

et al., 1993; Lemly, 1985, 1993a; c; 1997b; Hamilton et al., 1990; 2000b; Adams et al., 1998; 

Linville and Luoma, in press). Many studies suggest effects begin at lower concentrations, but 

10 μg Se/g can be considered the value of least uncertainty. When invertebrate tissues exceed 

10 μg Se/g dw the expectation is strong that adverse reproductive effects are occurring in 

sensitive upper trophic level species such as birds and fish. 

• 15-20 μg Se/g in food = Observed conditions that coincide with extinction of some fish species. 

This is the annual maximum concentration of Se in P. amurensis observed between 1995 and 

1996 near Carquinez Strait in Suisun Bay (Table 13; Figures 14 through 17) 

• 40 μg Se/g in food = Extinction of numerous fish species. In field studies, all but the most 

tolerant populations of fish species have been eliminated when Se concentrations in 

invertebrates reach 40 to 100 μg Se/g (Lemly, 1985; 1993a; 1997c; Saiki, 1986; Saiki and 

Lowe, 1987). So we might define values > 40 μg Se/g dw as invertebrate tissue Se 

concentrations where risks of extinction of multiple fish species are high. These are also the 

concentrations in prey at which less sensitive predator species show teratogenic effects (e.g. 

coots in Kesterson Reservoir) (Presser and Ohlendorf, 1987; Skorupa, 1998a). 

• 100 μg Se/g in food = Widespread invertebrate toxicity. Although large-scale invertebrate 

toxicity is probably not the most sensitive response to Se, it could be an additional outcome of 

extreme Se contamination. Very rarely are invertebrates found in ecosystems when Se 

concentrations in invertebrates are greater than 150 μg Se/g (Lemly, 1993a; 1997c; Saiki and 

Lowe, 1987). For the sake of discussion, we will assume 100 μg Se/g to be the level of 

outright, broad scale invertebrate toxicity.

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

Forecast Se loads, freshwater endmember Se concentrations, particulate Se concentrations, and 

generic bivalve Se concentrations are shown at three different Kd’s (transformation constants) and four 

110
different AE’s (generic bivalve assimilation efficiencies) in Appendix F, Tables F6 to F9. Table 28 

summarizes these projected concentrations of Se in particulate material and in generic bivalve tissue as 

a function of four combinations of Kd’s and AE’s (C1/AE4, C1/AE4, C2/AE2, C3/AE1). Forecasts are 

for three loading scenarios (6,800, 18,700 and 44,880 lbs per six months) for a SLD extension release 

and for a SJR discharge of a targeted load of 3,500 lbs Se per six months under three different climate 

regimes. Also included for comparison is a forecast of Bay-Delta conditions prior to refinery cleanup. 

 The forecasts show that, contamination of prey would be sufficient to cause widespread extinction 

of fish species (> 40 μg Se/g in food) during the low flow season of any year, but especially in dry 

years (Table 28), if Se transformation occurs at a Kd of 3 X 103 or higher and: 

• the proposed SLD extension discharges at 300 cfs, even if management succeeds in holding 

concentrations to 62.5 μg Se/L (44,880 to 18,700 lbs per six months). Some of these scenarios 

could also cause widespread elimination of invertebrates in addition to predicted effects on 

predators (> 100 μg Se/g in food). 

• the proposed SLD extension discharges at 150 cfs (half capacity) and with a drainage 

concentration of 50 μg Se/L (6,800 lbs per six months) and the highest reactivity of suspended 

sediment (C1/AE3 or C1/AE4) occurs. 

• sub-extinction threats to reproduction of birds and fish (concentrations between 10 and 40 μg 

Se/g dw in food) would result In low flow seasons from discharges of 6,800 lbs per six months

via a SLD extension. 

 For loading of 3,500 lbs per six months via the SJR, sub-extinct threats exist during the low flow 

season of a dry year at typical shallow-water bed sediments (C2) reactivity and during the low flow 

season of a wet year at the highest reactivity assumed (C1). 

 Concentrations less than 10 μg Se/g dw in food invertebrates (i.e., the threshold of effects of 

predators) are found only if (Table 28): 

• in the low flow season of both wet and dry years, the proposed SLD discharge is 150 cfs (half 

the capacity) and the drainage is treated to attain a concentration of 50 μg Se/L (6,800 lbs per 

six months) and if Se transformation values or reactivity is low (C3/AE1). 

• in the low flow season of both wet and dry years, the SJR discharges 3,500 lbs per six months 

and if Se transformation values or reactivity is the lowest found in any of the receiving waters 

studied previously (C3/AE1). 

111
• in wet years, if discharges of 6,800 lbs via a SLD extension or 3,500 lbs via the SJR per six 

months are released during high flows and reactivities are that of bed sediment or lower (C2 

and C3). At the lower load, a higher reactivity (C1/AE3 or C1/AE4) also result in prey of < 10 

μg Se/g, but not at 6,800 lbs Se. 

In general, SLD discharges that would meet demands for drainage pose risks to fish and bird 

reproduction and the risk of fish extinction via contamination of their invertebrate food (Table 28). If 

biogeochemical conditions like those 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 

filter-feeding 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 (reactivities that 

result in a Kd of < 103) in that such low Kd’s are not typical of the Bay-Delta. Similarly, the targeted 

load scenario for the SJR results in prey containing < 10 μg Se/g only if reactivities are low (C3/AE1) 

during low flow seasons. At other reactivities (C2/AE2, C1/AE3 or C1/AE4) during low flow seasons, 

concentrations in prey approach (i.e., 8.7 μg Se/g) or exceed 10 μg Se/g (12 to 38 μg Se/g). 

Loadings of Se from 6,800 to 18,700 lbs per six months, if released during the highest flows only, 

would result in exceedances of the effects levels only if the highest Kd’s, of 1 X 104

 (C1) were 

observed (i.e., if the particulate Se 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 Se 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 et al., 1979; 1985; Nichols et al., 1986; Peterson et al., 1989). Also during high inflows, 

highly contaminated particulate material from either the SJR or the SLD is most likely to add to the Se 

load in the estuary (although, at present, suspended particulates are not typically highly contaminated 

during high inflows). 

For comparison, forecasts of conditions in the Bay-Delta prior to refinery cleanup show exceedances of 

the 40 μg Se/g threshold during the low flow season of a dry year at high reactivity (C3/AE4) and of 

the 10 μg Se/g threshold at bed sediment reactivity (C2/AE2). During the low flow season of a wet 

112
year, 10 μg Se/g is exceeded at a high reactivity (C1/AE3 and C1/AE4). Even during high flows in 

wet years, this high reactivity produces prey with concentrations greater than 10 μg Se/g. 

 

Effects on predators based on selenium concentrations in food

We take two forecasts, one for a SLD extension load of 18,700 lbs Se per six months and one for a 

SJR targeted load of approximately 3,500 lbs per six months, forward to link uptake by bivalves and 

effects on predators (Table 29). Forecasts are shown for three climate seasons and for three 

transformations previously selected (C1/AE3, C2/AE2, and C3/AE1). This cumulative summary also 

shows the composite freshwater endmember Se concentrations and particulate Se concentrations at the 

head of the estuary for these scenarios. The forecast invertebrate Se bioaccumulation is compared to 

the guidelines for effects on fish and birds from contaminated food. In this case we assume clams 

constitute that food. 

The projection for the SLD scenario (18,700 lbs Se per six months) shows that (Table 29): 

• Composite freshwater endmember Se concentrations in the Bay-Delta would reach the USEPA 

criterion of 5 μg Se/L, on average, during a dry year and the low flow seasons. At the level of 

the guideline, effects on fish (predator) populations from contaminated food (9-266 μg Se/g 

dw) would be expected, no matter what the reactivity of the Se (i.e., concentrations posing a 

serious risk would be reached under all feasible biogeochemical conditions). 

• Composite freshwater endmember Se concentrations would fall between the USEPA guideline 

and the USFWS proposed criterion of 2 μg Se/L in the dry season of a wet year. If Se is of the 

lowest possible reactivity, bioaccumulation would not reach the 10 μg Se/g dw food guideline 

under these conditions. A typical estuarine Kd would result in exceedance of the 40 μg Se/g 

dw guideline and threaten an array of fish and birds with extinction from the estuary. So, in the 

most likely circumstances (those with precedent in the estuary) significant risk exists. 

• Even during high inflows, 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 Se per six months, SLD discharges usually 

result in waterborne and particulate Se concentrations that exceed biotic effects thresholds and 

concentrations of Se in bivalve prey of fish and birds that exceed dietary guidelines (10-40 μg Se/g) 

113
during the six months or more of each year when river inflows are reduced. This condition is the most 

likely if the transformation prevalent at present in the Bay-Delta is operable in the future. 

Biogeochemical transformation rates and AE’s are critical determinants of the degree of contamination 

of the food of predators in the Bay-Delta and need to be better understood. 

 The projection for the SJR scenario (approximately 3,500 lbs Se per six months) shows that: 

• Under the most likely biogeochemical conditions (Kd = 3 X 103

, C2) risks to predators are 

greatly reduced compared to SLD discharge scenarios. Invertebrate concentrations of Se would 

fall just within the 10 to 40 μg Se/g dw range of elevated risk to reproduction in critically dry 

years under the most likely reactivity scenarios. Risk at this or lower reactivity would be 

reduced in intensity compared to prior to refinery cleanup, based upon contamination of bivalve 

prey. 

• Contamination of food would be sufficient to suggest risk of fish extinctions (> 40 μg Se/g dw) 

or at the high end of the range defining risks to reproduction, if Kd’s were like those often 

observed for suspended material in the Bay-Delta (C1), in the low flow season. 

The 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 

Choice of predators

 White sturgeon, surf scoter, and scaup (greater and lesser) were chosen to forecast Se 

concentrations in predator tissue that would result from different Se loads to the estuary. There are 

three reasons for this choice: 

• These are the species for which the most data is available for the Bay-Delta (i.e., the Selenium 

Verification Study: White et al., 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 Se, and thus seem to 

receive the highest internal exposure. Changes in Se exposures in the Bay-Delta food web 

should have the greatest effect on concentrations of Se in these species. 

114

• The fish and birds with the greatest Se 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 Se 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 Se 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 bioaccumulation to bioaccumulation by prey (food). Urquhart and Regalado 

(1991) determined Se in white sturgeon, surf scoter, greater scaup, and lesser scaup at a number of 

times and locations when they or others also determined Se in bivalves. The bivalve Corbicula 

fluminea was collected from 1987 to 1990 in Suisun Bay (Urquhart and Regalado, 1991). Johns et al. 

(1988) 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). Potamocorbula 

amurensis invaded North Bay initially in 1986, and by the late 1980's was established as the dominant 

bivalve in the ecosystem. No data for Se concentrations in P. amurensis were collected until 1995; but 

1995 through 1996 average Se concentrations in this species might be used to estimate concentrations 

in 1990. 

 We have assumed that the bivalves listed above were a major food source for surf scoter, scaup, and 

white sturgeon during the period 1986 to 1990. The bivalve C. fluminea was collected during the 

Selenium Verification Study from 1987 to 1990 from Suisun Bay (White et al., 1987; 1988; 1989; 

Urquhart and Regalado, 1991). Johns et al. (1988) collected C. fluminea from Suisun Bay in 1986. 

The Selenium Verification Study collected the bivalve Mya arenaria from Humboldt Bay and from San 

Pablo Bay in 1988. Figures 26 through 28 show relations between bivalve Se concentrations and Se 

in the livers and flesh of these predators. Each data point represents data from a common year and 

common location (Table 30). Mean Se concentrations in the liver and flesh of white sturgeon, surf 

scoter, greater scaup, and lesser scaup are significantly and strongly correlated with mean Se 

concentrations in bivalves If data for P. amurensis is employed to match the predator data in 1990, 

the correlation remains strong. The 1990 concentrations in C. fluminea are not as strongly correlated 

as other years with the predators, but P. amurensis was the predominant benthos in 1990 in both San 

Pablo Bay and Suisun Bay. 

115
 The regressions in Tables 30 and 31 were employed to forecast Se concentrations in predators under 

the different conditions of loading and climate season employed previously. In Table 30, the mean 

bivalve Se concentration was matched to the mean tissue Se concentration for white sturgeon, surf 

scoter, greater scaup, and lesser scaup. Table 31 represents a further regression of the data. In this 

regression the mean for each year of data for the North Bay or Humboldt Bay for all bivalves is 

regressed for a specific predator. It is recognized that the uncertainty in this calculation is substantial 

because we are extrapolating linearly from the small set of data available. Nevertheless, the 

calculation adds an important and highly relevant perspective to the forecasts presented earlier. Once 

these concentrations are forecast they can be compared to toxicity thresholds known for the tissue Se 

concentrations in birds and fish. This line of evidence is a second demonstration, in addition to 

concentrations in food, of how Se might affect predators in the system. 

 

Selenium concentrations in predators

 Table 32 shows forecasts of hepatic (liver) concentrations of Se in white sturgeon, surf scoter, 

greater scaup, and lesser scaup that result from regression with forecast bioaccumulation by bivalves, 

in two possible Se discharge scenarios (18,700 lbs per six months for a SLD extension discharge and 

an approximately 3,500 lbs Se per six months for a targeted SJR discharge). The forecasts are for the 

low flow season of a dry year, which is the most relevant time period for the migratory predators (see 

discussion below). The forecasts include consideration of all three possible reactivity scenarios 

(C1/AE3, C2/AE2, and C3/AE1). Shown for comparison, is a range of threshold Se concentrations for 

adverse effects on predators based on Se concentrations in liver tissue. The guidelines illustrated show 

a range from 20 to 50 μg Se/g dw based on data compiled in Tables 13 through 15. 

 White sturgeon, surf scoter, greater scaup, and lesser scaup are all in the estuary during the fall and 

early winter, when Se 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 Se concentrations in bivalves in response to 

increased river inflows, so in most years that have been studied, high Se concentrations in bivalves 

extend into February or March. A further lag is expected in the response of predators to changing Se 

concentrations in their food. Thus, the burden of Se these migratory predators would carry as they 

leave the Bay-Delta would probably be reasonably close to that forecast in Table 32. The low flow 

116
condition forecasts may depict the high-end of the risk to these animals, but that is an ecologically 

reasonable expectation of exposure. 

 The Se concentrations in tissues of predators that occur when 18,700 lbs Se are released in six 

months from an SLD extension are well above thresholds for adverse effects (even when full latitude is 

given for uncertainties about linkages between tissue concentrations and effects). There is no 

condition when a SLD extension carrying such loads would not greatly threaten these species. The 

SJR targeted load of approximately 3,500 lbs per six months also threatens these species if partitioning 

of Se follows the suspended sediment partitioning observed in the past. If partitioning to particulate Se 

follows the Kd typical of shallow sediment, bivalve bioaccumulation would be similar to what 

probably existed prior to refinery cleanup, with a resultant forecast of risk similar to that forecast to 

exist prior to cleanup. This forecast is another line of evidence that the targeted load of 3,500 lbs Se 

per six months, if conveyed to the Bay-Delta by the SJR, would have the effect of replacing the Se 

scheduled for removal through treatment by the oil refiners in 1998 (Table 10). 

 

CONCLUSIONS 

Cumulative Impacts on the Bay-Delta 

 Some uncertainty characterizes transformations and other aspect of the analysis given above. 

However, enough is known about the biogeochemistry and biotransfer of Se that, using multiple lines 

of evidence, the relevant conditions and outcomes can be bracketed for the Bay-Delta. The model and 

forecasts demonstrate that many of the most likely combinations of load, hydrology, climate, Se 

reactivity, and Se bioavailability pose a significant ecological risk to the Bay-Delta. In general, SLD 

discharges that would meet demands for drainage pose risks to fish and bird reproduction and the risk 

of fish extinction via contamination of their invertebrate food. If biogeochemical conditions like those 

today in the Bay-Delta predominate during projected Se 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 Se undergoes reactions typical of low flow or longer residence time, highly 

problematic bioaccumulation is forecast to result. There are some conceivable scenarios of increased 

Se discharge to the Bay-Delta where the potential of risk is reduced. For example, the targeted load 

scenario for the SJR results in prey in the Bay-Delta containing Se concentrations less than the 

threshold of effects for predators based on food, but only if reactivity is low during low flow seasons. 

117
Most of those conditions are of low likelihood in that such low particulate and suspended matter 

reactivity is not typical of the Bay-Delta. Discharge of Se from the SJV would be predominantly 

selenate, rather than the selenite released by refineries prior to 1998. Transformation of selenate to 

particulate Se is observed throughout nature where residence times are extended. The efficiency of this 

transformation and the resulting particulate Se concentrations are key to forecasting Se 

bioaccumulation and effects. 

! Dry year and wet year, low flow season 

 The dry years and low flow seasons will be the ecological bottleneck (the times that will drive 

impacts) with regard to Se. Surf scoter, greater and lesser scaup, and white sturgeon 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 dry year compiles Se concentrations for each 

media employed in our analysis (water, sediment, invertebrate, predator), along with guidelines or 

concentrations where biotic effects are expected (Table 33). The forecasts show conditions at the head 

of the estuary for a range of inputs (6,800; 18,700; or 44,880 lbs released per six months). We assume

a particulate transformation of 3 X 103

 (C2) indicative of shallow sediment Bay-Delta conditions and a 

generic bivalve AE of 0.56 (AE2) to reflect bioaccumulation potential. In general, the lower range of 

guidelines for waterborne, particulate, dietary, and predator tissue Se is exceeded in every forecast 

considered in Table 33 where the input is from a proposed SLD extension. In these dry year/low flow 

season forecasts, the upper range of guidelines is exceeded in all forecasts except that for the 

concentration of a generic bivalve (food) at the lowest load considered (6,800 lbs per six months). 

However, that concentration in prey does result in exceedance of the guideline for white sturgeon and 

greater and lesser scaup liver. 

 If a SLD extension is constructed and it discharges 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 Se to the Bay-Delta via the SJR (for example at 3,500 lbs per six 

months), the risks are less than for those forecast for a proposed SLD extension. However, for the low 

flow season of a dry year, Se concentrations in prey and predators are forecast that are similar to Se 

concentrations observed (and forecast) during conditions in the Bay-Delta prior to refinery cleanup. 

118
These concentrations are in the range of threshold Se concentrations for adverse effects on predators 

based on both Se concentrations in prey (food) and in predator liver tissue. Thus, selenium from the 

SJV replaces, in terms of food web exposure and effects, the Se 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 result in human health advisories. 

 Concentrations less than the threshold of effects for predators based on food were found in two 

forecasts for the low flow season of both wet and dry years, but only if: 

o the proposed SLD discharge is 150 cfs (half the capacity) and the drainage is treated to 

attain a concentration of 50 μg Se/L (6,800 lbs per six months) and if Se transformation 

values or reactivity is low (C3/AE1) in the Bay-Delta; or 

o the SJR discharges 3,500 lbs per six months and if Se transformation values or reactivity is 

the lowest found in any of the receiving waters studied previously (C3/AE1). 

 The necessary low reactivity is unprecedented in the Bay-Delta during low flows, so this seems an 

unlikely scenario. 

! Wet year, low and high flow seasons

 High flow conditions afford some protection under certain forecast conditions. Under these 

conditions, there are some conceivable scenarios where the potential of risk can be reduced. 

Concentrations less than the threshold of effects for predators based on food are found in wet years, if 

discharges of 6,800 lbs or 18,700 lbs via a SLD extension or 3,500 lbs via the SJR per six months are 

released during high flows and reactivities are that of bed sediment or lower (C2 and C3). At the lower 

SJR input load, a higher reactivity (C1/AE3 or AE4) also results in prey of < 10 μg Se/g, but not at 

SLD input loads of 6,800 lbs or greater per six-month. 

 If concentrations in the SJR are regulated under a concentration management plan, increased SJR 

inflows will result in increased input 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 SJR (Figure 19). Higher concentrations result because the higher Se 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. 

119
 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 Se 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 et al., 1979; 1985; Nichols et al., 1986; Peterson et al., 1989). Also during high inflows, 

highly contaminated particulate material from the SJR and/or the SLD is most likely to add to the Se 

load in the estuary. 

! Implications for water quality criteria for the protection of aquatic life 

 In many forecasts, the considered load scenario results in Se concentrations in prey and predators 

that equal or exceed Se concentrations forecast and measured in the Bay-Delta prior to refinery 

cleanup. In some forecasts, Se concentrations in the Bay-Delta remained below the 2 μg Se/L water 

quality criterion proposed for the protection of aquatic life, but those predators using the specific 

bioaccumulation pathway from sediment and benthic/suspended biomass to bivalves were, 

nevertheless, impacted. Our forecasts suggest that even at waterborne Se concentrations at the head of 

the estuary of 1 μg Se/L, all risk of adverse effects cannot be eliminated. 

Extent and Sustainability of Agricultural Discharge from the San Joaquin Valley 

 Taking a broad view, two lines of evidence were used to show the general magnitude of the 

accumulated Se reservoir in the western SJV. Calculations at the lower range of projections show that 

long-term reduction in Se discharge would not be expected for 63 to 304 years, if Se were disposed of 

at a rate of approximately 42,500 lbs per year. Drainage of wastewaters outside of the SJV may slow 

the degradation of SJV resources, but drainage alone cannot alleviate the salt and Se buildup in the 

SJV, at least within a century, even if no further inputs of Se from the Coast Ranges occur. The 

amounts of ground water, salt, and Se that have accumulated in the internal reservoir of the SJV may 

make management of only the annual imbalance of input greater than output impractical. 

 However, forecasts of annual SJV agricultural discharges provide a basis for determining the upper 

and lower limits of Se discharge from the western SJV (Tables 6 to 9; 17). Secondarily, the projections 

provide the basis for determining the magnitude of Se load reductions that may become necessary to 

achieve a specific targeted load of Se for environmental or restoration targets or objectives. To 

120
narrow the range of possibilities in our analysis, agricultural inputs or discharges were divided into 

three groups depending upon management scenarios: 

! Supply-driven management. A range of 3,000 to 8,000 lbs Se per year was assumed to address

environmental protection via a targeted load that cannot be exceeded. For example, using 

different modes of conveyance: 

o Current load limits for the Grassland subarea are from 5,661 to 6,660 lbs Se per year. 

Grassland subarea loads modeled for the SJR as part of TMDL regulation to meet the 5 

μg Se/L concentration objective in the SJR 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; and Appendix C). 

o Although no environmental review of the impact of potential Westlands subarea loads 

has been done since the ecological disaster at Kesterson National Wildlife Refuge 

occurred, a Westlands subarea load estimate as part of evidentiary hearings is 8,160 lbs 

Se per year (assuming 200,000 affected acres; drainage generation of 0.3 acre-feet per 

acre per year; and a Se concentration of 50 μg Se/L) (Table 7). Thus, a load of 8,000 

lbs Se per year may be a lower limit of discharge via a proposed SLD extension. 

! Demand-driven load with management of land and/or drainage quality. A range of 15,000 to 

45,000 lbs Se per year was assumed to address agricultural needs, to some degree, for draining 

saline or waterlogged soils. In this scenario, the quality and quantity of the drainage are 

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 or subsurface drainage defined by the SJV 

Drainage Program for year 2000 with implementation of the management plan (demand driven 

volume) in conjunction with a concentration of 50 μg/L Se (controlled concentration), yields a 

Se load range of 19,584 to 42,704 lb Se per year (Table 6). 

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! Demand-driven load with minimum management. A range of 45,000 to 128,000 lbs per year 

seems 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 example, a range of loads projected 

from the amount of problem water defined by the SJV Drainage Program for year 2000 without 

implementation of the management plan (demand driven volume) in conjunction with a 

concentration of 150 μg/L Se (non-controlled concentration), yields a Se load range of 42,704 

to 128,112 lbs Se per year. 
Graphical tools such as presented in Appendix B (Figures, B2 to B3) could help model additional 

probable scenarios of drainage selected for each subarea. 

Implications and Monitoring Needs 

 Implications for water management using our approach and range of loading forecasts are: 

• 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; as noted earlier, 

critical dry years comprised 15 of those years. Any analysis of Se effects must take the 

influences of variable river inflows into account. 

• Selenium impacts in the Bay-Delta also could increase if water diversions increase or if SJR 

inflows increase with concomitant real-time discharge of Se that increases Se loading (i.e. the 

Se issue and the water management issues are tightly linked). 

• Construction of an extension of the SLD would increase Se exposures of Bay-Delta organisms 

under any scenario partly because the entire load is unequivocally conveyed directly to the 

Bay-Delta. The greatest risks occur if discharge is continuous through high and low flow 

periods. Discharges from a SLD extension are especially problematic if they are constant 

through low inflow periods, when the dilution capacity of the estuary subsides dramatically 

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 

impact of a SLD extension.

• Treatment also may be important in determining source loads impacts. Treatment technologies 

applied to source waters may affect both the concentration and speciation of the effluent. For 

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

enhanced Se food chain concentrations if speciation in the effluent changes to increase the 

efficiency of uptake. 

 We view low flow conditions as the bottleneck that will determine the effects of Se 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 Se are probably near their maxima when migratory 

species leave the estuary, enhancing risk of biological damage. Animals that will be most vulnerable 

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to Se effects probably include those that feed on filter-feeding benthos like bivalves and those that are 

active (i.e., preparing for reproduction or for which early life stages develop) in the estuary in 

September through March. 

 If water quality criteria are to be employed in managing Se inputs, the composite freshwater Se 

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 Se concentration that is the starting point for determining the exposure that 

Bay-Delta organisms will experience. 

 Various guidelines and criteria were employed as reference points in this report. These may not be, 

individually, realistic indications of ecological risk. For example, in the Bay-Delta neither the USEPA 

criterion of 5 μg Se/L nor the recommended USFWS criterion level of 2 μg Se/L alone, would be 

sufficient to protect the estuary if Se transforms to particulate concentrations at a Kd of greater than 

103

. The most effective interpretation includes monitoring data and development of guidelines for all 

critical media. We see the need for systematic long-term monitoring as crucial to protection of 

ecosystems receiving Se discharges. In addition to loads and water column concentrations, risk is 

affected by speciation, transformation to particulate forms, particulate concentrations, 

bioaccumulation, and trophic transfer to predators. Given below is a sampling plan that includes 

sampling of media and organisms that are specific to vulnerable food webs. Used in combination, such 

data and criteria might be the most useful way to manage Se in an ecosystem. 

 We propose that all processes that link Se load to predator effects be monitored as a feasible 

approach for site-specific analysis. The linked processes provide the necessary framework. 

Monitoring, as conceptualized below, would sample critical environmental components at a frequency 

relevant to each process to determine trends in Se contamination or changes in processes that 

determine fate and effects of Se. 

• In any site-specific analysis of Se impacts, it is important that “site” be defined by all 

components of its hydrologic unit (e.g., Lemly, 1999b). Hydrologic models would serve as a 

basis for developing the infrastructure of this hydrologic unit. Specifically, the Bay-Delta 

ecosystem is connected to the SJR ecosystem, thus warranting consideration of the 

vulnerability of downstream water bodies when considering evaluation of upstream source 

waters. Toxicity problems may not appear equally in all components of a hydrologic unit 

because some components may be more sensitive than others. For example, the SJR, as a 

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flowing water system may be less sensitive to Se effects (especially if selenate dominates 

inputs) than adjacent wetlands, the Delta or the Bay, where residence times and biogeochemical 

transformations of selenate are more likely. 

• Multiple-media guidelines provide, in combination, a feasible reference point for monitoring. A 

linked or combined approach would include all considerations that cause systems to respond 

differently to Se contamination. 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 of Se; concentrations of dissolved Se and suspended Se; Se 

speciation in water and sediment; assimilation capacities of indicator food chain organisms; and 

Se concentrations in tissues of prey and predator species. Determination of transformation 

efficiency and processes that determine Kd’s of Se in Bay-Delta and SJR are crucial to relate 

loads to bioaccumulation, rates of transfer, and effects. Trace elements sequestered in bed 

sediments and in algal mats would be a part of recommended mass balance considerations. 

• Invertebrates may be the optimal indicator to use in monitoring Se because they are practical to 

sample and are most closely linked to predator exposure. Knowledge of optimal indicators in 

the Bay-Delta and SJR are necessary to fully explore feeding relationships. Resultant 

correlations with Se bioaccumulation in food webs are a part of this process. 

• Determination of food web inter-relations will help identify the most vulnerable species. 

Specific protocols that include life cycles of vulnerable predators including migratory and 

mobile species would then document Se effects for the species most threatened. 

• Little is known about Se concentrations in the Delta, yet this is the system that could be most 

impacted by Se discharges from the SJV. This is the transition zone between the Bay and the 

largest potential source of Se. It is an area of great biological value itself and an area of great 

emphasis in CALFED’s restoration effort. The fate of Se in the Delta will be a key in 

determining the extent to which Se contamination will impede restoration of the estuary. 

• The fate and effects of Se in the SJR are not well known. Given the possibility of Se 

concentrations in this ecosystem that may occasionally be greater than the current criterion of 5 

μg/L or the proposed criterion of 2 μg/L, it will be essential to investigate and determine the 

fate and effects of Se in this system. In short, if management and regulatory measures to 

restore the SJR ecological resources to their former level of abundance are to be effective, then 

124
the biogeochemistry of Se, ecology, and hydrodynamics in this system must be further 

investigated and understood.

• A mass balance of Se through the estuary is crucial because internal (oil refinery) and external 

(agricultural drainage) sources of Se are changing as a result of management. In the past (1986 

to 1995), cumulative agricultural loading to the SJR was estimated at approximately 100,000 

lbs Se (Presser and Piper, 1998). Currently, Se is discharged through Mud Slough to the SJR at 

the rate of approximately 6,000 to 8,000 lbs per year. The ultimate fate of Se from these past 

and current agricultural discharges is not known. At a minimum, a mechanism for tracking Se 

loading via oil refineries and the SJR is needed based on SJR, Sacramento River, and BayDelta hydrodynamics. Monitoring needs to measure the on-going status of the system in terms 

of inputs, storage in sediment, throughput south via the Delta-Mendota Canal and California 

Aqueduct, and throughput north to the Bay. 

• Storms and high flow years will be times of increased regional discharge of drainage containing 

high concentrations and loads of Se. Violations of water quality criteria and load targets could 

result on a re-occurring basis, if the precipitation-dependence of the Se inflows is not 

recognized. 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. 

• In view of the analysis of the existing Se reservoir in the SJV, consideration of the degradation 

of groundwater reservoirs needs to be a factor in management scenarios. Short-term

management that results in more storage than leaching will result in more degradation of 

aquifers. Mass balance considerations should include a “storage” term, not only input and 

output terms. Monitoring and assessment of storage also will show if treating discharge on an 

annual basis will suffice to manage the current regional imbalance of water, salt, and Se. 

 We have demonstrated and thoroughly reviewed the justifications for a methodology that employs 

existing knowledge of each factor in a sequence of linked processes that control ecological effects of 

Se. We have incorporated these linked processes into an internally consistent evaluation using 

multiple lines of evidence. Any future analysis of impacts from Se discharges via the SJR or a 

proposed SLD extension to the Bay-Delta should be at least as complete and could profitably build 

from the framework presented here. For the Bay-Delta, this new tool is used in site-specfic forecasts to 

125
evaluate Se effects based upon the major processes leading from loads through consumer organisms to 

predators. We conclude that credible protective criteria need to be applicable to vulnerable food webs 

and to be based on contaminant concentrations in sources such as particulate material that most 

influence bioavailability. Bivalves appear to be the most sensitive indicator of Se contamination in the 

Bay-Delta. 

126
ACKNOWLEDGMENTS 

 We wish to acknowledge: 1) technical and policy reviews by Marc A. Sylvester, Water Resources 

Division of the U.S. Geological Survey; 2) technical reviews by Steve Hamilton, Biological Resources 

Division of the U.S. Geological Survey; and Joy Winckel of the U.S. Fish and Wildlife Service; and 3) 

grant review by Gail Louis and Philip Woods of the U.S. Environmental Protection Agency. This 

work was performed with the support of a U.S. Environmental Protection Agency interagency funding 

agreement (EPA/IAG DW 14955347-01-0) and cooperative funding agreements with Contra Costa 

County and Contra Costa Water District. We wish to thank Gail Louis, Eugenia McNaughton and 

Michael Boots of U.S. Environmental Protection Agency, John Kopchik of Contra Costa County, and 

Richard Denton of Contra Costa Water District for their support during the preparation of our model. 

Mark Huebner of the Water Resources Division provided technical support with data and figures. And 

lastly, the long-range vision of T. John Conomos within the U.S. Geological Survey and the goals of 

the Water Resources Division National Research Program have made this report possible. 

127
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171
FIGURES 
Coal Soils and Alluvium Oil Phosphorite

Power Generation Irrigation Refining Mining

Ash, Flue Gas

Scrubbing Subsurface drainage Wastewater

Belews Lake,

North Carolina

San Francisco

Bay-Delta

Estuary, California

Blackfoot 

River watershed,

Idaho

Kesterson NWR, 

San Joaquin River, 

Tulare Basin,

California

Organic carbon-enriched sediment

Geologic sources 

Anthropogenic

activity

Pollutants

Receiving waters 

(examples)

Species of 

concern

bluegill, sunfish,

bass, bullhead

coot, duck, grebe 

avocet, stilt, sculpin,

splittail, salmon 

trout, coot, horse,

sheep, elk, cow

scoter, scaup,

sturgeon, splittail,

flounder, salmon,

Dungeness crab

Selenium source 

deposits

Depositional environments Freshwater Seawater

Tailings, runoff

Figure 1. Conceptual model of Se pollution with examples of source deposits, anthropogenic activities, receiving water bodies, and biota at risk.
Figure 2. Conceptual model describing linked factors that determine the effects of selenium on ecosystems. The sequence of relations links 

environmental concentrations to biological effects. The general term “bioaccumulation” can be applied to all of the biological levels of selenium 

transfer through the food web, but in this report we use the term explicitly in reference to particulate/invertebrate bioaccumulation. 

Composite Source Load

(oil refinery discharges, agricultural drainage via

San Joaquin River or proposed San Luis Drain

extension, Sacramento River

Composite Volume

(Sacramento River and San Joaquin River)

Composite Freshwater Endmember Concentration

(head of estuary)

Dissolved species

(selenate, selenite, organo-Se)

Phytoplankton, algae, bacteria

suspended particulate material and bed sediment

(elemental Se, particulate organo-Se, adsorbed 

selenite/selenate)

Impaired reproduction, teratogenesis, selenosis

Bay-Delta Selenium Model

Partitioning (Kd)

Transformation

zooplankton

striped bass

clams amphipods

sturgeon

diving ducks

splittail

splittail

flounder

prey

predators

 ̧

bioaccumulation

trophic transfer

effects


Northern Subarea

Grassland Subarea

Westlands Subarea

Tulare Subarea

Kern Subarea

San Pablo 

Bay

South Bay

Delta

Mendota

Pool

to San Joaquin River

Drains

Drains

Drains/

Evaporation Ponds

Drains/

Evaporation Ponds

Sacramento River

New Exchequer Dam

New Don Pedro Dam

New Melones Dam

Crows Landing

Stanislaus R.

Tuolomne R.

Merced R.

Vernalis

Los Angeles

Mud Slough

SAN JOAQUIN

Carquinez

Strait

Delta Mendota Canal

California Aqueduct

Pine Flat Dam

Isabella Dam

Kings R.

Kern R.

Potential

San Luis 

Drain

Discharge 

Point

Sierra Nevada

Existing

San Luis Drain

Friant Kern Canal

Coast Ranges

Potential

San Luis Drain

Extension

Potential

San Luis Drain 

Extension

Kesterson N.W.R

Freeport

Suisun Bay 

San Francisco Bay - Estuary System

Clifton Court Forebay

Tracy

Pumps

Pacific

Ocean

Figure 5. Hydrologic connections of the San Francisco Bay-Delta Estuary with the San Joaquin 

Valley. The only natural outlet from the valley is the San Joaquin River. An extension of the 

San Luis Drain would provide a constructed outlet for agricultural drainage from the San Joaquin 

Valley to the Bay-Delta. Filled circles show locations of five major oil refineries. Enlarged 

arrows are for emphasis and are not representational of flow. Not to scale.

San Joaquin River

San Luis Drain

RECYCLE

N

North Bay

Sacramento-San Joaquin

Delta

Central

Bay

Honker Bay

Grizzly Bay

Grassland Grassland wetlands RIVER

Contra Costa Canal Delta

Pumps

Bypass

1981 to 1986 connection

currently, no discharge

Friant Dam
Selenium Concentration

Water Flux

Load

Concentration

fall summer El Nino

Selenium Load

Figure 6. Selenium concentration in drainage (i. e., source waters) as a function

of flow (I.e., water flux) and resultant Se load. This schematic representation from

current data depicts the effects of a large reservoir of Se on subsurface drainage.
0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6

Kestersons (ksts)

Kern

Tulare

Westlands

Grassland

Northern

high range low range

Kestersons per year

1 Kesterson = 17,400 lbs Se

Figure 7. Projected high and low range of annual selenium discharges from the five subareas of the western San Joaquin Valley

using current available data. Discharges are given in kestersons (ksts), where 1 kst equals 17,400 lbs. The kst unit is the

cumulative total of 17,400 lbs Se, which when released directly into KestersonReservoir caused ecotoxicity and visible

ecological damage. It is used here as a measure of potential ecological damage based on selenium load. 
Grassland (42 )

Northern (1.9 ) Tulare (1.4 )

Kern (4.3 )

Westlands (67 )

Projected Annual Selenium - high range

lbs per day

Figure 8. Projected high range of daily selenium discharges from the five subareas

shown as proportions of total discharge from the western San Joaquin Valley.
0

50000

100000

150000

200000 Cubic feet per second

0 30 60 90 120 150 180 210 240 270 300 330 360

Julian days (1/1/94 through 12/31/94)

TOTAL INFLOWS (SR +SJR) TOTAL OUTFLOW 

Sacramento - San

Joaquin Delta

Sacramento R.

at Freeport

San Joaquin R.

at Vernalis

Total

Outflow

Tracy +

CCtF

0

5000

10000

15000

20000

25000 Cubic feet per second

0 30 60 90 120 150 180 210 240 270 300 330 360

Julian days (1/1/94 through 12/31/94)

SJR@VERNALIS TRACY+CCtF TOTAL OUTFLOW 

Figure 9. The balance between water diversions (e.g., pumping at Tracy and Clifton Court

Forebay), total river inflow to the Bay-Delta, and the discharge of the San Joaquin River in

a dry year (1994).
0

50000

100000

150000

200000

Cubic feet per second

0 30 60 90 120 150 180 210 240 270 300 330 360

Julian days (1/1/96 through 12/31/96)

TOTAL INFLOWS (SR +SJR) TOTAL OUTFLOW 

Sacramento R.

at Freeport

Sacramento - San

Joaquin Delta

San Joaquin R.

at Vernalis

Total

Outflow

Tracy +

CCtF

0

5000

10000

15000

20000

25000

Cubic feet per second

0 30 60 90 120 150 180 210 240 270 300 330 360

Julian days (1/1/96 through 12/31/96)

SJR@VERNALIS TRACY+CCtF TOTAL OUTFLOW 

Figure 10. The balance between water diversions (e.g., pumping at Tracy and Clifton Court

Forebay), total river inflow to the Bay-Delta, and the discharge of the San Joaquin River in

a wet year (1996).
0

0.05

0.1

0.15

0.2

0.25

0.3

Selenium (

mg/L)

0 5 10 15 20 25 30 35

Salinity (psu)

Selenium Dilution in Bay-Delta

Existing Conditions: Annual average

Sacramento River

endmember

SeawatrendmemberRegional Se bsineMixigLandward Suisun BayCarquinezStrait San PabloBayComposite freshwaterendmmber(i.e. athad ofestuary)17.5psuSeaward

Figure 11.Hypotheical dilution profiles for Sein theBay/Delt. The rgional bseine profile shows Se concentrations thrugh thesuary sconcentrations n theSacrmento River arediluted by concentrations thePacific Ocean asidcte by salinties (practical sintyunits,p).The xample mixing profile shows the Seconcetration n ahypoteical averg feshwaterndmmberas it is dlutedby concentrations thePacific Ocean. Thiswas calculated from loads n volumes in the Sacramento Riverat 20 MAF perya plus refinery inputs ofapprximately 4,000 lbs Seper ya(typical ofawet yarpiorto refinry cleanup).

Landward Suisun Bay Carquinez Strait San Pablo Bay Seaward

Regional Se baseline

Mixing

Composite freshwater

endmember (i.e., at head

of estuary)

17.5 psu

Figure 11. Hypothetical dilution profiles for selenium in the Bay-Delta. 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 (practicalsalinity units, psu). The example mixing profile shows the selenium concentration in a hypothetical average freshwater endmember as it is

diluted by concentrations in the Pacific Ocean. This endmember was calculated from loads and volumes in the Sacramento River at 20 million

acre-feet (MAF) per year plus refinery inputs of approximately 4,000 lbs Se per year (typical of a wet year prior to refinery cleanup).
0 5 10 15 20 25 30 35

Salinity

0.00

0.06

0.12

0.18

0.24

0.30

Se (

μg/L)

Dissolved Selenium in San Francisco Bay

4/86 9/86

6/95

10/96

Figure 12. Dissolved selenium profiles as a function of salinity (practical salinity units, psu) in the BayDelta, comparing high and low flow seasons in 1986 (4/86 and 9/86) and in 1995-96 (6/95 and 10/96)
0 5 10 15 20 25 30 35

Salinity

0

1

2

3

4

September 1986 October 1996

7

8

9

Particulate Se (

μ g/g)

Se Particulate Concentrations vs. Salinity

Figure 13. Particulate selenium profiles as a function of salinity (practical salinity units, psu) in the

Bay-Delta, comparing high and low flow seasons in 1986 (9/86) and in 1995-96 (10/96).
0 2 4 6 8 10 12 14 16 18 20

Concentration of Se (μ g/g)

0

10

20

30

40

% of samples

Frequency Distribution of Se Concentrations

1986: Reference sites & SF Bay

C. fluminea

Reference

SF Bay

0 2 4 6 8 10 12 14 16 18 20

Concentration of Se (μ g/g)

0

10

20

30

40

% of samples

Frequency Distribution of Se Concentrations

Reference sites & SF Bay: 1995-97

Reference

P. amurensis

C. fluminea

SF Bay

Figure 14. Frequency distributions of selenium concentrations in (a) 129 composite samples of C. fluminea collected between

January 1985 and October 1986 and (b) 62 composite samples of P. amurensis collected between May 1995 and June 1997

from the Bay-Delta. Concentrations in bivalves from reference sites also are given. 

(a)

(b)
J FMAMJ J ASOND

95

J FMAMJ J ASOND

96

J FMAMJ

97

0

5

10

15

20

25

Se Concentration (

μ g/g)

0

100

200

300

(Thousands)

Delta Outflow (CFS)

Se Concentrations in Potamocorbula

compared to river inflows

Carquinez Straits

River inflow

San Pablo Bay

Figure 15. Selenium concentrations in replicate composite samples of P. amurensis from 1995

through 1997 as a function of Delta outflow. Flows are averaged on a monthly basis. 
38° 00’

122°30’ 122°15’ 122°00’

Suisun

Bay

Carquinez

Strait

5 mi

8 km

0

0

San Pablo

Bay

4.0

8.1

14.1

8.0

14.0

20.0

0 - 2 (m)

-

-

-

7.9

7.5 7.3

6.9

8.1

8.1

8.3

8.7

7.5

9.2

9.6

7.5

9.2

9.6

10.3

10.0

8.9

20.0

6.7

6.1 8.2

5.7

16.8 11.0

Figure 16. Selenium concentrations in replicate composite samples of Potamocorbula

amurensis at 22 locations in the Bay-Delta during October 1996. Bivalve selenium

concentrations are given in μg Se/g, dry weight.
English SoleHerringLF Smelt No. Anchovy STR Flounder SPK Sanddab PS SculpinYF Goby WHT Sturgeon

Fish Species

0

3

6

9

12

15

Selenium (

μ g/g dry wt.)

Se Concentrations in Fish

from the North Bay 1986

Flesh Liver Whole

Herring

Smelt

Flounder

Sculpin

*Data from Department of Fish and Game

Goby

English Sole

Anchovy

Sanddab

Sturgeon

** includes San Pablo, Suisun, Grizzly and Honker Bays

Figure 17. Selenium concentrations in fish samples collected from the North Bay during 1986. Data from California

Department of Fish and Game Selenium Verification Study (White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991)
0 20 40 60 80 100 120 140

Se (average) in Liver (μ g/g dry wt)

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

Se in Bird Liver Tissue

Suisun and San Pablo Bays (1986-1990)

Figure 18. Average selenium concentrations in bird liver samples collected from Suisun Bay and San Pablo Bay from 1986 to 1990. Data from California

Figure 18. Average selenium concentrations in bird liver samples collected from Suisun Bay and San Pablo Bay from 1986 to 1990. Data

from California Department of Fish and Game Selenium Verification Study (White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991).

Species marked with an asterisk were collected in Suisun Marsh.
0

0.2

0.4

0.6

0.8

1

1.2

1.4

Composite FW endmember (

μ g/L Se)

0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5

SJR Input (μ g/L Se)

Wet year Dry year

Concentration Management Scenarios

Low flow season

Wet year

Dry year

Figure 19. Forecasts of composite freshwater endmember selenium concentrations for a series of concentration management scenarios

for the SJR in low flow seasons of both wet and dry years.
0 

1 

2 

3 

4 

5

Composite FW endmember, (

μ

g/L Se)

0 

2400 

4800 

7200 

9600 

12000 

Se input load (lbs)

J F M A M J J A S O N D

lbs Se SLD[36,720 lb/yr] lbs Se SJR[32,936 lb/yr]

lbs Se SJR[16,468 lb/yr] SLD @ 62.5 μ g/L

SJR @ 2 μ g/L SJR @ 1 μ g/L

Monthly Forecasts

(Wet year, 1997)

SLD input (62.5 μ g/L) 

SJR input (2 μ g/L)

SJR input (1 μ g/L)

month

month

Figure 20. Forecasts of monthly composite freshwater endmember selenium concentrations under three discharge scenarios

(San Joaquin River at 1 and 2 μg Se/L; San Luis Drain at 62.5 μg Se/L) contrasted to input concentrations and loads of selenium. 
0

1

2

3

4

5

Composite FW endmember, (

mg/L Se)

0 5 10 15 20 25 30 35

Salinity (psu)

October 1997 (wet year) Forecast

SLD extension or SJR conveyance

SeawatrendmemberRegional Se bsineMixigLandward Suisun BayCarquinezStrait San PabloBayComposite freshwaterendmmber(i.e. athad ofestuary)17.5psuSeaward

Figure 11.Hypotheical dilution profiles for Sein theBay/Delt. The rgional bseine profile shows Se concentrations thrugh thesuary sconcentrations n theSacrmento River arediluted by concentrations thePacific Ocean asidcte by salinties (practical sintyunits,p).The xample mixing profile shows the Seconcetration n ahypoteical averg feshwaterndmmberas it is dlutedby concentrations thePacific Ocean. Thiswas calculated from loads n volumes in the Sacramento Riverat 20 MAF perya plus refinery inputs ofapprximately 4,000 lbs Seper ya(typical ofawet yarpiorto refinry cleanup).

Carquinez Strait (17.5 psu)

Figure 21. Dilution of selenium through the estuaryas a function of salinity (practical-salinity units, psu) in October 1997 (wet year). 

Carquinez Strait is assumed to be about half seawater salinity (17.5 practical-salinity units). The composite freshwater endmember 

selenium concentrations are forecast for the SJR at 1 and 2 μg Se/L and for a SLD extension at 62.5 μg Se/L. 

SLD input (62.5 μg/L)

SJR input (2 μg/L) SJR input (1 μg/L)
0

5

10

15

20

25

Composite FW endmember ( 

mg/L Se)

0 20000 40000 60000 80000

lbs Se, SJR (targeted) or SLD input

high flow (wet) low flow (wet) low flow (dry)

Seasonal Forecasts

6,800 lbs

SLD

18,700 lbs

SLD

44,880 lbs

SLD

89,760 lbs

SLD

3,500 lbs

SJR

Figure 22. Forecasts of seasonal composite freshwater endmember concentrations under five discharge scenarios for the high

flow season of a wet year and the low flow seasons of wet and dry years. Input agricultural selenium loads released through a

SLD conveyance are from 6,800 to 89,760 lbs per six months. The SJR forecast releases 3,500 lbs Se per six months. 
0 

5000 

10000 

15000 

20000 

25000 

30000 

35000 

40000 

45000 

50000 

Se load (lbs from all sources)

0 1 2 3 4 5 

Total River Inflow (MAF in 6 months)

Se concentration range,wet year Se concentration range, dry year

Composite FW Endmember, mg/L Se

(low flow season, head of estuary)

10

8

5 4

3

2

1

0.3

Dry year

1.3 MAF

Wet year2.3 MAF

Figure 23. Calculation of eight composite freshwater endmember selenium concentrations as derived from different combinations

of total input load and total river inflow. River inflows are the composited mass of water that reaches the estuary in a six-month

period. The range of inflows and input loads are typical of different climate regimes (wet year or dry year) during the six-month 

dry season. 
0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35

Dissolved Se (μg/L)

0

1

2

3

September 1996 October 1996

7

8

Particulate Se (

μg/g)

Se Particulate vs. Dissolved Concentrations

San Francisco Bay September 1986 and October 1996

Kd = 10,000

Kd = 1,000

Figure 24. Suspended particulate selenium concentrations as a function of total dissolved selenium concentrations.

Lines describing predicted particulate concentrations using Kd’s of 1 X 103 and 1 X 104 are superimposed on the plots.
0 5 10 15 20 25 30 35

Salinity

0.00

0.50

1.00

1.50

2.00

2.50

3.00

3.50

4.00

Particulate Se (

μg/g)

Particulate Se: Observed vs. Predicted

Suisun Bay: October 1996

Observed

Kd = 10,000

Kd = 3000

Kd = 1000

Figure 25. Particulate selenium concentrations as occurring landward (salinity, psu = 0) to seaward (salinity, psu = 35) in the BayDelta. Three different Kd’s forecast three different trend lines for particulate concentrations using dissolved Se concentrations 

(Figure 24). The observed October 1996 particulate data is superimposed on the projections. 
0 2 4 6 8 10

Selenium in Bivalves (μ g/g dry wt.)

0

50

100

150

200

250

300

Selenium in Scoter Liver (

μ g/g dry wt.)

Bivalves vs. Scoter Liver

Figure 26. Relation between bivalve selenium concentrations and selenium in surf scoter liver. Data from California

Department of Fish and Game Selenium Verification Study (White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991).
0 3 6 9 12 15

Selenium in Bivalves (μ g/g dry wt.)

0

5

10

15

20

Selenium in Sturgeon Flesh (

μ g/g dry wt.)

Bivalves vs. Sturgeon Flesh

Potamocorbula

Figure 27. Relation between bivalve selenium concentrations and selenium in sturgeon flesh. Data from California

Department of Fish and Game Selenium Verification Study (White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991).
0.00 2.60 5.20 7.80 10.40 13.00

Selenium in Bivalves (μ g/g dry wt.)

0

10

20

30

40

Selenium in Sturgeon Liver (

μ g/g dry wt.)

Bivalves vs. Sturgeon Liver

Potamocorbula

Figure 28. Relation between bivalve selenium concentrations and selenium concentrations in sturgeon liver. Data from California

Department of Fish and Game Selenium Verification Study (White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991).
TABLES
Table 1. Chronology of authorizing, planning, regulatory, and evidentiary events for construction of a valleywide drain or a San Luis Drain. 

Date Agency or Industry Event 

1950 U.S. Bureau of Reclamation 

(USBR) 

Begins Central Valley Project (CVP) 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 (SJV) 

1960 Federal Law (Public Law 86-488) ‡ Authorizes San Luis Unit (SLU) of Central Valley Project 

(CVP) and makes provision for constructing interceptor drain to 

the S.F. Bay-Delta 

1962 USBR Definite Plan Report for SLU (includes capacity for other areas) 

1965 State of California ‡ Proposes expansion of drainage plans to install valley-wide 

master drain 

1965 

to 

present 

U.S. Congress * Includes a rider to CVP 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 SLU drainage waters 

1967 State of California Declines to participate in valley-wide master drain 

1968 USBR Begin (1) CVP water deliveries to the San Luis Service Area 

and (2) construction of San Luis Drain (SLD) for use by 

Westlands Water District 

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

1970 USBR and U.S. Fish and Wildlife 

Service (USFWS) 

Designate Kesterson Reservoir, a regulating reservoir for the 

San Luis Drain, as a new USFWS National Wildlife Refuge 

1972 USBR EIS on SLU filed with Council on Environmental Quality 

1975 USBR Completes 85-mile SLD to Kesterson, 120 miles of collector 

drains, and 1200-acre reservoir; agrees to supplemental EIS on 

impacts of SLD from SLU 

1975 USBR * Halts construction of remainder of SLD due to Federal budget 

restrictions and increasing environmental concerns regarding 

discharge to the Delta 

1975 USBR and state water agencies ‡ Recommend completion of the SLD to the SF Bay/Delta 

1977 Federal Law (Public Law 95-46) * Authorizes study of problems related to completion of SLD 

1977 USBR * Asks USEPA about requirements for a waste discharge permit 

for SLD 

1979 USBR and California water 

agencies * ‡ 

Issues study of alternatives and final report recommending 

construction of drain; issues First Stage EIR for discharge at 

Suisun Bay (Chipps Island) 

1981 USBR * ‡ Begins drainwater flow into Kesterson Reservoir; begins San 

Luis Special Study to fulfill state requirements for obtaining a 

permit for discharge of SJV drainage to the SF Bay/Delta at 

Chipps Island in Suisun Bay 

1983 USFWS Advises USBR of bird deformities/deaths at Kesterson Resv. 

1984 USFWS and USGS * Studies show environmental damage from selenium at 

Kesterson Reservoir 

1985 Secretary of U.S. Department of 

Interior (USDOI) and California 

Governor * 

Establishes 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 SLD; initiates National Irrigation Water Quality 

Program to study effects of agricultural drainage on refuges 

across the western U.S. 
Table 1. continued 

1986 USBR Closes SLD; issues EIS for cleanup alternatives for Kesterson 

Reservoir 

1986 Barcellos Judgment, U.S. District 

Court ‡ 

Calls for a Drainage Plan, Service Facilities, and a Drainage 

Trust Fund 

1987 Federal and State Interagency 

Committee, San Joaquin Valley 

Drainage Program (SJVDP) * 

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

environmental groups and coastal communities opposition, 

future studies limited to in-valley options 

1988 USBR as ordered by State of 

California 

Fills and grades Kesterson Reservoir as part of Kesterson 

Cleanup Program 

1990 Federal and State Interagency 

Committee 

Completes SJVDP Management Plan for in-valley solutions to 

drainage problem 

1991 Federal and State Interagency 

Committee 

Forms San Joaquin Valley Drainage Implementation Program 

and signs MOU to help implement in-valley recommendations; 

state CDWR is lead agency 

1992 USBR ‡ As part of Barcellos Judgment, submits Draft EIS for San Luis 

Unit Drainage Program; EIS suggests in-valley approaches and 

stated “the social and environmental unacceptability” of 

completing a drain “precludes further consideration”; court 

rejects EIS as not complying with judgment 

1992 Federal Law 102-575 (CVPIA) Calls for water for protection of fish and wildlife and land 

retirement in the SJV 

1993 U.S. House of Representatives 

(Subcommittee on Natural 

Resources) 

Oversight Hearing on agricultural drainage issues in the Central 

Valley including re-use of a portion of SLD by Grassland 

subarea 

1993 Porgans, Carter, U.S. Fish and 

Wildlife Service, and 

environmental groups 

Petition state over adequacy of EIS’s for operation of privately 

owned drainage evaporation ponds where unavoidable bird loss 

was occurring 

1994 Wanger Decision, U.S. District 

Court * ‡ 

Decides to send the salty water north; calls for initiation of 

process to obtain a discharge permit for the SLD to the SF 

Bay/Delta 

1995 USBR; Contra Costa County et al. Appeals Wanger decision; environmental groups intervene; 

decision pending 

1995

- 

1996 

USBR and San Luis Delta-Mendota 

Water Authority 

Issues Environmental Assessment (FONSI) for re-use of SLD 

by Grassland subareas; 28-miles of SLD reopens to convey 

drainage to the San Joaquin River 

1996 State Water Resources Control 

Board ‡ 

State re-emphasizes that valley-wide drain is best technical and 

feasible solution for water-quality and salt balance in the SJV, 

but calls for NPDES permit 

1997 State Department of Water 

Resources 

Starts preparing update of SJVDP Management Plan due to nonimplementation 

1999 State Department of Water 

Resources 

Declares SJVDP to have been unsuccessful 

1999 USBR, State Department of Water 

Resources and State Water 

Resources Control Board Water 

Right Decision 1641 * ‡ 

Recommend completion of the SLD to S.F. Bay/Delta or other 

out-of-valley alternative; call for MOU to initiate environmental 

review for consideration of discharge application for the SLD 

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

completing SLD 

2000 Hug, et al., 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 

‡ recommendation for completion of drainage facility (i.e., San Luis Drain); * call for environmental review 

or notice of environmental concerns; CVP includes the San Luis and Delta-Mendota Service Areas.
Table 2. Chronology of investigative and regulatory events for the San Francisco Bay/Delta concerning 

selenium. 

Date Agency or Industry Event 

1975 Report to Association of Bay Area 

Governments (regional monitoring 

program, Risebrough et al., 1977) 

Samples of transplanted Mytilus edulis show 

some of highest concentrations in Carquinez 

Strait 

1982 and 1985 U.S. Fish and Wildlife Service Elevated Se concentrations found in scoter 

and scaup from South and North Bay 

1985 California State Water Resources Control 

Board 

Initiates 5-year Selenium Verification Study

for intensive sampling of biota in areas of 

concern including Bay-Delta and San 

Joaquin River 

1985-1986 U.S Geological Survey and U.S Bureau of 

Reclamation 

Samples of Corbicula fluminea and Macoma 

balthica show enrichment in North Bay 

1986 California Department of Water 

Resources and Cutter (1989) 

Sampling shows internal sources of Se from 

refineries in the mid-estuary 

1986 California Department of Water 

Resources and U.S. Geological Survey 

Invasion of the Asian clam (Potamocorbula 

amurensis) in Suisun Bay changes benthic 

macroinvertebrate community 

1986-1991 California Department of Fish and Game 

and U.S. Fish and Wildlife Service 

As part of SVS, sampling shows elevated 

levels of Se in scoter, scaup, white sturgeon, 

starry flounder, Dungeness crab and Bay 

shrimp 

1986 California 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 California Department of Water 

Resources and Cutter and San DiegoMcGlone (1990) 

Sampling shows anthropogenic Se source is 

52% to 92% of total Se 

1988 California San Francisco Bay Regional 

Water Quality Control Board 

(CSFBRWQCB) 

Directs oil refineries to investigate selenium; 

crude oils from the San Joaquin Valley are 

targeted as source; call for Se control 

technologies rather than best management 

practices of waste streams 

1988 California 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 U.S. Environmental Protection Agency Establishes San Francisco Estuary Project as 

part of National Estuary Program 

1988-1989 California San Francisco Bay Regional 

Water Quality Control Board 

Determines water-quality standards not met 

in the North Bay to develop comprehensive 

conservation and management plan by 1992 

1989 U.S. Environmental Protection Agency Because of bioaccumlation in predators, 

overrules regional board and places North 

Bay on 304(l) list as substantially impaired 

by point sources of Se; mandates control 

strategies to be implemented to reduce loads 

resulting in standards being met within 3 yrs. 

1991 California San Francisco Bay Regional 

Water Quality Control Board 

Issues Se mass limits in NPDES permits 

including 50 μg/L daily concentration 

maximum limit 
Table 2. continued 

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 U.S. Environmental Protection Agency Promulgates 5 μg Se/L standard for BayDelta because salt water objective of 71 μg/L 

is underprotective 

1992 U.S Geological Survey Modeling studies show importance of 

phytoplankton-particulate-bivalve foodweb 

to predator tissues Se concentrations 

1992 Oil Refiners Appeal permits and sue regional board 

1992 USEPA Promulgates 5 ppb Se standard in National 

Toxics Rule 

1992 California San Francisco Bay Regional 

Water Quality Control Board 

Proposes Basin Plan Amendment that takes 

iterative mass reduction approach 

1993 California San Francisco Bay Regional 

Water Quality Control 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 

1993 to present Oil Refiners Research and implement Se reduction 

technologies on mandated time schedule 

1993 and 1994 San Francisco Estuary Institute Issues annual report regional monitoring 

program for trace substances 

1994 California San Francisco Bay Regional 

Water Quality Control 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 U.S. Geological Survey (and Interagency 

Ecological Program for the SacramentoSan Joaquin Estuary) 

Sampling in North Bay shows elevated Se 

concentrations in Potamocorbula amurensis 

1996 U.S. Fish and Wildlife Service Issues recovery plan for Sacramento/San 

Joaquin Delta native fishes 

1998-2000 CALFED Ecosystem Restoration Plan for Bay-Delta 

1998, amended 

in 2000 

U.S. Environmental Protection Agency in 

consultation with U.S. Fish and Wildlife 

Service 

Issues California Toxics Rule withholding 

rule on Se 

1998 California San Francisco Bay Regional 

Water Quality Control 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 Bay-Delta 

2000 California State Water Resources Control 

Board 

Lists Bay-Delta as toxic hot spot 

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. 
TABLE 3. Measured and estimated selenium concentrations in shallow ground water and subsurface 

drainage in Westlands Water District, Grassland Drainage Problem Area, Tulare subarea, and Kern 

subarea. 

Source and Sampling ppb Se 

San Luis Drain and agricultural sumps 

SWRCB, 1985 (WQ No. 85-1) 

San Luis Drain, discharge (measurement average, 1983-1984) 330-430 

USGS, 1985 (Presser and Barnes, 1985) 

San Luis Drain discharge, 1984 340 

Westlands subarea drainage sumps 140-1,400 

Grassland subarea drainage sumps 8-4,200 

Testimony (Stevens and Bensing, 1994; Wanger, 1994; WWD, 1996) 

Westlands subarea

San Luis Drain discharge (1981-1984 range) 230-350 

Westlands Water District compilation of USGS data (depending on grid size) 208-277 (range of means)

Westlands Water District estimate 300 

Westlands Water District 1993 survey of 63 locations within 42,000 drained acres 163 (mean) 

Westlands Water District estimate of drainage with treatment 50 

U.S. Bureau of Reclamation (conservative estimate) at least 150 ppb 

CCVRWQCB (1996a,b) 

Grassland Drainage Problem Area

Subsurface tile drainage estimate 150 

Subsurface tile drainage modeling estimate 120 

Subsurface drainage sumps (annual survey of measurements 211 (mean); 134 (median)

1994 drainage leaving problem area (surface plus subsurface) modeled estimate 80 (average) 

SJVDP ( 1990) 

Grassland subarea 

Year 1990 Estimated subsurface discharge to San Joaquin River 150 

Year 2040 Estimated subsurface discharge to San Joaquin River 75 

USGS observation wells, 10-50 feet (Gilliom et. al., 1989) 

Panoche Creek alluvial fan (Grassland and Westlands subareas)

Murietta field well 320-7,300 

Murietta field subsurface drains 800-1,000 

15-year field wells 96-1,000 

15-year field subsurface drains 400 

CCVRWQCB (1990 a, b) 

Tulare and Kern Basins Evaporation Ponds (1988 and 1989) 

Inflows to evaporation ponds <1 – 760 

Evaporation ponds <1 – 6,300 

USGS Observation wells, 12-25 feet (Fujii and Swain, 1995) 

Tulare and Kern subareas 

Alluvial fan zone 

West-side alluvium 

East-side alluvium 

(median) (maximum) 

 8 520 

 < 1 25 

Basin zone 

West-side basin 

East-side basin 

 3 240 

 <1 320 

Tulare Lake Zone 

Northeastern margin 

Southern/western margin 

Lake bed 

 <1 4 

 34 1,000 

 < 1 2 
Table 4. Conversion factors for selenium and salt or Total Dissolved Solids (TDS). 

Selenium (Se) Salt or Total Dissolved Solids (TDS) 1 ppb Se =1 μg Se/L 1 ppm TDS = 1 mg salt/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 μgrams Se/acre-foot at 1 ppb Se 1.23 grams Se/ acre-foot at 1 ppb Se 1,234 grams salt/acre-foot at 1 ppm salt 454 grams = 1 lb 454 grams = 1 lb 0.00272 lbs Se/acre-foot at 1 ppb Se 2.72 lbs salt/acre-foot at 1 ppm salt [1 ppb Se = 0.00272 lbs Se/acre-foot] [1 ppm salt= 2.72 lbs salt/acre-foot] 

2000 lbs = 1 ton 1 ppm salt = 0.00136 tons salt/acre-foot 

Volume 

1 cubic foot per second (cfs) = 1.98 acre-feet/day 
TABLE 5. Annual acre-feet or million acre-feet (MAF) and selenium loads from the upstream drainage source (Drainage Problem Area or Gra

Project site B) and downstream sites for Mud and Salt Sloughs, and the San Joaquin River at Crows Landing (state compliance point for SJR) a

Wateryear Upstream Drainage Source (problem acres 65,200 to 103,390) 

(drained acres 47,500 to 51,000) (historic drainage quality average* 1986-1994 64 ppb) acre-feet ppb Se lbs Se 

Mud and Salt Sloughs acre-feet ppb Se lbs Se 

San Joaquin River at Crows Landing (USEPA 5 ppb Se standard exceeded > 50% of the year in 1987, 1988, 1989, 1990, 1991 and 1994; drainage prohibition of 8,000 lbs/year enacted in 1996) MAF ppb Se lbs Se 

San Joaquin MAF 

1986 67,006 52 9,524 284,316 8.6 6,643 2.67 1.6 11,305 5.22 1987 74,902 54 10,959 233,843 12.0 7,641 0.66 4.9 8,857 1.81 1988 65,327 57 10,097 230,454 13.0 8,132 0.55 6.2 9,330 1.17 1989 54,186 59 8,718 211,393 14.1 8,099 0.44 6.3 7,473 1.06 1990 41,662 65 7,393 194,656 14.6 7,719 0.40 5.6 6,125 0.92 1991 29,290 74 5,858 102,162 14.0 3,899 0.29 4.5 3,548 0.66 1992 24,533 76 5,083 85,428 12.6 2,919 0.30 3.7 3,064 0.70 1993 41,197 79 8,856 167,955 15.0 6,871 0.89 3.5 8,379 1.70 1994 38,670 80 8,468 183,546 16.0 7,980 0.56 4.8 7,270 1.22 1995 57,574 76 11,875 263,769 14.9 10,694 3.50 1.6 14,291 6.30 1996 52,978 70 10,034 267,344 13 9,697 1.44 3.0 10,686 3.95 1997 37,483 62.5 7,097 not

available 

30 Mud only 

not available 

4.18 2.9 8,667-

9,054 

6.77 

1998 45,858 66.9* 9,118 not

available 

27 Mud only 

not available 

5.13 1.6 13,445-

15,501 

8.5 

Daily range 

0.4 to 286 (1986-1995) 15 to 134 (1997 and 1998) 

0.5 to 59 (1986-1995) 3 to 104 (1997 and 1998) 

956 to

73,458 acre-feet (1997-1998) 

0.4 to 17 (1986 –1995) 0.1-8.2 (1997 and 1998) 

DATA SOURCES: 1-Drainage Problem Area) California Central Valley Regional Water Quality Control Board, 1996b; c; 1998d; e; f; g; h; 200board in 1996 recompiled data from 1985 through 1995; therefore earlier versions of the regional board’s data may be quoted in some examples

Channel Project monthly reports (see website, http://www.mp.usbr.gov/; select projects, then select GBP) and annual reports (USBR et al., 1997
Table 6. Load scenarios using data from the SJV Drainage Program (1990a) and 50 ppb, 150 ppb, and 300 ppb 

assigned selenium concentrations. 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 our analysis, the distinction between problem water and subsurface drainage helps in 

assigning water-quality. The SJVDP defined scenarios of without future (i.e., no implementation of recommended 

plan) and with future (i.e., implementation of recommended plan). A third condition defined for use in our 

projections is called with targeted future which applies a factor of 0.20 acre-feet/acre/year of generated drainage, 

estimating the lowest, although probably not realistic, irrigation water return. The year 2000 projection for problem 

water is calculated here applying a factor of 0.4 acre-feet per acre per year; this projection was not part of the SJVDP 

consideration. 

Loading Scenario 

(five subareas 

Northern, Grassland, 

Westland, Tulare, 

and Kern)

Total problem 

acres or 

tile drained 

acres

Factor 

acre-feet/acre/year

Total 

problem 

or 

drainage 

acre-feet 

lbs Se 

(assigned 

50 ppb)

lbs Se 

(assigned 

150 ppb) 

lbs Se 

(assigned 

300 ppb)

1990 

Without Future

Subsurface drainage 

133,000 0.60-0.75 100,000 13,600 40,800 81,600 

1990 

With Future

Subsurface drainage 

133,000 0.40 53,200 7,235 21,706 43,411 

2000 

Without Future

Subsurface drainage 

269,000 Northern 0.75 

Tulare 0.65-0.70 

Others 0.50-0.55 

163,000 22,168 66,504 133,008 

2000 

With Future

Subsurface drainage 

360,000 0.40 144,000 19,584 58,752 117,504 

2000 

With Targeted Future

Subsurface drainage 

360,000 

(hypothesized 

from above case) 

0.20 

(hypothesized for 

minimum drainage) 

72,000 9,793 29,376 58,753 

2000 

Without Future

Problem Water 

444,000 0.70 

(range 0.60-0.75) 

314,000 42,704 128,112 256,224 

2000 

Apply 0.4 acrefeet/acre/year future 

factor

Problem Water

444,000 0.40 177,600 24,154 72,460 144,922 

2040 

Without Future

Subsurface drainage 

386,000 Northern 0.75 

All others 0.55 

(i.e., minimum 

improvement) 

223,000 

(243,000) 

30,328 90,984 181,968 

2040 

With Future

Subsurface drainage 

759,000 0.40 (hypothesized) 303,600 41,290 123,869 247,738 

2040 

Without Future

Problem Water 

951,000 0.75 

(steady increase) 

666,000 90,576 271,728 543,456 
TABLE 7. Our calculations of selenium concentrations in discharge from SJV Drainage Program subareas 

based on evidence presented by Westlands Water District or currently available ranges of measurements for 

drainage volume (acre-feet) and selenium load (i.e., measured values after the SJV Drainage Program database 

measurements in 1986-1989; see footnotes for source), except for Northern subarea where there was no 

recommended management plan by the SJV Drainage Program (1990a) (see footnote). Only one set of values 

for the Westlands Water District drainage volume and selenium load was presented in evidence (see minimum). 

Since no updated measurements are available for Westlands Water District, the condition for the maximum load 

was calculated using an assigned* concentration of 150 ppb to the volume of drainage presented in evidence. 

Subarea 

or area

Drainage 

 volume 

(acre-feet/ 

year) 

Minimum 

(lbs Se/ 

year) 

Calculated

minimum 

ppb Se

Maximum

(lbs Se/ 

year) 

Calculated

maximum 

ppb Se

Calculated 

maximum and 

minimum 

(lbs Se/acre-foot)

problem 

 acres 

Northern 26,000 350 5 700 10 0.014- 0.027 

Grassland 

Farmers 

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 (avg) 91 1.7 519 9.8 0.005- 0.027 

Kern 2,292 (avg) 1,089 175 1,586 254 0.475- 0.692 

Total 145,268 16,490 42,785 

Data Sources for subareas (also see Appendices A and B) 

Northern: a nominal 5 ppb and 10 ppb selenium concentrations; drainage volume is from SJVDP, 1990, Table 3 

for year 2000. 

Grassland: minimum is value measured for WY 1997 as part of the Grassland Bypass Channel Project and 

maximum is 17,250 lbs Se measured for the San Joaquin River at Vernalis for WY 1995 (CCVRWQCB, 1998). 

Westlands: minimum is for condition presented as evidence for Westlands Water District and maximum 

condition is the same volume of drainage, but with an assigned concentration of 150 ppb. 

Tulare and Kern: personal communication (Anthony Toto, CCVRWQCB, 1/98) of measurements for volume 

and selenium concentration for 1993 to1997 from which an average volume (1993-1997) was calculated and the 

minimum and maximum lbs Se were selected as the range. 
Table 8. Projections of selenium loads from the western San Joaquin Valley under different drainage scenarios. 

A kesterson (kst) is 17,400 lbs of Se, the cumulative load that caused visible ecological damage when released 

to a wetland (Kesterson National Wildlife Refuge, California). 

Scenario: Subarea or subareas 

discharging to a proposed San Luis Drain 

extension 

annual 

selenium load 

(lbs Se/year) 

kestersons/year 

(kst/year) 

cumulative 

kestersons (ksts in 

 5 years) 

Grassland

(based upon current data) 6,960 – 

 15,500 0.4 – 0.89 2.0 – 4.45 

Westlands (based upon 50 to 150 μg Se/L 

in drainage and 60,000 acre-feet) 8,000 – 

 24,500 0.46 – 1.41 2.3 – 7.05 

Grassland + Westlands (from above) 14,960 – 

 40,000 0.86 – 2.30 4.3 – 11.5 

Valleywide Drain (current conditions and 

Westlands projection) 16,490 – 

 42,785 0.95 – 2.46 4.75 – 12.3 

Vallywide 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 

TMDL or TMML management (Load 

targeted for environment, Grassland subarea) 1,394 – 

 6,547 0.08 – 0.38 0.4 – 1.9 
Table 9. Load of Se discharged if a constant concentration is maintained in the SJR and conveyed to the BayDelta under high (3 MAF per year) and low (1.1 MAF per year) flow regimes. Approximately 220,000 acrefeet/year represents the annual volume of flow from a proposed extension of the SLD at maximum capacity or a 

small SJR input to the Bay-Delta in a dry year. 

Selenium Concentration 

in the SJR or a SLD 

extension 

@ 3.0 (million acre-feet/ 

year) 

Load (lbs Se/year) 

@ 1.1 million acre-feet/ 

year ) 

Load (lbs Se/year) 

@ 216,810 acre-feet/year 

 (300cfs) 

Load (lbs Se/year) 

0.1 μg Se/L 816 299 60 

1.0 μg Se/L 8,160 2,990 598 

2.0 μg Se/L 16,320 5,980 1,197 

5.0 μg Se/L 40,800 14,960 2,992 

 50 μg Se/L -------- -------- 29,920 

 150 μg Se/L -------- -------- 89,760 

 300 μg Se/L -------- -------- 179,520 
Table 10. Annual and daily oil refinery Se loads for the Bay-Delta for the period 1986 to 1992 

and 1999. Cleanup of discharges and further permitting was required by 1998. 

Oil refinery 1986-1992 

lbs Se/year 

(range) 

1986-1992 

lbs Se/day 

(range) 

1999 

lbs Se/year 

1999 

lbs Se/day 

Equilon Enterprises LLC at 

Martinez (formerly Shell Oil) 1,203-2,595 3.3-7.1 440 1.2

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 Corporation 354-1,687 0.97-4.6 327 0.90

TOTAL 3,103-7,457 8.5-20.4 1,115 3.05

1986-1992 data: CSFRWQCB, 1992 and 1993 

1999 data: CSFRWQCB, personal communication, Johnson Lam, 9/19/00 
Table 11. Partitioning between dissolved Se and particulate or sediment Se in 

ecosystems for which reliable analytical data is available. 

Ecosystem TSediss

μg/L 

TSeSed

μg/g 

TSeSed/ 

Tsediss (Kd) 

Reference 

Kesterson 

Reservoir 

(terminal pond) 

14 55 4 X 103 Presser and Piper, 1998 

Belews Lake ~11 ~15 1.3 X 103 Lemly, 1985

Benton Lake

Pool 1 Channel 

4 10 2.5 X 103 Zhang and Moore, 1996 

Benton Lake

Pool 2 

10.4 3.5 0.34 X 103 Zhang and Moore, 1996 

Benton Lake

Pool 5 

0.74 0.35 0.5 X 103 Zhang and Moore, 1996 

Constructed 

Wetland 

<5 - 30 2.1 - 6.7 0.3 X 103 Hansen et al., 1998 

SLD (means) 62.5 55 0.9 X 103 This report

Delaware: Tidal 

Freshwater 

0.17 - 0.35 0.6 - 1.5 4 X 103 Reidel and Sanders, 1998 

Diatoms 1.1X105 Reinfelder and Fisher, 

1991 

Dinoflagellate 4.0 X 103 Reinfelder and Fisher, 

1991 

Great Marsh, 

Delaware 

0.01 - 0.06 0.3 - 0.7 3 X 103 – 

1 X 104

Velinsky & Cutter, 1991 

Bay-Delta SPM 

(suspended 

particulate 

matter) 

1986/1995/1996 

0.1 - 0.4 1 - 8 1 – 4 X 104 Cutter et al., in 

preparation 

Bay-Delta 

sediment 

0.1 - 0.3 0.2 - 0.5 1 - 5 X 103 Johns et al., 1988 
Table 12. Selenium concentrations in fish (μg/g dry weight) from the Bay-Delta (North Bay including Suisun, S

Honker Bays) and Humboldt Bay (Selenium Verification Study, White et al., 1987; 1988; 1989; Urquhart and ReLocation/Date flesh (μg Se/g, dry weight) liver (μg Se/g, dry weight) w

average std

dev. 

n average std

dev. 

n 

North Bay (January-June, 1986)white sturgeon 7.8 3.1 10 9.2 2.9 10English sole 3.0 0.2 4 starry flounder 4.6 1.0 7 9.2 2.2 7longfin smelt Pacific staghorn sculpin 2.5 0.2 8 6.7 1.0 8 Pacific herring speckled sanddab northern anchovy yellowfin goby 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 42yellowfin goby 2.0 NA 1 4.3 NA 1 Humboldt Bay (February and June, 1986) English sole 1.8 0.22 3 7.8 NA 1 starry flounder 0.9 1 3.6 1longfin smelt Pacific staghorn sculpin 1.6 0.13 4 3.9 0.46 3 Pacific herring 1.6 0.08 2 speckled sanddab n = number of samples; NA = not applicable 
TABLE 13. Examples of thresholds for Se effects (health, reproductive, teratogenesis, or survival) in fish 

based on concentrations of Se in food; the example of massive poisoning at Kesterson Reservoir, California 

also applies to aquatic birds. Selenium concentrations in the most abundant benthic prey (food) organism

in the Bay-Delta are given for comparison. 

Concentration 

in food 

(μg Se/g, dry 

weight)

Approach Response Observed Reference(s)

0.1 - 0.5 μg/g Lab Nutritionally sufficient range. Additional 

nutritional benefits often observed up to 1 μg/g. 

Diets containing < 0.1 μg/g often associated 

with deficiency syndrome. 

cited in Lemly, 1998a 

(Hodson and Hilton, 1983) 

3 - 8 μg/g Lab, field, 

and synthesis 

Reproductive impairment 

(similar threshold for birds, Skorupa and 

Ohlendorf, 1992; Skorupa, 1998b; see also 

Table 15). 

e.g., Engberg et al., 1998; 

Skorupa, 1998a; b; Lemly,

1998a; b; Hamilton et al., 

1996; 2000b 

2 - 5 μg/g Belews Lake, 

North 

Carolina 

(1996) 

Teratogenesis in fry of four recovering fish 

species 

Lemly, 1993b; 1997b 

5 μg/g Lab Winter stress syndrome (includes mortality) in 

juvenile bluegill 

Lemly, 1993b 

9 - 13 μg/g Lab, field, 

and synthesis 

Reduced growth and/or mortality in rainbow 

trout and bluegill 

Cited in Hamilton et al., 

2000a (Goettl and Davies, 

1978; Hilton et al., 1980; 

Cleveland et al., 1993); 

Skorupa, 1998b 

5 - 10 μg/g in 

prey (fish) 

18 μg/g in prey

(fish) 

Lab 

Freshwater 

Brackish 

water 

Growth and survival affected in chinook salmon 

(swim-up) larvae (SLD diet) 

Growth reduced of chinook salmon fingerlings 

(SLD diet) 

Hamilton et al., 1990 

30 - 35 μg/g Synthesis Complete reproductive failure in adult sensitive 

species (e.g., bluegill) 

Cited in Skorupa, 1998b 

(Coyle et al., 1993; Woock 

et al., 1987) 

20 - 80 μg/g Belews Lake, 

North 

Carolina 

(1973-1984) 

Massive poisoning of fish community: 16 of 20 

species disappear; two species rendered sterile, 

but persisted as aging adults; one occasionally

re-colonized as adults; and one unaffected. 

Deformities in survivors. Some recovery after 

Se removal. 

Cumbie and VanHorn, 

1978; Lemly, 1985; 1997b; 

1998a 

>100 μg/g Kesterson 

Reservoir, 

California 

Massive poisoning of fish and birds, including 

deformities in coots, grebes, ducks, and stilts. 

Saiki and Lowe, 1987; 

Ohlendorf, 1989; Presser 

and Ohlendorf, 1987. 

Se concentrations in the most abundant benthic prey organism in the Bay-Delta

4 - 20 μg/g Bay-Delta 

1985-1986 

1995-1996 

(Suisun 

Bay/San 

Pablo Bay) 

Range of Se concentrations in the 

predominant bivalve in the North Bay are 

sufficient to load eggs beyond teratogenic 

thresholds and approach the lower 

thresholds for systems where fish were 

eliminated by Se poisoning. 

Selenium Verification 

Study; Johns et al, 1988; 

Linville and Luoma, in 

press 
TABLE 14. Examples of thresholds for Se effects (health, reproductive, teratogenesis, or survival) in fish 

based on Se concentrations in tissues of fish. Selenium concentrations in tissue of white sturgeon from the 

Bay-Delta are given for comparison. 

Effect/Threshold Location 

Concentration in Tissue 

(μg Se/g, dry weight) Reference(s)

 Deformities/tissue Field • 

• 

• 

10 - 20 μg/g in whole homogenate; 

6 - 12 μg/g in muscle (fillets) 

20 - 40 μg/g in viscera. 

Lemly, 1998a 

Percent deformed larvae, 

fry, juveniles, or adults 

(e.g., centrarchids)/ 

whole-body 

Field • 

• 

• 

• 

• 

• 

5 - 10 μg/g whole-body = onset of deformities 

(<6%) in larvae, fry, juveniles, and adults. 

11 - 20 μg/g whole-body = <11% deformities in 

juveniles and adults

25 - 35 μg/g whole body = rapid rise in rate of 

deformities in larvae of some species (35-65%) 

40 - 50 μg/g - rapid rise in rate of deformities = 

20 - 30% in juveniles and adults. 

30 - 40 μg/g whole body = 80% deformities in 

larval fish

70 - 90 μg/g whole body = 70% deformities in 

juveniles and adults

Lemly, 1997a 

Growth and survival of 

salmon (larval; 

fingerling)/whole-body

Lab (SLD 

diet) and 

synthesis 

• 4 - 6 μg/g whole-body Hamilton et al., 

1990; also cited in 

2000a 

Survival of razorback 

sucker larval fish/wholebody

Field • 4 - 14 μg/g whole body Hamilton, et al., 1996 

Thresholds

• whole body • 

(sensitive species)

Synthesis 4 - 6 μg/g 

Skorupa, 1998b 

Thresholds

• 

• 

• 

• 

• 

• 

• 

• 

• 

• 

whole body, 

skeletal muscle, 

liver 

ovary and egg 

 larvae and fry

Synthesis 5 - 7 μg/g 

6 - 8 μg/g 

15 - 20 μg/g 

5 - 10 μg/g (6 - 17 μg/g, terata) 

 8 - 12 μg/g (5 - 12 μg/g, terata)

Lemly, 1998b 

Thresholds

• 

• 

• 

• 

whole body

ovary

Synthesis 6 (coldwater) - 9 (warmwater) μg Se/g 

 17 μg Se/g 

Deforest et al., 1999 

Thresholds

• whole body Synthesis • 4 - 12 Engberg et al., 1998 

Selenium concentrations in white sturgeon tissue (μg Se/g, dry weight) from the Bay-Delta

White sturgeon 

1989-1990 (Suisun, 

San Pablo, Grizzly, and 

Honker Bays) 

Field • 30 μg Se/g in liver (average, n=42) 

(range 6 – 80 μg/g) 

• 15 μg Se/g in flesh (average, n=62)

(range 2 - 50 μg/g)

Selenium 

Verification Study 

(Urquhart and 

Regalado, 1991) 

White sturgeon 

San Pablo Bay 

Field • ovaries 3 - 29 μg Se/g 

• plasma 5 - 9 μg Se/g 

• egg yolk components 3 - 90 μg Se/g 

Kroll and Doroshov, 

1991 
Table 15. Examples of thresholds for Se effects (health, reproductive, teratogenesis, or survival) in birds based upon 

Se concentrations in different tissues of birds. Thresholds based on diet are also included. Selenium concentrations in 

tissues of bird species from Kesterson Reservoir and the Bay-Delta are given for comparison. 

Selenium in tissue 

(μg/g, dry weight)

Embryo Deformity 

Threshold

Hatchability 

Threshold

Reference(s)

Egg 13 – 24 (mean egg) 

(field, western and northern 

plains, U.S.) 

Skorupa and Ohlendorf, 1991 

Egg 12 – 15 

(lab, mallard and chicken) 

Heinz, 1996

Egg 10

(Kesterson Reservoir, California) 

Skorupa and Ohlendorf, 1991; 

Skorupa, 1998a; b 

Egg 6 (mean)

(Salton Sea, California) 

Skorupa, 1998a; b 

Egg 4 – 10 

(Tulare Basin, California) 

Skorupa, 1998a; b 

Egg 

(taxa specific) 

duck, 15-20 

stilt, 18-25 

avocet, 38-60 

- 

6 – 7 

- 

Skorupa, 1998a; c; pers. comm.., 

2000 

Egg 

(impaired reproduction*) 

>6 to > 9* Engberg et al., 1998; Skorupa, 

1998a; b; Lemly, 1998b 

Liver 14 – 19 Heinz et al., 1989; Heinz, 1996 

Liver 23 – 32 (terata) Lemly, 1998b

 Liver** >30** Skorupa, 1998b 

Diet 4 - 8 Heinz et al., 1989; Heinz, 1996 

Diet 6 - 9 Ohlendorf, 1989 

Diet 3 - 8 Lemly, 1998b 

Se concentration range in bird (ducks, coots, grebes, stilts) tissue (μg Se/g, dry weight) 

 From Kesterson Reservoir, California (1983-1984)

Egg 2-180 Ohlendorf et al., 1986a; b; 

Skorupa, 1998a 

Liver 3-360 Presser and Ohlendorf, 1987 

Se concentration (average/range) in bird tissue (μg Se/g, dry weight) from the Bay-Delta (1986-1990)

Liver 

surf scoter

(Suisun Bay)

n = 71 

average = 145 

 (1986) 80/37-113 

 (1987) 84/13-167 

 (1988) 193/134-244 

 (1989) 240/137-368 

 (1990) 127/78-190 

 (White et al., 1987; 1988; 1989; 

Urquhart and Regalado, 1991) 

Liver 

surf scoter

 (San Pablo Bay) 

n = 62 

average = 123 

 (1986) 74/ 41-148 

 (1987) 113/65-196 

 (1988) 135/62-176 

 (1989) 162/81-217 

 (1990) 130/84-192 

Selenium Verification Study 

(1986 – 1990) 

(White et al., 1987; 1988; 1989; 

Urquhart and Regalado, 1991) 

Liver 

(greater and lesser scaup, 

Suisun Bay)

n = 39 

average =41 

 (1986) 14-86 

 (1987) 8-48 

(range only)

(1988) 85/35-114 

(White et al., 1987; 1988; 1989) 

Liver 

(scaup, San Pablo Bay) 

n = 31 

average = 32 

 (1986) 12-23 

 (1987) 11-47 

(range only)

(1988) 46/26-87

 (White et al., 1987; 1988; 1989) 

**Presented as reproductive impairment and juvenile and adult toxicity. Also at Ouray National Wildlife Refuge, Utah, a 

range of 40 to 50 μg Se/g in bird liver was associated with adult mortality (Skorupa, 1998b). Review of experimentally

induced selenosis in mallards proposed a diagnostic Se liver criterion of 66 μg Se/g (Albers et al., 1996). 
Table 16. Selenium loads employed in forecasts of Se impacts. Loads were calculated for a six-month 

season. Annual loads would be two times higher if Se discharge is continuous (i.e., at a constant rate). 

Agricultural inputs fall into three groups depending on management strategy: supply-driven management 

(3,000 to 8,000 lbs Se/year); demand-driven load with management of land and/or drainage quality (15,000 

to 45,000 lbs Se/year); and demand-driven load with minimum management (45,000 to 128,000 lbs Se/year). 

INPUTS TO BAY/DELTA 

(μg Se/L or parts per billion) 

(cfs cubic feet per second) 

(MAF million acre-feet) 

FLOW: Year/season 

WET YEAR/HIGH 

FLOW 

(lbs Se discharged in six 

months) 

FLOW: Year/season 

WET YEAR/LOW 

FLOW 

 (lbs Se discharged in 

six months) 

FLOW: Year/season 

CRITICALLY 

DRY/LOW FLOW 

(lbs Se discharged in 

six months) 

Agricultural Drainage 

via San Joaquin River

(targeted load) 

via SLD 50 μg/L, 150 cfs 

(0.05 MAF/season) 

via SLD 62.5 μg/L, 300 cfs 

(0.11 MAF/season) 

via SLD 150 μg/L, 300 cfs 

(0.11 MAF/season) 

via SLD 300 μg/L, 300 cfs 

(0.11 MAF/season) 

3,400-3,600 lbs/season 

6,800 

18,700 

44,880 

89,760 

3,400-3,600 lbs/season 

6,800 

18,700 

44,880 

89,760 

3,400-3,600 lbs/season 

6,800 

18,700 

44,880 

89,760 

SAN JOAQUIN RIVER

(maximum recycling) 

3-5 lbs/season 3-5 lbs/season 3-5 lbs/season 

Oil Refineries 680 lbs/season 680 lbs/season 680 lbs/season 

Sacramento River 141 lbs/season 250 lbs/season 1,850 lbs/season 
Table 17. Comparison of Se hazard in the Bay-Delta and other environments. Values are Se concentrations 

in μg Se/g dry wt. 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 BayDelta, bird egg concentrations are converted from bird liver. Data sources are Lemly, 1995; 1996a; b; 1997a; b; 

c for western U.S. sites and this report and *Kroll and Doroshov, 1991 for the Bay-Delta. 

Site Water; 

Hazard 

Sediment; 

Hazard 

Invertebrates;

Hazard 

Fish Eggs; 

Hazard 

Bird Eggs; 

Hazard 

Score; 

Hazard 

Ouray Refuge (Leota), 

Utah 

<1 - 3 

Low 

0.7 - 1.0 

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 - 3.0 

Low 

3 - 33 

High 

8 - 27 

High 

1 - 17 

Moderate 

21 

High 

Belews Lake, pre-1986, 

North Carolina 

5 - 20 

High 

4 - 12 

High 

15 - 57 

High 

40 - 159 

High 

20 

High 

Belews Lake, 1996

North Carolina 

<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 

3.0 - 15.8 

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 - 11.2 

High 

5.6 - 46.2 

High 

16 

High 

Ridges Basin Reservoir, 

Colorado and New 

Mexico 

1 - 10 

High 

1 - 8 

High 

5 - 75 

High 

5 -100 

High 

5 - 100 

High 

25 

High 

Southern Ute Reservoir, 

Colorado and 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 - Mod 

4 - 20 

High 

3 – 29*

High

Moderate - 

High 

17 

High 

Rating protocol Water Sediment Invertebrate Fish eggs Bird eggs Total 

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
Table 18. Calculation of a composite freshwater endmember concentration of Se (ug Se/L) from inputs of the Sacramento River (Sac R), 

the San Joaquin River (SJR), and oil refineries under conditions simulating those prior to refinery cleanup. Forecasts 

contrast wet and dry years; and high and low flow seasons. Load is expressed in lbs Se per six months. 

Volume Volume Concentration Load Load Contribution Volumes Concentration Concentration at

MAF billion L ug Se/L billion ug lbs Se Sum Sum FW Endmember Carquinez Strait

billion ug billion liters ug Se/L at 17.5 psu

ug Se/L

Prior to Refinery Cleanup Scenarios (No SLD extension)

Wet Year (1997 data), High Flow Season (six months, December through May)

Sac R. 17 20961 0.04 838 1,850

SJR 3 3699 1 3699 8,160

SLD 0 0 0

Refineries 0.005 6.165 150 925 2,040

5,462 24,666 0.22 0.11

Wet Year (1997 data), Low Flow Season (six months, June-November)

Sac R. 2.3 2835.9 0.04 113 250

SJR 0.1 123.3 1 123 272

SLD 0 0 0 0

Refineries 0.005 6.165 150 925 2,040

1,161 2,965 0.39 0.20

Critically Dry Year (1994 data), Low Flow Season (six months, June-November)

Sac R. 1.62 1997.46 0.04 80 176

SJR 0.1 123.3 1 123 272

SLD 0 0 0

Refineries 0.005 6.165 150 925 2,040

1,128 2,127 0.53 0.27
Table 19. Calculation of a composite freshwater (FW) endmember concentration of Se (ug Se/L) from inputs of the Sacramento River (Sac R.),

the San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and oil refineries under different load scenarios. Forecasts are 

for a wet year (1997) during the high flow season. Load is expressed in lbs Se per six months. Forecasts 1a through 1d use a SLD extension

and assume a 2 MAF SJR inflow reaches the Bay-Delta. The final forecast assumes no SLD extension and a SJR inflow of 1.1 MAF.

Volume Volume Concentration Load Load Contribution Volumes Concentration Concentration at

MAF billion L ug Se/L billion ug lbs Se Sum Sum FW Endmember Carquinez Strait

billion ug billion liters ug Se/L at 17.5 psu

1. Scenarios: Wet Year (1997 data), High Flow Season (six months, December - May), Refinery cleanup

a) SLD at 150 cfs, 50 ppb Se (6,800 lbs SLD load in six months). 

Sac R. 17 20961 0.04 838 1,850

SJR 2 2466 1 2466 5,440

SLD 0.05 61.65 50 3083 6,800

Refineries 0.005 6.165 50 308 680

6,695 23,495 0.28 0.14

b) SLD at 300 cfs and 62.5 ppb Se (18,700 lbs SLD load in six months). 

Sac R. 17 20961 0.04 838 1,850

SJR 2 2466 1 2466 5,440

SLD 0.11 135.63 62.5 8477 18,700

Refineries 0.005 6.165 50 308 680

12,090 23,569 0.51 0.26

c) SLD at 300 cfs and 150 ppb Se (44,880 lbs SLD load in six months). 

Sac R. 17 20961 0.04 838 1,850

SJR 2 2466 1 2466 5,440

SLD 0.11 135.63 150 20345 44,880

Refineries 0.005 6.165 50 308 680

23,957 23,569 1.02 0.51

d) SLD at 300 cfs and 300 ppb Se (89,760 lbs SLD load in six months). 

Sac R. 17 20961 0.04 838 1,850

SJR 2 2466 1 2466 5,440

SLD 0.11 135.63 300 40689 89,760

Refineries 0.005 6.165 50 308 680

44,302 23,569 1.88 0.94

Targeted SJR load of 7,180 lbs Se annually; 3,590 lbs Se in six months

Sac R. 17 20961 0.04 838 1,850

SJR 1.1 1356.3 1.2 1628 3,590

SLD 0 0 0 0 0

Refineries 0.005 6.165 50 308 680

2,774 22,323 0.12 0.06
Table 20. Calculation of a composite freshwater (FW) endmember concentration of Se (ug Se/L) from inputs of the Sacramento River (Sac R),

the San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and oil refineries under different load scenarios. Forecasts are

for a wet year (1997) during the low flow season. Se load is lbs Se per six months. Forecasts 2a through 2d use a SLD extension and

assume little SJR inflow reaches the Bay-Delta. The final forecast assumes no SLD extension and a 0.5 MAF SJR inflow.

Volume Volume Concentration Load Load Contribution Volumes Concentration Concentration at

MAF billion L ug Se/L billion ug lbs Se Sum Sum FW Endmember Carquinez Strait

billion ug billion liters ug Se/L at 17.5 psu

a) SLD at 150 cfs and 50 ppb Se (6,800 lbs SLD load in six months). 

Sac R. 2.3 2835.9 0.04 113 250

SJR 0.001 1.233 1 1 3

SLD 0.05 61.65 50 3083 6,800

Refineries 0.005 6.165 50 308 680

3,505 2,905 1.21 0.60

b) SLD at 300 cfs and 62.5 ppb Se (18,700 lbs SLD load in six months). 

Sac R. 2.3 2835.9 0.04 113 250

SJR 0.001 1.233 2 2 5

SLD 0.11 135.63 62.5 8477 18,700

Refineries 0.005 6.165 50 308 680

8,901 2,979 2.99 1.49

c) SLD at 300 cfs and 150 ppb Se (44,880 lbs SLD load in six months). 

Sac R. 2.3 2835.9 0.04 113 250

SJR 0.001 1.233 2 2 5

SLD 0.11 135.63 150 20345 44,880

Refineries 0.005 6.165 50 308 680

20,769 2,979 6.97 3.49

d) SLD at 300 cfs and 300 ppb Se (89,760 lbs SLD load in six months). 

Sac R. 2.3 2835.9 0.04 113 250

SJR 0.001 1.233 2 2 5

SLD 0.11 135.63 300 40689 89,760

Refineries 0.005 6.165 50 308 680

41,113 2,979 13.80 6.90

Targeted SJR load at 6,800 lbs Se annually; 3,400 lbs Se in six months; no SLD.

Sac R. 2.3 2835.9 0.04 113 250

SJR 0.5 616.5 2.5 1541 3,400

SLD 0 0 0 0 0

Refineries 0.005 6.165 50 308 680

1,963 3,459 0.57 0.28
Table 21. Calculation of a composite freshwater (FW) endmember concentration of Se (ug Se/L) from inputs of the Sacramento River (Sac R.),

San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and oil refineries under different load scenarios. Forecasts are 

for a critically dry year (1994) during the low flow season. Se load is lbs Se per six months. Forecasts 3a through 3d use a SLD extension

and assume little SJR inflow reaches the Bay-Delta. The final forecast assumes no SLD extension and a 0.5 MAF SJR inflow.

Volume Volume Concentration Load Load Contribution Volumes Concentration Concentration at

MAF billion L ug Se/L billion ug lbs Se Sum Sum FW Endmember Carquinez Strait

billion ug billion liters ug Se/L at 17.5 psu

3. Scenarios: Critically Dry Year (1994 data), Low Flow Season (June - November), Refinery cleanup

a) SLD at 150 cfs and 50 ppb Se (6,800 lbs SLD load in six months).

Sac R. 1.3 1602.9 0.04 64 141

SJR 0.0005 0.6165 2 1 3

SLD 0.05 61.65 50 3083 6,800

Refineries 0.005 6.165 50 308 680

3,456 1,671 2.07 1.03

b) SLD at 300 cfs and 62.5 ppb Se (18,700 lbs SLD load in six months). 

Sac R. 1.3 1602.9 0.04 64 141

SJR 0.0005 0.6165 2 1 3

SLD 0.11 135.63 62.5 8477 18,700

Refineries 0.005 6.165 50 308 680

8,850 1,745 5.07 2.54

c) SLD at 300 cfs and 150 ppb Se (44,880 lbs SLD load in six months). 

Sac R. 1.3 1602.9 0.04 64 141

SJR 0.001 1.233 2 2 5

SLD 0.11 135.63 150 20345 44,880

Refineries 0.005 6.165 50 308 680

20,719 1,746 11.87 5.93

d) SLD at 300 cfs and 300 ppb Se (89,760 lbs SLD load in six months).

Sac R. 1.3 1602.9 0.04 64 141

SJR 0.0005 0.6165 2 1 3

SLD 0.11 135.63 300 40689 89,760

Refineries 0.005 6.165 50 308 680

41,063 1,745 23.53 11.76

Targeted SJR load of 6,800 lbs Se annually; 3,400 lbs Se in six months.

Sac R. 1.3 1602.9 0.04 64 141

SJR 0.5 616.5 2.5 1541 3,400

SLD 0 0 0 0 0

Refineries 0.005 6.165 50 308 680

1,914 2,226 0.86 0.43
Table 22. Calculation of a composite freshwater endmember concentration of Se (ug Se/L) from inputs of the Sacramento River (Sac R), the San

Joaquin River (SJR), and oil refineries, under a restoration scenario. Se load is lbs Se per six months. Assume greater SJR inflows enter the Bay-Delta

to aid fish migration and the SJR input is held constant at 0.5 ppb Se. High flow season conveys 75% of SJR annual flow; low flow season, 25%. 

Volume Volume Concentration Load Load Contribution Volumes Concentration Concentration at

MAF billion L ug Se/L billion ug lbs Se Sum Sum FW Endmember Carquinez Strait

billion ug billion liters ug Se/L at 20 psu

ug Se/L

Restoration Scenarios (No SLD extension, refinery cleanup)

Wet Year (1997 data), High Flow Season, conveys 75% of SJR inflow (six months, December-May)

Sac R. 17 20961 0.04 838 1,850

SJR 2.25 2774.25 0.5 1387 3,060

SLD 0 0 0

Refineries 0.005 6.165 50 308 680

Total 19.255 23741.42 50.54 2534 5,590 2,534 23,741 0.11 0.05

Wet Year (1997 data), Low Flow Season, conveys 25% of SJR inflow (six months, June-November)

Sac R. 2.3 2835.9 0.04 113 250

SJR 0.75 924.75 0.5 462 1,020

SLD 0 0 0 0

Refineries 0.005 6.165 50 308 680

Total 3.055 3766.815 50.54 884 1,950 884 3,767 0.23 0.12

Dry Year (1994 data), High Flow Season, conveys 75% of SJR inflow (six months, December-May)

Sac R. 5 6165 0.04 247 544

SJR 0.82 1011.06 0.5 506 1,115

SLD 0 0 0

Refineries 0.005 6.165 50 308 680

Total 5.825 7182.225 50.54 1060 2,339 1,060 7,182 0.15 0.07

Dry Year (1994 data), Low Flow Season, conveys 25% of SJR inflow (six months, June-November)

Sac R. 1.6 1972.8 0.04 79 174

SJR 0.28 345.24 0.5 173 381

SLD 0 0 0

Refineries 0.005 6.165 50 308 680

Total 1.885 2324.205 50.54 560 1235 560 2,324 0.24 0.12
Table 23. Summary of forecasts of Se concentrations in a composite freshwater endmember entering the BayDelta under different conditions. Load is expressed in lbs per six months. SLD loads are for the SLD only; 

targeted load and “restoration” scenario is for the SJR only. CF is a composite concentration in all sources of 

freshwater at the head of the estuary (i.e. near the discharge point of a proposed SLD extension); CE is a 

composite concentration at 17.5 practical-salinity units (psu), usually near Carquinez Strait during the low flow 

season. 

Forecast 

Year/Season 

Prior to 

refinery

cleanup 

SLD: Half 

capacity, 

50 μg/L 

SLD: Full 

capacity, 

62.5 μg/L 

SLD: Full 

capacity, 

150 μg/L 

SLD: Full 

capacity, 

300 μg/L 

Targeted 

Load 

SJR 

“Restoration” 

in SJR 

0.5 μg Se/L 

Wet/High

 Load 

(lbs/6 mo) 

6,800 18,700 44,880 89,760 3,590 3,060

 Conc.F 

 (μg/L)

0.22 0.28 0.51 1.02 1.88 0.12 0.11

 Conc.E 

 (μg/L)

0.11 0.14 0.26 0.51 0.94 0.06 0.05

Wet/Low

 Load (lbs/6 

mo) 

6,800 18,700 44,880 89,760 3,400 1,020

 Conc.F 

 (μg/L) 

0.39 1.21 2.99 6.97 13.8 0.57 0.23

 Conc.E 

 (μg/L)

0.20 0.60 1.49 3.49 6.9 0.28 0.12

Dry/Low

 Load 

(lbs/6 mo) 

6,800 18,700 44,880 89,760 3,400 381

 Conc.F 

 (μg/L)

0.53 2.07 5.07 11.9 23.5 0.86 0.24

 Conc.E 

 (μg/L)

0.27 1.03 2.54 5.93 11.8 0.43 0.12

Criteria 2 to 5 μg Se/L 
Table 24. Summary of forecasts of Se concentrations in particulate material under different conditions. Load 

is expressed in lbs Se/six months. SLD scenario loads are for the SLD only; the targeted load and “restoration” 

scenario are for the SJR only. C1 is the concentration forecast at a Kd of 104

, typical of suspended sediment; C2 

is the concentration forecast at a Kd of 3X103

, typical of shallow-water bed sediment; C3 is the low reactivity 

concentration forecast at a Kd of 103. All concentrations are those at the head of the estuary (near the release 

point of a proposed SLD extension). 

Forecast 

Year/Season 

Prior to 

refinery 

cleanup 

SLD: Half 

capacity, 

50 μg Se/L 

SLD: Full 

capacity, 

62.5 μg 

Se/L 

SLD: Full 

capacity, 

150 μg Se/L

SLD: Full 

capacity, 

300 μg Se/L

Targeted 

Load 

SJR 

“Restoration”

in SJR 

0.5 μg Se/L 

Wet/High

 Load 

(lbs/6 months) 6,800 18,700 44,880 89,760 3,500 3,060

 C1

 (μg Se/g) 2.2 2.8 5.1 10.2 18.8 1.2 1.1

 C2

 (μg Se/g) 0.66 0.84 1.53 3.06 5.6 0.36 0.33

 C3 

 (μg Se/g) 0.22 0.28 0.51 1.02 1.88 0.12 0.11

Wet/Low

 Load 

(lbs/6 months) 6,800 18,700 44,880 89,760 3,400 1,020

 C1

 (μg Se/g) 3.9 12.1 29.9 69.7 138 5.7 2.3

 C2

 (μg Se/g) 1.2 3.63 8.97 20.9 41.4 1.71 0.69

 C3 

 (μg Se/g) 0.39 1.21 2.99 6.97 13.8 0.57 0.23

Dry/Low

 Load 

(lbs/6 months) 6,800 18,700 44,880 89,760 3,400 381

 C1

 (μg Se/g) 5.3 20.7 50.7 118.7 235 8.6 2.4

 C2

 (μg Se/g) 1.6 6.21 15.2 35.6 70.6 2.58 0.72

 C3 

 (μg Se/g) 0.53 2.07 5.07 11.9 23.5 0.86 0.24

Guidelines 1.5 to 4 μg Se/g 
Table 25. Forecast of particulate Se concentrations at the head of the Bay-Delta estuary: 

• in years with different climate regimes; 

• in different seasons; and 

• for alternative speciation and biogeochemical behavior patterns. 

The scenarios considered are: 

• a SLD extension discharge of 18,700 lbs per six months (full capacity, 62.5 μg Se/L); and 

• a SJR discharge of a targeted load of 3,590 lbs per six months for a wet year (1.2 μg Se/L) and 3,400 lbs per 

six months for a dry year (2.5 μg Se/L). 

Forecasts are compared to conditions prior to refinery cleanup. 

Forecast Composite 

Freshwater 

Endmember Se 

(μg/L) 

Particulate Se (μg/g) 

low reactivity 

Kd: 103

 (C3) 

Particulate Se (μg/g) 

shallow sediment 

Kd: 3 X 103 (C2) 

Particulate Se (μg/g) 

biotransformed 

suspended matter 

Kd: 104 (C1) 

SLD 

Wet Year 

High Flow

Season 

0.46 0.5 1.5 5.1 

Wet Year 

Low Flow

Season 

3.0 3.0 9.0 30.0 

Critically 

Dry Year

Low Flow

Season 

5.1 5.1 15.2 50.7 

SJR (targeted load) 

Wet Year

High Flow

Season 

0.12 0.12 0.36 1.2 

Wet Year 

Low Flow

Season 

0.57 0.57 1.71 5.7 

Critically 

Dry Year

Low Flow

Season 

0.86 0.86 2.58 8.6 

Prior to refinery cleanup 

Wet Year 

High Flow

Season 

0.22 0.22 0.66 2.2 

Wet Year 

Low Flow

Season 

0.39 0.39 1.2 3.9 

Critically 

Dry Year

Low Flow

Season 

0.53 0.53 1.6 5.3 

Criteria 2 – 5 1.5 – 4.0 1.5 – 4.0 1.5 – 4.0 
Table 26. Laboratory-derived physiological constants for Se bioaccumulation by several species of 

bivalve and composite values for a generic bivalve (data from Luoma et al., 1992; Reinfelder et al., 

1997). 

Species Feeding rate

(grams 

food/grams 

tissue/day) 

Assimilation 

Efficiency 

(AE %)

Rate Constant 

of Loss 

ke (d-1) 

AE/ ke

Oyster 70 ± 6

Clam 

(Macoma balthica) 80 ±7 0.03 ± 0.001 24.6

Clam 

(Mercenaria mercenaria) 92 ± 2 0.01 ± 0.004 92.0

Mussel 

(Mytilus edulis) 74 ± 8 0.02 ± 0.007 37.0

Generic bivalve 

(from diatom) 0.2 79 0.02 39

Sorbed Se 0.2 40 0.02 20

Elemental Se 0.2 23 0.02 10 
Table 27. Selenium concentrations in a generic bivalve when exposed to different concentrations of particulate 

organo-Se or particulate elemental Se (constants from Luoma et al., 1992 and Reinfelder et al., 1997). 

Exposure to 

different 

concentrations 

of: 

Particulate 

Concentration 

(μg Se/g) 

Absorption 

Efficiency 

(speciation) 

Rate 

Constant of 

Loss 

(d-1) 

Tissue 

Concentration at 

Steady State 

(μg Se/g) 

Reference 

 particulate 

 organo-Se

Luoma et al., 

1992; Reinfelder 

et al., 1997 

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

particulate

elemental Se

Luoma et al., 

1992; Reinfelder 

et al., 1997 

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

Particulate concentrations of Se range from 0.3 to 3 μg Se/g dw in brackish Bay-Delta and 0.3 to 8 μg Se/g dw 

at the head of the estuary (Cutter, 1989 and Cutter et al., in preparation). 
Table 28. Summary of forecasts of Se concentrations in a generic bivalve under different conditions. Load is 

expressed in lbs per six months. SLD scenario loads are for the SLD only. The targeted load and “restoration” 

scenario are for the SJR only. C1 is the concentration forecast at a Kd of 104

, typical of suspended sediment; C2 

is the concentration forecast at a Kd of 3 X 103

, typical of shallow-water bed sediment; C3 is the low reactivity 

concentration forecast at a Kd of 103

. Four assimilation efficiencies have been assumed for each Kd: AE4 = 0.8; 

AE3 = 0.63; AE2 = 0.55; and AE1 = 0.35. All concentrations are those at the head of the estuary (near the 

release point of a proposed SLD extension) 

Forecast 

Year/Season 

Prior to refinery 

cleanup 

SLD: Half 

capacity, 

50 μg/L 

SLD: Full 

capacity, 

62.5 μg/L 

SLD: Full 

capacity, 

150 μg/L 

Targeted 

Load in 

SJR 

Particulate

bivalve 

Particulate

bivalve 

Particulate

bivalve 

Particulate

bivalve 

Particulate

bivalve 

Wet/High

 Load 

(lbs/6months) 6,800 18,700 44,880 3,500

 C1-AE4

 (μg/g) 

2.2

22 

2.8

19

5.1

34

10

68

1.2

8.0

 C1-AE3

 (μg/g) 

2.2

17 

2.8

15

5.1

27

10

54

1.2

6.3

 C2-AE2

 (μg/g)

0.66

4.5 

0.84

3.9

1.5

7.0 

3.1

14

0.36

1.7

 C3-AE1 

 (μg/g) 

0.22

0.96 

0.28

0.8

0.5

1.5

1.0

3.0

0.12

0.4

Wet/Low

 Load 

(lbs/6 months) 6,800 18,700 44,880 3,500

 C1-AE4

 (μg/g) 

3.9

39 

12

81

30

199

70

465

5.7

38

 C1-AE3

 (μg/g) 

3.9

31 

12

64

30

157

70

366

5.7

30

 C2-AE2

 (μg/g)

1.2

8.0 

3.6

17

9.0

41

21

96

1.7

7.8

 C3-AE1 

 (μg/g) 

0.39

1.7 

1.2

3.5

3.0

8.7

7.0

20

0.57

1.7

Dry/Low

 Load 

(lbs/6 months) 6,800 18,700 44,880 3,500

 C1-AE4 

 (μg/g) 

5.3

53 

21

138

51

338

119

793

8.6

57

 C1-AE3

 (μg/g) 

5.3

42 

21

109

51

266

119

625

8.6

45

 C2-AE2

 (μg/g)

1.6

11 

6.2

28

15

70

36

163

2.6

12

 C3-AE1 

 (μg/g) 

0.53

2.3 

2.1

6.1

5.1

15

12

35

0.9

2.5

Guidelines 1.5 - 4.0/ 10 - 40 μg Se/g 
Table 29. Forecast of Se concentrations bioaccumulated by a generic bivalve at the head of the Bay-Delta 

estuary: 

• in years with different climate regimes; 

• in different seasons; and 

• for alternative speciation and biogeochemical behavior patterns. 

The scenarios considered are: 

• a SLD extension discharge of 18,700 lbs per six months (full capacity, 62.5 μg Se/L); and 

• a SJR discharge of a targeted load of 3,590 lbs per six months for a wet year (1.2 μg Se/L) and 3,400 lbs per 

six months for a dry year (2.5 μg Se/L). 

Forecasts are compared to conditions prior to refinery cleanup. 

Forecast Composite 

Freshwater 

Endmember 

Se (μg/L) 

Low reactivity: 

Kd: 103

 

(C3/AE1) 

Particulate Se

[Bioaccum. Se] 

(μg/g) 

Shallow sediment: 

Kd: 3 X 103 

(C2/AE2) 

Particulate Se

[Bioaccum. Se] 

(μg/g) 

Suspended matter: 

Kd: 104 

(C1/AE3)

Particulate Se

[Bioaccum. Se] 

(μg/g) 

SLD

Wet Year 

High Flow

Season 

0.5 0.5

1.5 

1.5

7 

5.1

27 

Wet year 

Low Flow Season 3.0 3.09 

9.0

41 

30

157 

Critically Dry 

Year

Low Flow Season 

5.1 5.1

15 

15.2

70 

51

266 

SJR (targeted load) 

Wet Year 

High Flow

Season 

0.12 0.12

0.4 

0.36

1.7 

1.2

6.3 

Wet year 

Low Flow Season 0.57 0.571.7 

1.7

7.8 

5.7

30 

Critically Dry 

Year

Low Flow Season 

0.86 0.86

2.5 

2.6

12 

8.6

45 

Prior to refinery cleanup 

Wet Year 

High Flow

Season 

0.22 0.22

0.96 

0.66

4.5 

2.2

17 

Wet year 

Low Flow Season 0.39 0.391.7 

1.2

8.0 

3.9

31 

Critically Dry 

Year

Low Flow Season 

0.53 0.53

2.3 

1.6

11 

5.3

42 

Criteria (water 

and particulate

 food) 

2 – 5 1.5-4.0

10-40 

1.5-4.0

10 - 40 

1.5-4.0

10 – 40 
Table 30. Regression equations for bivalves vs. bivalve predators. Data from Selenium Verification

Studies (White, et al., 1987; 1988;1989; Urquart and Regalado, 1991).

Scoter Regression Output: Scoter

North Bay Constant -10.98 North Bay

Bivalves Avg. ppm Se Std Err of Y Est 9.07 Bivalves Avg. ppm Se Regression Output:

avg. ppm Se Flesh R Squared 0.77 avg. ppm Se Liver Constant -41.57

4.8 12.5 No. of Observations 8 4.8 92.8 Std Err of Y Est 51.07

2.77 12.5 Degrees of Freedom 6 2.77 92.8 R Squared 0.74

2.2 4.0 2.2 15.5 No. of Observations 8

5.13 21.3 X Coefficient(s) 7.12 5.13 137.0 Degrees of Freedom 6

2.01 3.0 Std Err of Coef. 1.57 2.01 12.5

5.73 37.8 5.73 228.0 X Coefficient(s) 36.06

6.87 51.8 6.87 263.8 Std Err of Coef. 8.83

7.90 35.8 7.90 174.3

Scaup

North Bay Regression Output: Scaup

Bivalves Avg. ppm Se Constant -2.80 North Bay Regression Output:

avg. ppm Se Flesh Std Err of Y Est 5.19 Bivalves Avg. ppm Se Constant -8.14

4.8 7.1 R Squared 0.59 avg. ppm Se Liver Std Err of Y Est 13.19

2.77 7.1 No. of Observations 6 4.8 25.8 R Squared 0.64

2.2 3.9 Degrees of Freedom 4 2.77 25.8 No. of Observations 6

5.13 12.0 2.2 9.7 Degrees of Freedom 4

2.01 6.57 X Coefficient(s) 3.42 5.13 29.1

5.73 23.93 Std Err of Coef. 1.42 2.01 13.57 X Coefficient(s) 9.63

5.73 65.12 Std Err of Coef. 3.61

WHITE STURGEON WHITE STURGEON Regression Output:

North Bay Regression Output: North Bay Constant -7.15

Bivalves Avg. ppm Se Constant 1.04 Bivalves Avg. ppm Se Std Err of Y Est 9.49

avg. ppm Se Flesh Std Err of Y Est 2.38 avg. ppm SeLiver R Squared 0.62

4.8 7.81 R Squared 0.66 4.8 9.20 No. of Observations 4

2.77 7.81 No. of Observations 6 2.77 9.20 Degrees of Freedom 2

5.13 9.84 Degrees of Freedom 4 6.87 14.19

5.73 7.47 7.90 35.50 X Coefficient(s) 4.33

6.87 12.38 X Coefficient(s) 1.68 Std Err of Coef. 2.41

7.90 16.81 Std Err of Coef. 0.60

 '88, '89 & '90 scoter data matched to Replaced Corbicula from 1990

Potamocorbula, (replace Corbicula) with Potamocorbula

Scoter Regression Output: WHITE STURGEON Regression Output:

Bivalves Avg. ppm Se Constant Bivalves Avg. ppm Se Constant -3.50

avg. ppm Se Liver Std Err of Y Est avg. ppm Se Liver Std Err of Y Est 4.63

4.80 92.8 R Squared 4.80 9.20 R Squared 0.91

2.77 92.8 No. of Observations 2.77 9.20 No. of Observations 4.00

2.20 15.5 Degrees of Freedom 6.87 14.19 Degrees of Freedom 2.00

5.13 137.0 11.63 35.5

2.01 12.5 X Coefficient(s) 19.28 R Squared 0.91 X Coefficient(s) 3.15

11.63 228.0 Std Err of Coef. 3.21 Std Err of Coef. 0.70

11.63 263.8

11.63 174.3

R Squared 0.86
Table 31. Data employed in regression of Se concentrations in bivalves vs. Se concentrations in bivalve predators.

Means from diiferent years are aggregated; North Bay is Suisun Bay and San Pablo Bay. Both flesh and liver are

shown for predators. Bivalves are from different species (Corbicula fluminea*; Mya arenaria**; Macoma balthica***;

and Potamocorbula amurensis****) and different studies ( White et al., 1987*; 1988*; 1989*; Urquhart and Regalado,

1991*, Johns et al., 1988*; Luoma and Linville, 1997****; Linville and Luoma, in press****). Selenium as ppm is 

equivalent to micrograms Se per gram. All values are for dry weight.

Scoter Scaup WHITE STURGEON 

North Bay North Bay North Bay

Bivalves Avg. ppm Se Avg. ppm Se Avg. ppm Se

Date avg. ppm Se Flesh Liver Flesh Liver Flesh Liver

1986 4.8* 12.5 92.8 7.1 25.8 7.81 9.20

1986-Humboldt 2.2** 4.0 15.5 3.9 9.7

1987 5.13* 21.3 137.0 12.0 29.1 9.84

1988-Humboldt 2.0*** 3.0 12.5 6.57 13.57

1988 5.73* 37.8 228.0 23.93 65.12 7.47

1989 6.9* 51.8 263.8 12.38 14.19

1990 7.9* 35.8 174.3 16.81 35.50

 1995-1996 11.6**** 35.8 174.3 16.81 35.50
Table 32. Forecasts of Se concentrations in bivalves and resulting Se concentrations in livers of surf 

scoter, greater and lesser scaup, and white sturgeon under two Se discharge conditions: 1) the SLD 

scenario is for 18,700 lbs per six months (37,400 lbs per year) and 2) the SJR scenario is for a 

targeted load of 3,500 lbs per six months (7,000 lbs per year) (SJR conditions defined earlier). All 

forecasts are for six months of discharge during the low flow season of a critically dry year. 

Forecast concentrations are compared to average Se concentrations in these organisms (Corbicula 

fluminea, 1988-1990; Potamocorbula amurensis, 1995-1996; surf scoter, greater and lesser scaup, 

and white sturgeon, 1989-1990) in the Bay-Delta and to thresholds for adverse effects described 

earlier. Forecasts for predators were predicted by extrapolation from regressions between bivalve 

and predator concentrations using data from 1986 to 1990 (Tables 30 and 31). 

Load

Scenario

Load in 

six months

(lbs Se) 

Bioaccumulation 

by bivalves 

(μg Se/g dry wt) 

Selenium Concentration in Liver

(μg Se/g dw)

 Scoter Scaup Sturgeon 

SLD 

1. Low 

Reactivity 

(C3/AE1)

2. Shallow 

Sediment 

(C2/AE2)

3. Suspended 

Sediment 

(C1/AE3)

18,700 

18,700 

18,700 

15 

70 

266 

248 

1293 

5017 

136 

664 

2546 

45 

221 

848 

SJR 

Target Load 

1. Low 

Reactivity 

(C3/AE1)

2. Shallow 

Sediment 

(C2/AE2)

3. Suspended 

Sediment 

(C1/AE3)

3,500 

3,500 

3,500 

2.5 

11.8 

45 

10 

187 

818 

16 

105 

424 

5 

35 

141 

Average 

Concentration

1988-1990 

1995-1996 

(μg Se/g dw)

Corbicula

fluminea = 8 

Potamocorbula 

amurensis =12 

164 64 30 

Threshold for 

Effects 

(μg Se/g dw) 

10 - 40 20 - 50 20 - 50 20 - 50 
Table 33. Relation of Se loads, composite freshwater endmember Se concentrations, particulate Se 

concentrations, Se bioaccumulation by bivalves, Se bioaccumulation by two predators (sturgeon and scaup) 

and Se guidelines or concentrations at which effects are expected. Forecasts are for: 

• discharges from a SLD extension or the SJR; 

• 

• 

concentrations in the North Bay near the site of input (i.e., head of estuary) with instantaneous mixing; 

and 

the low flow season of a dry year. 

Conditions prior to refinery cleanup are given for comparison.

Forecast

Dry year/ 

low flow

season 

(lbs Se/six 

months) 

Composite 

freshwater 

endmember 

(μg Se/L) 

Particulate 

(μg Se/g dw) 

Kd = 3 X 103 

(C2) 

Bioaccumlation, 

generic bivalve 

(μg Se/g dw) 

AE2 (0.55) 

White 

Sturgeon 

Liver 

(μg Se/g dw)

Greater and 

Lesser 

Scaup 

Liver 

(μg Se/g dw)

SLD 

6,800 2.1 6.2 28 87 261

18,700 5.1 15 70 221 664

44,880 12 36 163 519 1557

SJR (targeted load) 

3,500 0.86 2.6 11.8 35 105

Prior to refinery cleanup 

0.53 1.6 11 30 65

Guidelines 1-5 1.5 – 4.0 10 - 40 20 – 50 20 – 50 
APPENDIX A 

San Joaquin Valley Historic Planning and Geologic Inventory 

 
APPENDIX A 

San Joaquin Valley Historic Planning and Geologic Inventory 

CONTENTS

Envisioned Discharges and Salt Loads 3 

Planning................................................................................................................................................3 

Specific Estimates ................................................................................................................................5 

Current Management............................................................................................................................7 

Geologic Inventory and Reservoir of Selenium in the San Joaquin Valley 8 

Selenium Geologic Inventory and Mass Balance.................................................................................8 

Prediction of Long-Term Selenium Reservoirs....................................................................................9 

Estimates Based on Alluvial Fill—Soils Scenario 9

Estimate Based on Panoche Creek Runoff—Runoff Scenario 10 

Characteristics and Timing of Selenium’s Release as Drainage: Source Waters ..............................12 

Mobility of Selenium: Source Flow, Concentration, and Load .........................................................12 

Control and Timing ............................................................................................................................13 

FIGURES 

A1. Map of San Luis Unit of the Central Valley Project (USBR, 1981). 

A2. Schematic of Ultimate Waterflow Conditions of the San Luis Unit (USBR, 1978). 

A3. Envisioned salt discharges and drainage volume from the San Luis Unit to the San Luis 

Drain during the period 1995 to 2095 (USBR, 1983). 

A4. Conceptual water budget for the western San Joaquin Valley (USBR, 1989; adapted from 

CH2M HILL, 1988). 

A5. Surface water salt inflow/outflow (railroad cars per day) from the western San Joaquin Valley 

(printed with permission, SJV Drainage Implementation Program, 1998). 

A6. Schematic of selenium sources of the Coast Ranges and the reservoir of selenium within the 

western San Joaquin Valley. If the discharge from the valley is assumed to be approximately 

42,500 lbs per year, loading to the Bay-Delta would take place, at a minimum, for 63 to 304 years 

at the lower range of projections. Data compiled from Presser et al., 1990; Presser and Piper, 

1998; and this report. 

A7. Schematic of relation of rate of selenium oxidation and oxygen flux. 

A8. Schematic of relation of selenium load and water flux. 

A9. Selenium load (lbs) for Drainage Problem Area (DPA)/ Grassland Bypass Project Area, Crows 

Landing, and Vernalis for WY 1986 through WY 1998a and 1998b. Lower bar represents 6600 

lbs. selenium. Upper bar represents 8,000 lbs selenium. 

 1 Appendix A 
A10. CIMIS (California Irrigation Management Information System) station #124 (Panoche, Fresno 

County) precipitation for WY 1986 through 1998 (CDWR, 1986-1998). Base average for 1986 

to 1994 is 7.13 inches. 

A11. Monthly selenium load targets (lbs) for SLD discharge to Mud Slough for WY 1997 and 1998. 

TABLES 

A1. Historical (SJVDP, 1975; USBR, 1977 and 1978) Prediction of Drainage from San Luis Unit 

(San Luis Service Area and the Delta-Mendota Service Area). The defined ultimate or maximum

condition is drainage of 300,000 acres. 

A2. Forecast selenium reservoir in San Joaquin Valley based on soils of the Panoche Fan. 

A3. Forecasts of Se generated during storms of WY 1998 for Panoche Creek. Storm 

 runoff for WY 1998 was measured for Panoche Creek at highway I-5 by USGS (USGS, 

 1999; Kratzer et al., in press). Historic data for Se loads for Panoche Creek have not been 

 previously available. Sampling was done during the storms of WY 1998 on a limited basis 

 (Kratzer et al., in press). Extrapolations have been made here using the integrated area under the 

hydrograph for WY 1998. Loads measured for WY 1998 may represent maximum infrequent 

loading via Panoche Creek rather that being representative of annual historic loading (see text for 

more details). The forecast Se loads for WY 1998 form the basis of one of the forecasts of the Se 

reservoir in the western San Joaquin Valley (see Table A4, one large magnitude storm per 10, 50 

or 100 years). Flow data with asterisks are approximated from gage height measurements 

making load values generated from these flows also approximate. Loads for WY 1997 are given 

for comparison. Storm runoff from Panoche Creek for WY 1997 was measured at the San Luis 

Drain inflow by Grassland Area Farmers (USBR et al., 1998). 

A4. Forecast selenium reservoir in San Joaquin Valley based on storm runoff from Panoche Creek 

(see Table 3A for data used for extrapolation).

2
APPENDIX A 

San Joaquin Valley Historic Planning and Geologic Inventory 

Envisioned Discharges and Salt Loads 

Planning

Agricultural development has continued in the western SJV despite salinized soils. Lands were 

classified in the San Luis Unit (SLU) (Figure A1) starting in 1954 as to their suitability for crop 

productivity and management cost (USBR, 1978; Ogden, 1988). The SLU includes agricultural lands 

that total over 700,000 acres in the Westlands, Panoche, Broadview, Pacheco, and San Luis Water 

Districts of the Grassland and Westlands subareas (USBR, 1981). Limiting factors were soil, 

topography, and drainage. Lands were considered flawed because of the presence of alkali (i.e., salt), 

hardpan (i.e., impeded drainage), and roughness (i.e., uneven land surface). The irrigation service area 

that required drainage continued to increase. By 1962, 12% of the SLU was comprised of Class 4 

lands (i.e., lands known to have a reduced payment capacity for irrigation/drainage improvements 

based on agricultural return). These were mainly in areas directly affected by erosion from the Coast 

Ranges to the west (USBR, 1978). A larger segment of Class 3 lands (i.e., lands known to require 

difficult and costly management) were identified adjacent to the valley trough. Through time, 

agriculture has expanded increasingly into Class 4 lands. This expansion into Class 4 lands was 

controversial since these lands were considered to require the most capital for drainage removal and 

have the least ability to pay for drainage improvements. Recent plans again include further expansion 

of the place of use for CVP water supplies by WWD (CH2MHILL, 1997). 

Historic estimates of drainage needs (i.e., estimates of envisioned rates of flow or volume of 

drainage in acre-feet to lower the water table) provide an interesting context for modern estimates. 

Although the amounts of drainage for conveyance out of the SJV have increased since planning began 

in 1955, the design capacity of the main component of a drainage facility has remained relatively 

unchanged through time [i.e., 300 cubic feet per second (cfs)]. However, estimates vary for the rate of 

flow for the north and south ends of the drain (100 cfs in the south and 450 cfs in the north). Given 

below are examples of the many sets of values for drainage volume and drained acreage that exist 

throughout the planning history for a drain, but our review is by no means exhaustive. For example, 

references are mainly documentation by or for federal agencies and joint federal and state efforts (e.g., 

 3 Appendix A 
Hydroscience, 1977; USBR, 1978; SJV Interagency Drainage Program, 1979a; CH2M Hill, 1985; SJV 

Drainage Program, 1990a; USBR, 1992; SJV Drainage Implementation Program, 1998). A parallel set 

of reports that document early state planning efforts are not as extensively cited (e.g., CDWR, 1965a; 

b; 1969; 1974; 1978; CSWRCB, 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 the high water 

table (SJV Interagency Drainage Program, 1979a; SJV Drainage Program, 1990a). Evaluations of 

alternative geographic disposal areas showing engineering and net revenue disposal benefit of different 

drainage conveyances (e.g., USBR, 1955; 1962; CDWR, 1965a; SJV Interagency Drainage Program, 

1979b; Brown and Caldwell, 1986), mainly address management aspects, not source loads estimates. 

Comparison of the amount of volume discharged per subareas is useful as a measure of hydrologic 

balance and hence, the volume of drainage expected. For example, 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 lands 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 Se. Achieving 

hydrologic balance also would not achieve salt balance. Salts would continue to accumulate in the 

soils and aquifers of the SJV. 

Besides estimates of flow and volume, historical documentation gave estimates of water quality 

(i.e., milligrams per liter total dissolved solids or specific conductance) on which to base annual 

discharge of salt (i.e., tons salt/year). Selenium analyses on which to base loads of Se were not 

available until the mid-1980’s (Presser and Ohlendorf, 1987). The amounts of salt projected for 

discharge from the SJV, as a whole, help identify the magnitude of the salt build-up. Difference in the 

amounts of salt discharged per subarea help identify differences due to geology and hydrology in the 

affected areas. The affect of salinity on receiving waters is not considered here, only the magnitude of 

source salinity loads. Both the levels of salt and nitrate (7,604 tons of nitrate [NO3 + NO2 (N)] during 

the worst case year of 2020) were considered problematic in historical water-quality studies of the SLD 

(USBR, 1978; SJV Interagency Drainage Program, 1979a; b). Salt would aggravate problems of 

salinity intrusion into the Delta thereby interfering with beneficial uses of Delta waters and nitrates 

4
would disturb the balance of nutrient levels in the estuarine system thereby causing eutrophication and 

high turbidity levels. Limited data on toxicity and concentrations of other constituents of concern (e.g., 

nitrate, phosphate, pesticides, dissolved oxygen, boron, arsenic, heavy metals) present in agricultural 

drainage are listed in historical reports (CDWR, 1965a; SJV Interagency Drainage Program, 1979a; b; 

Brown and Caldwell, 1986; USBR, 1984b through h), but are not included here. 

 

Specific Estimates

 Both the SJV Interagency Drainage Program in 1975 and the USBR in 1977 and prepared estimates 

of discharge for the SLU (USBR, 1978). The 1970’s planners envisioned an agricultural drainage 

canal with a design capacity of 300 cfs and a length of 197 miles. Estimates of the quantity of the SLU 

drainage discharge were calculated through the year 2080 (i.e., approximately 100 years into the 

future) and of quality through the year 2030 (Table A1). Maximum quantities of drainage were not 

anticipated for “at least another 100 years” in the original plan. But revised estimates showed the 

“ultimate” (i.e., maximum) quantity of drainage would be available by 2030 (Table A1). A hydrologic 

schematic of the Ultimate Waterflow Conditions developed for the SLU shows a drain discharge of 

144,200 acre-feet/year from 300,000 acres underlain by subsurface drainage pipes (Figure 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. As “equilibrium conditions” were approached between soil and water, concentrations of 

dissolved minerals in the drainage water were expected to decrease”. The model also predicted salt 

concentration (mg/L total dissolved solids, TDS) would decrease by 50% after 40 years of drainage. 

The prediction was for the annual discharge of salt from the SLU would increase from 43,710 tons 

salt/year at the start of drainage provision to a maximum of 1.5 million tons salt/year after 40 years of 

discharge, as the volume of drainage water discharged increased (USBR, 1978). 

 In 1979, a final report was prepared by the SJV Interagency Drainage Program recommending 

completion of a valley-wide drain (i.e., encompassing five areas, North, Delta-Mendota, San Luis, 

Tulare Lake, and Kern County) which would discharge into the Bay-Delta at Chipps Island. The report 

also included a first stage environmental impact report (SJV Interagency Drainage Program, 1979a, b). 

Estimates of expected annual quantities of drainage ranged from 57,000 acre-feet in 1985 to 668,000 

acre-feet in 2085 when acres drained were expected to reach over one million acres. Estimated tons of 

salt requiring disposal ranged from 3.1 million to 3.9 million tons of salt/year for a valley-wide drain. 

 5 Appendix A 
 In 1983, the USBR estimated drainage quantity and quality (i.e., concentration of salt, seven major 

elements, and twelve minor elements, but Se data was absent) for expected discharge to the SLD from

the SLU during the period 1995 to 2095 (USBR, 1983) (Figure A3). Water-quality projections were 

based on concentration averages in the SLD for the period September 1982 to January 1983 (USBR, 

1983), before the discovery of deformities at Kesterson NWR. Estimates of drainage volume ranged 

from 84,525 acre-feet in 1995 to 274,270 acre-feet in 2095 for the combined discharge from the San 

Luis Service Area (equivalent to WWD; 48,885 to 192,105 acre-feet) and the Delta-Mendota Service 

Area (encompassing Grassland subarea and other northern water districts; 35,660 to 82,158 acre-feet). 

A steady rise in discharge was predicted from 1995 to approximately year 2035 when the rate of 

increase slows but continues rising through the projected year 2095 (Figure A3). The worst-case 

scenario was to occur in year 2020 when 1.8 million tons of salt/year was to be discharged in 201,025 

acre-feet of drainage. 

 In 1988, salt and water inflows and outflows to the SJV were conceptualized (CH2MHILL, 1988) 

(Figure A4). Calculations specific to the 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 (e.g., evapotranspiration), sources (e.g., canal imports), or reservoirs 

(e.g., confined aquifer). The annual salt accumulation determined for the semi-confined aquifer in 

1988 for all five subareas was 3.3 million tons of salt/year. The annual accumulation per subarea 

ranged from 1,000 tons salt/year to 1.5 million tons/year, due to differing hydrology, geology, and 

drainage options (see later discussion). An analysis for the Westlands subarea showed 44% of the salt 

was from dissolution of salts internal to the SJV, 49% imported from outside sources including 

irrigation water and 7% 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 Se because of its location on the Panoche 

alluvial fan (Presser et al., 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 show high proportions of imported salt to 

internal salt and relatively low salt accumulations because of the availability of the SJR for salt 

discharge. A 1989 analysis for the SJV Drainage Program estimated that salt is accumulating at a rate 

of approximately 100,000 tons salt/year in the Grassland subarea (SJV Drainage Program, 1989). On a 

recent detailed basis, calculations for the lower SJR basin, that includes the Grassland subarea and 

6
recycling to and from the SJR, show a doubling of salt within the basin every five years despite 

drainage to the SJR (net gain of 207,000 tons salt/year of a mean salt inflow of 917,000 tons/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 (SJV Drainage Implementation 

Program, 1998) (Figure A5; one railroad car is equivalent to 100 tons salt). The total annual imported 

salt was 1.5 million tons/year. This value does not include the calculated 620,000 tons salt/year 

discharged out of the valley through the SJR (SJV Drainage Implementation Program, 1998). No data 

were given for internal salt or the status of subarea salt reservoirs. 

 The input of 1.5 million tons salt/year calculated as part of the 1997-re-evaluation, is the value 

quoted in 1978 by the San Luis Task Force that reviewed the management, organization, and operation 

of the SLU to determine the extent to which the SLU conforms to the purpose and intent of Public Law 

86-488. The task force noted that planning documents had 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). 

Current Management

 The current implemented agricultural wastewater management plans for the five SJV Drainage 

Program subareas are: 

• The Northern (26,000 drained acres) and Grassland (51,000 drained acres) subareas discharge 

agricultural drainage to the SJR. A state permit has been in place since 1998 to regulate drainage 

from the Grassland subarea to the SJR through use of a portion of the SLD as a conveyance facility 

(CCVRWQCB, 1998a). The SLD has been renamed the Grassland Bypass Channel for this project 

for re-use of a 28-mile section of the drain. 

• Westlands subarea (5,000 drained acres, relieving 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 (SJV Drainage 

Program, 1989) although it has temporal storage, displacement, and distribution components to it. 

 7 Appendix A 
Degradation of groundwater aquifers is expected to occur. Ground water with dissolved solids of 

greater than 2,500 mg/L is considered un-usable for irrigation (SJV 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 (CSWRCB, 1996a). State permits have regulated evaporation pond 

discharges since 1993 with various areas of mitigation wetlands required (CCVRWQCB, 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 (SJV Drainage 

Implementation Program, 1999d) showed the number of individual basins and pond operators 

decreasing by approximately 60%, but the surface area of ponds decreasing only from 6,715 to 

4,895 acres, 

Geologic Inventory and Reservoir of Selenium in the San Joaquin Valley 

Selenium Geologic Inventory and Mass Balance

 Salt (and by inference, Se) enriched sediment has been accumulating on the alluvial fans of the SJV 

for 1.0 to 1.2 million years, originating from Coast Range sources of marine sedimentary rocks (Bull, 

1964; Deverel and Gallanthine, 1989; Gilliom et al., 1989; Andrei Sarna-Wojcicki, U.S. Geological 

Survey, Menlo Park, CA, personal communication, 7/23/98). Figure A6 visually illustrates some of 

the characteristics of the geologic sources of Se in the Coast Ranges, the SJV irrigation and drainage 

system, and potential Se reservoirs (i.e., Se inventory components). A summary of Se concentration 

and load data that are the basis of the conceptual model of Se sources, transport, and mobility is given 

in Figure A6. 

 The SJV has a net negative annual water budget (evaporation exceeds precipitation). Prior to 

development of the water management system, a permanent shallow groundwater table only occurred 

in groundwater discharge zones near the SJV 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. 

8
 An estimate of the time necessary to discharge the accumulated Se from the aquifers and alluvial 

fans of the SJV can provide some perspective on the size of the geologic and hydrologic reservoirs of 

Se. Estimates of the geologic and hydrologic reservoirs of Se within the alluvial fans and in the valley 

also provide perspective on the amount of Se potentially available for discharge via a drainage 

conveyance. Such estimates are necessary to understand the minimum bounds on how much Se would 

be discharged over the course of time should an out-of-valley conveyance system be built. 

Prediction of Long-Term Selenium Reservoirs

 Recent data collection in the area of the Panoche Creek alluvial fan has enabled a preliminary 

calculation of the reservoir of Se within the alluvial fans of the SJV; that is, the Se potentially available 

for discharge via a drainage conveyance over the long-term. To determine the time necessary to 

discharge the accumulated Se from the alluvial fans of the SJV, two methodologies for estimating the 

reservoirs are given: 

1) based on known concentrations of Se in soils of the western SJV (especially the Panoche Fan or 

“problem acreage”) and neglecting the amount of Se in the groundwater reservoir; 

2) based on suspended and dissolved Se loads brought down in runoff from the Coast Ranges in the 

area of the Panoche Creek alluvial fan.

Estimates Based on Alluvial Fill—Soils Scenario 

 General surveys of Se concentrations in soils across the western United States show an average of 

0.34 micrograms Se per gram or parts per million (ppm). Across the conterminous United States the 

average is 0.26 ppm (Shacklette and Boerngen, 1984). Surveys of Se concentrations in soils of the 

western SJV were conducted in 1982 and 1985 (Tidball et al., 1986; 1989). The interfan area below 

Monocline Ridge and between Panoche Creek in the north and Cantua Creek in the south showed the 

highest Se concentrations (maximum ungridded value 4.5 ppm). The geometric mean for the Panoche 

Creek alluvial fan is 0.68 ppm Se (1985, 721 sites, 1.6 kilometer interval, 66-72 inch depth). Tidball et 

al. (1986; 1989) also found a geometric mean of 0.14 ppm for the SJV western slope (1983, 297 sites, 

10 kilometer intervals, 0-12 inch depth). 

The Se concentration in soils was extrapolated to estimate the amount of Se in the soil reservoir of 

the Panoche Creek alluvial fan. An average concentration of 0.68 ppm Se was employed along with 

several estimates of affected acreage, soil densities, and soil depths. Selenium deposition under the 

 9 Appendix A 
various conditions ranges from 2.7 to 356 million pounds (lbs) Se (Table A2). If a removal rate of 

42,785 lbs Se/year is hypothesized (see later discussion, Appendix B), it would take 63 to 8,321 years 

to discharge the soil reservoir of Se in the Panoche Creek alluvial fan (Table A2) (Figure A6). This 

estimate does not factor in the loading that would occur over the course of that time due to further 

weathering and runoff from the Coast Ranges, nor the amount of Se in the groundwater reservoir. 

 

Estimate Based on Panoche Creek Runoff—Runoff Scenario 

 No complete sets of data (i.e., flow, Se concentration in water and sediment, and amounts of 

sediment) exist for Panoche Creek prior to 1997. Reconnaissance in 1987 to 1988 (Presser et al., 1990) 

showed dissolved Se concentrations of 44 to 57 μg/L in runoff samples. Suspended sediment Se 

concentrations were relatively low (1.2 to 2.9 ppm Se), but the volume of sediment relatively high 

(10% or 91,500 mg/L). Estimation of runoff transported in the SLD in water year (WY) 1995 (a water 

year begins on October 1st), when extreme flooding in the Coast Ranges caused the drain to be used to 

collect runoff, showed a Se load of 1,750 lbs Se eventually discharged to the SJR (CCVRWQCB, 

1996a; b; Presser and Piper, 1998). This amount represents 22% of the annual 8000-lb Se prohibition 

for discharge to the SJR enacted by the state in 1996. The runoff load for the one major storm of WY

1997 was estimated at 137 lbs Se based on monitoring downstream channels (USBR et al., 1998; Table 

B8). This amount represents 1.9% of the annual load discharged to the SJR in WY 1997. In 1998, 487 

lbs was estimated transported by Coast Ranges runoff, representing 5% of the total load discharged 

though the Grassland Bypass Channel Project (USBR et al., 1999). These latter data represent 

approximations of anecdotal events and only should be used to assess the order-of-magnitude for 

runoff loads during an extremely wet year in WY 1995 (total precipitation greater than 11.5 inches) 

and a short duration series of storms (total precipitation of 0.6 inches) in WY 1997. 

10

 The rate of sediment and Se loading has been under study at Panoche Creek only since September 

1997 (U.S. Geological Survey, 1999; Kratzer et al., in press). The recently installed gaging station 

provides flow data and hydrographs for WY 1998 storms. Storms of WY 1998 were the result of an El 

Nino 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 Se loads (U.S. Geological Survey, 1999; Kratzer et al., in 

press). The flow data are integrated with these Se concentration data to forecast dissolved and total Se 

loads, with suspended Se loads calculated by difference (Table A3). The forecast Se load measured in 
runoff discharged from Panoche Creek for two storms was 5,995 lbs Se (Table A3). Estimation of two 

intervening storms shows a total of 2,050 lbs. The total of the these forecast runoff loads of Se for WY

1998 is 8,045 lbs, with 16% of the load as the dissolved fraction and 84% as the suspended fraction. 

Although the concentration of Se in suspended sediment is relatively low (1-2 ppm Se) (Presser et al., 

1990; T. Presser, unpublished data), the large volume of material leads to a high load in the particulate 

material as compared to the dissolved load. Calculations cannot be made at this time to estimate the 

load of Se discharged from the watershed to receiving waters to compare to input loads because of the 

lack of adequate downstream monitoring stations. So influx and efflux cannot be directly compared. 

However, 8,045 lbs Se/year source influx measured in the extremely wet year of 1998 is comparable to 

the state limitation on discharge from the SJV via the SJR, that is, an efflux of 8,000 lbs Se/year 

(CCVRWQCB, 1996c). In general though, under average rainfall amounts, the annual load from these 

natural sources is calculated to be a small percentage of the Se load potentially discharged from the 

SJV (USBR et al., 1999). Only when source loads from the Coast Ranges are considered in sum (see 

below) or during a year in which a large magnitude storm occurs, are the influx amounts significant 

compared to efflux amounts currently regulated. 

 The Se discharge data for Panoche Creek for WY 1998 were extrapolated to give estimates of the 

amount of Se 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 one 

large magnitude storm in 10 years, one large magnitude storm in 50 years, or one large magnitude 

storm in 100 years. Table A4 shows amounts of total Se, dissolved Se, and suspended Se deposited 

under those conditions. The range of dissolved Se deposition over 0.5 million years is 13 to 86 million 

lbs Se and over the course of 1.1 million years, 28 to 188 million lbs Se. The range of suspended Se 

deposition over the course of 0.5 million years is 67 to 449 million lbs Se and over the course of 1.1 

million years, 147 to 989 million lbs Se. The range of total Se deposition over the course of 0.5 

million years is 80 to 535 million lbs Se and over the course of 1.1 million years, 175 to 1,177 million 

lbs Se. If the removal rate is hypothesized as 42,785 lbs Se/year (0.043 M lbs Se/year) (see later 

discussion, Appendix B), then it would take 1,870 to 27,510 years to discharge the reservoir of Se in 

the Panoche Fan based on total Se deposition from runoff (Table 4) (Figure A6). Ranges based on 

dissolved Se deposition from runoff are 304 to 4,394 years and based on suspended Se deposition from

runoff are 1,566 to 23,116 years. These estimates do not factor in the loading that would occur over 

 11 Appendix A 
the course of that time due to further weathering and runoff from the Coast Ranges. The estimate does 

attempt to include Se in the groundwater reservoir. 

Characteristics and Timing of Selenium’s Release as Drainage: Source Waters 

Mobility of Selenium: Source Flow, Concentration, and Load

 The behavior and speciation of Se, and hence its solubility and mobility, are determined by a 

combination of processes including inorganic (e.g., weathering of the Coast Ranges) and organic (e.g., 

oxidation by bacteria) reactions. Oxidative reactions are partly responsible for Se mobility from source 

geologic formations of the Coast Ranges and the adjacent derived alluvial fans of the SJV (Figure A7)

(Presser et al., 1990; Gilliom et al., 1989; Presser, 1994b). Selenium is oxidized to selenate, a form

readily soluble in water and hence 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 Se remains in its highest oxidation state (i.e., +6, 

SeO4

=

) (Figure A7). Source agricultural drainage waters are selenate-dominated, a fact of major 

significance in determining the mobility of Se in surface water and groundwater systems and, hence, 

the extent and impact of Se in drainage water discharges (e.g., subsurface drainage) from those 

systems. 

 The effect of the large reservoir of Se on recent subsurface drainage flow (i.e., potentially 

discharged source waters) is illustrated in Figure A8. Figure A8 is generalized from data collected 

(USBR et al., 1999) during frequent sampling of drainage source water (i.e., current agricultural 

discharges to the SJR in WY 1997 and 1998 from the Grassland subarea). Flow or discharge increases 

with increased water flux (i.e., applied irrigation or precipitation). The concentration of Se in the 

discharged source agricultural wastewater increases as water flux increases. Only at elevated water 

fluxes seen during extremely wet years (i.e., the maximum rainfall occurring in a February over a 50-

year record) does a dilution effect occur, lowering the concentration. The higher concentrations of Se 

discharged under high flow conditions are an indication of the magnitude of the Se 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 (Figure A8). The combined 

effect of increasing concentration and increasing flow as water flux increases assures an increase in Se 

load discharged as more irrigation water is applied or more precipitation falls. 

12
Control and Timing 

 The highest annual loads from agricultural drainage in the SJV (Figures A9) are discharged in years 

of normal or above average precipitation (CCVRWQCB, 1996b; c; 1998d; e; f; g; h; 2000b; c; CDWR, 

1986-1998) (Figure A10) (also see later discussion). Regulatory load targets also are highest during 

February, March, April, and May, reflecting agricultural practices (Figure A11) (USBR, 1995; 

CCVRWQCB, 1996c; 1998a). It is possible that dilution afforded during wetter years by the increased 

volume of water in rivers could decrease salt and Se concentrations at compliance points in the SJR, or 

especially in the Bay-Delta, seaward from the inflows of the Sacramento River. The extent of dilution 

depends upon clean water inputs relative to SJR loads. Se and salt concentrations do not necessarily 

decrease in wet years in agricultural drainage water itself, or in agricultural drainage canals where 

discharge is predominantly Se-laden water. 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 SJR). The effect could be larger loads 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 SLD was planned and throughout many of the later planning reports (e.g., 

SJV Interagency Drainage Program, 1979a; b). Recently, the SWRCB 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 SJV is crucial to meeting 

the Bay-Delta water-quality standards including salinity (CSWRCB, 1997). Further documentation in 

the DEIR of future drainage systems conceptualizes the temporary control of drainage discharges 

stored in the soil profile using a system of valves, weirs, and sumps. A similar management technique 

using “DOSIR” valves is in practice in the Grassland subarea to enable storage of subsurface drainage 

[Grassland Area Farmers (GAF), 1997; USBR et al., 1999]. Grassland area farmers in discussions with 

regulators have pointed out the effect of this type of storage technique by calculating the amount of Se 

they have not discharged to the SJR on an annual basis (e.g., WY 1997, 3,680 lbs Se not discharged 

compared to 7,097 lbs Se discharged) (USBR et al., 1999). These types of drainage management 

activities emphasizes the importance of the consideration of the reservoir of Se and of documenting the 

Se inventory as opposed to focusing on short-term averages of discharges representing annual leaching 

to sustain a year-to-year farming effort. 

 13 Appendix A 


0

50000

100000

150000

200000

250000

300000

Drainage (acre-feet)

0

0.5

1

1.5

2

Salt (million tons)

1995 2015 2025 2045 2065 2085

Year

SALT DMC-SA SLU-SA DMC+SLU

Envisioned Drainage

Figure A3. Envisioned salt discharges and drainage volume from the San Luis Unit to the San Luis Drain

during the period 1995 to 2095 (USBR, 1983).

Figure A5. Surface water salt inflow/outflow (railroad cars per day) from the western

San Joaquin Valley (printed with permission, SJV Drainage Implementatin Program, 1998).
Panoche Alluvial Fan 0.68 ppm(max. 4.5 ppm)

TulareFormation

Kreyenhagen 

Formation 11 

ppm 

(maximum, 45 

ppm)

Moreno Formation 9.1 

ppm 

(max 35 

ppm) (surficial 

samples)

Kreyenhagen Formation

Moreno Formation 12 ppm (maximum, 34 ppm) (core samples)

Tulare Formation 1.4 

ppm 

(maximum,, 2.6 

ppm)

Panoche

Formation 1.0 

ppm

San Joaquin River

San Francisco Bay/Delta

COAST RANGES

Panoche Formation

SIERRA NEVADA

N

RUNOFF

1-2 ppm

2-60 ppb

aggradation

erosion

Load limit: 6,600 lbs Se

Prohibition: 8,000 lbs Se

USEPA criterion for the 

protection of aquatic life: 

5 ppb Se

sumps 140-4,200 ppb 43-105 ppb

DRAINS

Load 0.5 million years, 1 storm/100 years

Discharge 42,785 lbs Se/year 304 - 4,394 years

Load 7 feet soil /160,000-444,000 acres

Discharge 42,785lbs Se/year 63 - 180 years

SAN JOAQUIN VALLEY 

RESERVOIR (water, soil, biota)

San Joaquin 

River Outlet

330-430 ppb

3 - 11 million lbs Se

13 - 188 million lbs Se

wells 96-7,300 ppb

Seeps

<2 – 3,500 ppb

Figure A6. Schematic of selenium sources of the Coast ranges and the reservoir of selenium within the western San Joaquin Valley

If the discharge rate from the valley is assumed at approximately 42,500 lbs per year, then loading to the Bay-Delta could take place for

63 to 304 years, at the lower range of reservoir projections (see Tables A2 and A4). Data compiled from Presser et al., 1990; Presser

and Piper, 1998; and this report. 

Scenarios:
Selenium Concentration

Water Flux

Load

Concentration

fall summer El Nino

Figure A8. Schematic of selenium load and selenium concentration as a 

function of water flux.

Selenium Load

Rate of Selenium Oxidation

Oxygen Flux

Asymptote

a

b

Figure A7. Schematic of selenium oxidation rate as a function of oxygen flux.
Figure A9. Selenium load (lbs) for Drainage Problem Area (DPA)/ Grassland Bypass Project 

Area, Crows Landing, and Vernalis for WY 1986 through WY 1998a and 1998b. Lower bar 

represents 6,600 lbs selenium. Upper bar represents 8,000 lbs selenium

Figure A10. CIMIS (California Irrigation Management Information System) station # 124 

 precipitation for WY 1986 through 1998. Base average for 1986 to 1994 is 7.13 inches.

0 

5000 

10000 

15000 

20000 

Selenium (lbs)

86 87 88 89 90 91 92 93 94 95 96 97 98a 98b

Water Year

DPA/GBP Crows Landing Vernalis

Selenium @ DPA/GBP, Crows Landing

and Vernalis

0 

2 

4 

6 

8 

10 

12 

14 

16 

18 

Precipitation (inches)

86 87 88 89 90 91 92 93 94 95 96 97 98

WATER YEAR

BASE AVG. 86-94 (7.13")

CIMIS Precipitation 1986-1998
0

200

400

600

800

1000

1200

Selenium, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

 348 lbs 348 lbs

 389 lbs

 533 lbs

 866 lbs

 1066 lbs

 799 lbs

 666 lbs

 599 lbs 599 lbs

 533 lbs

 350 lbs

LOAD TARGETS

SLD discharge to Mud Slough

WY 1997 and 1998 Load Targets

YEAR TOTAL = 6,660 lbs Se

MONTHLY TOTAL = 7,096 lbs Se

Figure A11. Monthly selenium load targets (lbs) for SLD discharge to Mud Slough for WY 1997

and 1998.
Table A1 Historical (USBR, 1978) prediction of drainage from San Luis Unit (San Luis Service 

Area and the Delta-Mendota Service Area). The ultimate or maximum condition is drainage of 300,000 acres. 

SJV Interagency Drainage Program 1975 estimated acre-feet/year

USBR 1977 estimated acre-feet/year 

USBR modeled* tons salt/year 

1980 20,000 3,100 43,7101985 - 8,700 159,2101990 47,000 19,000 317,3002000 64,000 33,100 521,4002010 71,000 107,400 1,385,4602020 78,000 152,300 1,538,230 2030 88,000 154,100 1,094,1102040 98,0002050 107,0002060 114,0002070 122,0002080 129,000Ultimate 150,000* Model predictions verified by sampling and analyses of drainage waters (USBR, 1978) 
TABLE A2 Forecast selenium reservoir in San Joaquin Valley based on soils of the Panoche Fan. 

Panoche Creek Alluvial Fan Soils Scenario 

Acreage Depth

Meters* 

Density grams/ cm2* 

Soil Se** (ppm) 

Reservoir Million lbs Se (M lbs Se) 

ksts (17,400 lbs Se = 1 kst) 

Assumed removal rate 42,785 lbs Se/year*(*see Table 5 or generalized 314,000 AF@50 ppb) 

YeloaBa

Problem acreage (SJVDP, 1990a) 

444,000 2

(6.6 feet) 

2.0 0.68 10.8 621 42,785 lbs/year 

(0.043 M lbs/year) 

25

444,000 2 1.46 0.68 7.7 442 42,785 lbs/year 

(0.043 M lbs/year) 

18

444,000 15

(50 feet) 

1.46 0.68 59 3,391 42,785 lbs/year 

(0.043 M lbs/year) 

1,3

444,000 91

(300 feet) 

1.46 0.68 356 20,460 42,785 lbs/year 

(0.043 M lbs/year) 

8,3

Panoche Fan Acreage* 

160,000 2 1.46 0.68 2.7 155 42,785 lbs/year 

(0.043 M lbs/year) 

63 

160,000 15 1.46 0.68 20.3 11,667 42,785 lbs/year 

(0.043 M lbs/year) 

47

160,000 91 1.46 0.68 123 7,069 42,785 lbs/year 

(0.043 M lbs/year) 

2,8

*Bull, 1964 ** Tidball et al., 1986; 1989 
TABLE A3. Forecasts of Se generated during storms of WY 1998 for Panoche Creek. Storm runoff for WY 1998 

was measured for Panoche Creek at highway I-5 by USGS (USGS, 1999; Kratzer et al., in press). Historic data for 

Se loads for Panoche Creek have not been previously available. Sampling was done during the storms of WY 1998 

on a limited basis (Kratzer et al., in press). Extrapolations have been made here using the integrated area under the 

hydrograph for WY 1998. Loads measured for WY 1998 may represent maximum infrequent loading via Panoche 

Creek rather that being representative of annual historic loading (see text for more details). The forecast Se loads for 

WY 1998 form the basis of one of the forecasts of the Se reservoir in the western San Joaquin Valley (see Table A4, 

one large magnitude storm per 10, 50 or 100 years). Flow data with asterisks are approximated from gage height 

measurements making load values generated from these flows also approximate. Loads for WY 1997 are given for 

comparison. Storm runoff from Panoche Creek for WY 1997 was measured at the San Luis Drain inflow by 

Grassland Area Farmers (USBR et al., 1998). 

Storm hours cfs 

(cubic 

 feet 

per sec) 

start 

cfs 

(cubic 

 feet 

per sec) 

maximum

cfs 

(cubic 

 feet 

per sec)

end 

Dissolved Se 

lbs 

Suspended Se 

lbs 

Total Se 

lbs 

WY 1998 

February 3-4, 1998 34.8 310 8,000 750 640 3,850 4,490 

February 6-7, 1998 28 1,800 2,800 200 179 699 878 

February 8, 1998 6,500* 1,800 

February 19-20, 1998 1,600* 250 

February 21-22, 1998 28.5 2 1,400 220 76 236 312 

February 23-24, 1998 21.8 510 2,100 180 67 248 315 

SUBTOTAL WY 1998 

(measured storms) 

962 (16%) 5,033 (84%) 5,995 

TOTAL WY 1998 

(all storms) 

8,045 

WY 1997 

February 25, 1997 137 

TOTAL WY 1997 137 
TABLE A4 Forecast selenium reservoir in San Joaquin Valley based on storm runoff from Panoche Creek (see Table 3A for data used f

Panoche Creek Alluvial Fan Deposition  and Recharge Scenario 

million lbs Se TOTAL  (dissolved plus suspended) 

million lbs Se DISSOLVED (dissolved16% of total) 

million lbs Se SUSPENDED (suspended84% of total) 

ksts (17,400 lbs Se = 1 kst) (range) 

Assumed Removal Rate M lbs Se/ year (see Table 5, 42,785lbs/year) 

0.5 million years 1 large magnitude storm year/10 years TOTAL 345-535 55-86 290-449 3,161-30,747 0.043 0.5 million years 1 large magnitude storm year/50 years TOTAL 140-387 22-62 118-325 1,264-22,241 0.043 0.5 million years 1 large magnitude storm year/100 years TOTAL 80-188 13-30 67-158 747-10,804 0.043 1.1 million years 1 large magnitude storm year/10 years TOTAL 759-1,177 121-188 638-989 6,954-67,644 0.043 1.1 million years 1 large magnitude storm year/50 years TOTAL 240-499 38-80 201-420 2,184-28,678 0.043 1.1 million years 1 large magnitude storm year/100 years TOTAL 175-415 28-66 147-348 1,609-23,850 0.043 
APPENDIX B 

San Joaquin Valley Agricultural Drainage Projections 

 
APPENDIX B 

San Joaquin Valley Agricultural Drainage Projections 

CONTENTS 

Projected Loadings from Historic Data and Evidentiary Testimony 4 

Westlands Water District and Subarea.......................................................................................4 

Projections from Historic Data .........................................................................................................4 

Projections from Evidentiary Testimony ..........................................................................................5

Grassland Subarea (WY 1986-1996) ...................................................................................................6 

Projections from Historic Data .........................................................................................................6 

Grassland Bypass Channel Project (Reuse of the San Luis Drain, WY 1997 to present) ................8 

Westlands Subarea in Combination with Grassland Subarea ............................................................10 

Projections from San Joaquin Valley Drainage Program Management Options 11 

Projections from Currently Available Data 12 

Estimates of Capacity of Drainage Conveyance (i.e., proposed SLD extension) 15 

Total flux from Agricultural Drainage Discharge (lbs Se/day) 15 

FIGURES 

B1a. Annual selenium load projections (lbs) at 50 (μg Se/L) for drainage discharges from the 

Northern, Grassland, Westlands, Tulare, and Kern subareas. 

B1b. Annual selenium load projections (lbs) at 150 (μg Se/L) for drainage discharges from the 

Northern, Grassland, Westlands, Tulare, and Kern subareas. 

B1c. Annual selenium load projections (lbs) at 300 (μg Se/L) for drainage discharges from the 

Northern Grassland, Westlands, Tulare, and Kern subareas.

B2a. Projected drainage volume and annual selenium loads for variable selenium concentrations 

(50,150,300 μg/L) for the Northern subarea.

B2b. Projected drainage volume and annual selenium loads for variable selenium concentrations 

(50,150,300 μg/L) for the Grassland subarea. 

B2c. Projected drainage volume and annual selenium loads for variable selenium concentrations 

(50,150,300 μg/L) for the Westlands subarea. 

B2d. Projected drainage volume and annual selenium loads for variable selenium concentrations 

(50,150,300 μg/L) for the Tulare subarea. 

B2e. Projected drainage volume and annual selenium loads for variable selenium concentrations 

(50,150,300 μg/L) for the Kern subarea. 

 1 Appendix B 

B3a. Projected drainage volume and annual selenium loads for select minimum and maximum

selenium concentrations for the Northern subarea. 
B3b. Projected drainage volume and annual selenium loads for select minimum and maximum

selenium concentrations for the Grassland subarea. 

B3c. Projected drainage volume and annual selenium loads for select minimum and maximum

selenium concentrations for the Westlands subarea. 

B3d. Projected drainage volume and annual selenium loads for select minimum and maximum

selenium concentrations for the Tulare subarea. 

B3e. Projected drainage volume and annual selenium loads for select minimum and maximum

selenium concentrations for the Kern subarea. 

B4a. Projected minimum annual selenium loads (lbs perday) for the Northern, Grassland, Westlands, 

Tulare, and Kern subareas. 

B4b. Projected maximum annual selenium loads (lbs perday) for the Northern, Grassland, Westlands, 

Tulare, and Kern subareas. 

TABLES 

B1. Westlands Water District historical selenium loading.

B2. Projections of annual selenium loading in the San Luis Drain using evidentiary evidence and 

selenium concentrations of 50, 150, and 300 μg/L for WWD drainage and 62.5 μg/L for 

Grassland Area drainage 1) if drainage to the San Luis Drain is to resume by Westlands Water 

District; and 2) if drainage to the San Luis Drain is to resume by Westlands Water District and 

drainage by the Grassland Area Farmers to the San Luis Drain is to continue. 

B3. Grassland subarea discharge to the San Joaquin River for year 2000 and year 2040 using San 

Joaquin Valley Drainage Program drainage volumes and selenium concentrations for Zones A, 

B, and C. 

B4. Annual acre-feet, selenium concentrations, and selenium loads from the Grassland Area 

Farmers Drainage Problem Area. 

B5. Annual acre-feet, selenium concentrations, and selenium loads from Mud and Salt Sloughs. 

B6. Annual acre-feet, selenium concentrations, and selenium loads measured at the San Joaquin 

River near Patterson/Crows Landing.

B7. Annual acre-feet, selenium concentrations, and selenium loads measured at the San 

Joaquin River near Vernalis. 

B8. San Luis Drain Re-use Project/Grassland Bypass Channel Project (1997-2001)

B9. San Luis Drain Re-use Project/Grassland Bypass Channel Project WY 1997 Average Monthly 

Drainage Volumes and Selenium Concentrations, Annual Discharge, and Load Targets 

B10. San Luis Drain Re-use Project/Grassland Bypass Channel Project WY 1998 Average Monthly 

Drainage Volumes and Selenium Concentrations, Annual Discharge, and Load Targets

B11. Acreage used for planning purposes in 1985-1990 by the SJVDP (SJVDP, 1989, Table 1-1) 

B12. The SJVDP 1990 and year 2000 irrigated acreage, abandoned acreage, problem acreage and 

cost for problem water reduction based on implementation of the recommended SJVDP 

Management Plan (1990). The without future (i.e., no implementation of a management plan) 

includes abandonment of lands due to salinization. 

B13. The SJVDP 1990, 2000, and 2040 volumes of drainage with no drainage improvement (0.75 

acre-feet/acre) or minimal improvement (0.55 acre-feet/acre). The conditions without 

implementation of SJVDP management plan is designated by the SJVDP as the without future

alternative and includes abandonment of lands due to salinization. An additional calculation is 

2
made for Westlands based on upslope contributions to the tile drained acreage from non-tile 

drained acreage (SWRCB, 1985). 

B14. Calculated volume of drainage using a drainage improvement factor of 0.40 acre feet per acre 

per year. The alternative with implementation of the SJVDP management plan is designated by 

the SJVDP as the with future alternative. An additional calculation is made for Westlands based 

on upslope contributions to the tile drained acreage from non-tile drained acreage (SWRCB, 

1985). 

B15a. Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley 

Drainage Program problem water volumes (without future alternative, 0.60 to 0.75 acrefeet/acre/year) and a 50-μg/L Se concentration in drainage discharge. 

B15b. Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley 

Drainage Program problem water volumes (without future alternative, 0.60 to 0.75 acrefeet/acre/year) and a 150-μg/L Se concentration in drainage discharge. 

B15c. Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley 

Drainage Program problem water volumes (without future alternative, 0.60 to 0.75 acrefeet/acre/year) and a 300-μg/L Se concentration in drainage discharge. 

B16a. Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley 

Drainage Program subsurface drainage volumes (without future alternative, 0.60 to 0.75 acrefeet/acre/year) and Se concentrations of 50, 150, and 300 μg/L. 

B16b. Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley 

Drainage Program subsurface drainage volumes (with future alternative, 0.40 acre-feet per acre 

per year) and Se concentrations of 50, 150, and 300 μg/L. 

B16c. Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley 

 Drainage Program subsurface drainage volumes, our with targeted future alternative (0.20 acrefeet per acre per year), and Se concentrations of 50, 150, and 300 μg/L. 

B17. Our projections of annual selenium loading for subareas for year 2000 using Se concentrations 

of 50 ppb, 150 ppb, and 300 μg/L and SJVDP volumes of problem water without future

alternative, of drainage volumes in the without future alternative, of drainage volumes in the 

with future alternative, and with targeted future alternative. 

B18. Summary of projections of annual selenium loads by SJVDP subareas for year 2000 (for details 

concerning drainage volumes and acreage used in calculations see Tables 13, 16a, b, c). 

Scenarios 1, 2, 3: assigned selenium concentrations of 50, 150, 300 μg/L Se and SJVDP 

estimates of drainage volume. 

B19. Tulare subarea historical selenium. 

B20. Tulare subarea historical selenium.

B21. Kern subarea historical selenium.

B22. Planned capacity of the San Luis Drain or valley-wide drain. 

B23a. San Joaquin Valley Drainage Program generalized projected annual selenium discharge from

the western San Joaquin Valley to a San Luis Drain extension to the San Francisco Bay-Delta. 

A selenium concentration of 50 μg/L Se was hypothesized to be attainable with treatment; a 

concentration of 150 μg/L Se is assigned to subsurface drainage. 

B23b. Projected low-range annual selenium discharges from the western San Joaquin Valley to a San 

Luis Drain extension to the San Francisco Bay-Delta. 

B23c. Projected high-range annual selenium discharges from the western San Joaquin Valley to a San 

Luis Drain extension to the San Francisco Bay-Delta. 

 3 Appendix B 
APPENDIX B 

San Joaquin Valley Agricultural Drainage Projections 

Projected Loadings from Historic Data and Evidentiary Testimony 

 Envisioned drainage volumes were presented in earlier discussions concerning the sustainability of

discharge from the SJV and the conditions of water-quality in ground- water aquifers (Appendix A). 

Presented here are projections for the Westlands, Grasslands, Tulare, Kern, and Northern subareas 

based on limited available measurements of drainage discharge and planning estimates. 

Westlands Water District and Subarea

Projections from Historic Data 

 Westlands subarea projections are based on limited historic measurements of drainage discharge 

from WWD into the SLD from 1981 until closure of the SLD in 1986 and planning estimates used in 

hearing testimony by WWD. Using a historical range of 330 to 430 μg Se/L concentration, the Se load 

from the initial hook-up of subsurface drains to the SLD during 1981 through 1985 was 6,283-8,187 

lbs Se annually (Table B1). These amounts are higher than those estimated in the USBR Kesterson 

Program 1986 Environmental Impact Statement (EIS) as having occurred over the 57-month period of 

SLD operation (January 1981-September 1985, average of 4,776 lbs Se/year) (USBR, 1986). A recent 

compilation from WWD indicates a discharge of 38,450 acre-feet from January 1981 through May 

1986 (WWD, 1998). The estimate of the total amount of Se discharged to Kesterson Reservoir from

1981-1985 was 22,660 lbs (USBR, 1986). The estimated input of Se includes 17,400 lbs that were 

distributed in the water, biota, and sediment of Kesterson Reservoir and 5,280 lbs of Se contained in 

95,271 cubic yards of bed sediment still residing in the SLD. Selenium transferred from the 

seleniferous agricultural drainage water-column to the sediment contributed to the Se load remaining in 

the bed sediment. The 17,400-lbs amount is hereafter referred to as one kesterson (kst). This amount 

represents a unit of measure of potential cumulative hazard to wildlife based on load directly released 

4
into an ecosystem (Presser and Piper, 1998). It will be used later for comparison to provide a historical 

perspective. 

Projections from Evidentiary Testimony 

 Evidence presented in 1996 referred to estimates prepared in 1965 for planned discharges from

WWD, before emphasis was placed on efficient on-farm water management in the 1980’s (WWD, 

1996). Table B1 shows the planned discharge in 1980 in comparison to the Se loading estimated to 

have occurred from 1981 to 1985. The 1980’s plans were expressed as volumes of drainage or 

acreage to be drained. If the 330-430 μg Se/L concentration range is used in conjunction with 

estimates of 38,000 acre-feet of annual drainage discharge, then plans were for discharge of 34,109-

44,445 lbs Se/year from 76,000 acres in WWD (WWD, 1996). Using these estimates, the amount of 

drainage generated per acre is 0.50 acre-foot/acre. Calculated amounts of Se per acre (0.449-1.02 lbs 

Se) or acre-foot (0.898-1.17 lbs Se) for the planned drainage are also given in Table B1. 

 Since the closure of the 85-mile segment of the SLD in 1986, WWD drainage waters have been 

stored in the subsurface (Jones and Stokes, 1986a; b; SJV Drainage Program, 1989; 1990a). Data for 

Se concentrations in drainage presently are not available. The quality of the ground water is 

endangered by such practices, of course. The eventual loss of use of the groundwater basin beneath the 

SLU has been predicted at various stages of the planning process as a justification for the out-of-valley 

drain. Trade-offs were to be among lands kept in production, water export from the Bay-Delta, 

ground-water quality, and SJR degradation (USBR, 1978). The SJV Drainage Program in 1990 

estimated the remaining life of the semi-confined aquifer beneath the Westlands subarea (576,000 

acres) at a mean of 110 years (aquifer water-quality greater than 2,500 ppm TDS at a thickness of from

150 to 220 feet at current pumping rates). Minimum life remaining in some areas of the western SJV 

was as low as 25 years. 

 Several evidentiary proceedings concerning the disposition of drainage from WWD and the SLU 

have resulted in judgments and testimony concerning the quantity of drainage (Table B2) (WWD,

1996). Annual drainage discharge from the SLU of the CVP was estimated as part of the Barcellos 

decision (1986) to be an amount of discharge not greater than 100,000 acre-feet and not less than 

60,000 acre-feet (USBR, 1992). Using assigned Se concentration of 50, 150, 300 μg Se/L, the amount 

of annual loading from the SLD would range from 8,160-81,600 lbs Se/year (Table B2). 

 5 Appendix B 
 Estimates presented in testimony in 1996 of drainage from WWD include 42,000 acres in the 

northeastern corner of WWD, where subsurface drains have been installed but are not connected to the 

SLD. The evidence stated that an additional 29.5 miles of SLD will be constructed to reach this area if 

drainage is to be provided for all areas of WWD needing drainage. Data for the annual volume of 

drainage (1,900-2,300 acre-feet) to be discharged upon initial reconnection to the SLD from WWD is 

not well justified, but is presented for comparison to those estimates given by WWD in 1980 (i.e., 

7,000 acre-feet/year). The evidence presented shows a total problem acreage of 200,000 acres for 

WWD, with 60,000 acre-feet of drainage generated annually (WWD, 1996). This estimate represents a 

0.3 acre-feet/acre rate of generation of drainage. Using assigned Se concentrations of 50, 150, and 300 

μg Se/L, projected Se loads of 8,160 to 48,960 lbs Se/year were calculated for WWD, with an initial 

hook-up contributing 258 to 1,877 lbs Se (Table B2). 

 

Grassland Subarea (WY 1986-1996)

Projections from Historic Data

Although provision of a drainage outlet was initially focused on WWD, parts of the Grassland 

subarea are within the SLU for which drainage is required (USBR, 1992). The larger historical area of 

the Grassland designated for the SLU is referred to as the Delta-Mendota Service Area (i.e., irrigation 

service from the Delta-Mendota Canal) as opposed to the San Luis Service Area (i.e., irrigation service 

from the San Luis Canal portion of the California Aqueduct). Essentially, the Grassland problem area 

considered here contains approximately 50,000 acres with a subsurface drainage system in a total of 

100,000 acres in production. The area generates a blended subsurface drainage for discharge to the 

SJR. The SJV Drainage Program 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) (SJV 

Drainage Program, 1990a). Zone A generates drainage of poor enough quality to impair state 

beneficial uses of receiving waters and therefore is the focus for 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 the already complex historical alignments (USBR, 

1992; Environmental Defense Fund, 1994). 

The Se discharge to the SJR from the state-designated Grassland Drainage Area has been 

monitored since 1986 and is continuing currently (CCVRWQCB, 1996b; c; 1998 d; e; f; g; h; 2000b;c; 

6
Henderson et al., 1995; USBR et al., 1998; 1999). Discharge occurred in the same configuration 

through the period 1986 to 1996 (drains to Grassland wetlands to SJR). Tables B4-B7 give summaries 

of the data for Se loads on a water-year basis from 1986 to 1998. An annual 8000-lb Se prohibition 

(CCVRWQCB, 1996c and 1998a) has been imposed by the state and an annual load target of 6,600 lbs 

Se for discharge to the SJR has been initiated by the USBR (1995) (also See Appendix A, Figure A9). 

The WY 1997 and 1998 Se loads measured further downstream in the SJR at Crows Landing is 

applicable to the state 8,000-lb prohibition limitation for Se discharge to the SJR effective October 1, 

1996 (CCVRWQCB, 1998b). The Se load for the SJR at Crows Landing was 8,667 lbs Se in WY 1997 

(CCVRWQCB, 1998h) and 15,501 lbs Se in WY 1998 (USBR et al., 1999). 

Selenium is persistently discharged from the Grassland area to the SJR, but Se load values are 

dependent on the monitoring site location within the Grassland area (Tables B4-B7). The upstream

drainage source discharge represents managed components of flow and load. Annual data are not 

available for individual farm-field sumps to represent source-area shallow groundwater conditions and 

thus show long-term variability in Se concentrations. The downstream sites reported here are the SJR 

at Crows Landing/Patterson (CL/PATT, approximately 50 miles downstream from the farm

agricultural discharge sumps), and the SJR at Vernalis (VERN, approximately 130 miles downstream

from the agricultural discharge). Data for WY 1986 to WY 1998 generally can be related to physical 

variables that affect drainage conditions (e.g., Appendix A, Figure A10, annual rainfall measured at 

station #124, compiled from CDWR database). 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 in 1997. Specific variables affecting Se load are discussed later in Appendix D. 

Detailed analysis of loads for WY 1986 to 1988 reported an annual average of 10,850 lbs Se per 

year (Environmental Defense Fund, 1994). The range of annual loads for WY 1986 to 1998 for the 

managed source discharge is from 5,083 to 11,875 lbs Se/year (Table B4). For the same time period, 

the range of annual loads for the state compliance point for the SJR at Crows Landing is 3,064-15,884 

lbs Se/year (Table B6). The range of loads for the SJR at Vernalis, the entrance to the Bay-Delta, from

WY 1986 to WY 1998 is 3,558 to 17,238 lbs Se/year (Table B7). The higher loads in recent years are 

noteworthy because they occur after issuance of 1) state control plans for agricultural drainage issued 

in 1985 and 2) joint federal-state agricultural drainage management plans issued in 1990. Loads from

the Grassland subarea have exceeded the annual 8,000-lb-prohibition for Se discharge to the SJR since 

its enactment in 1996. For WY 1986 through WY 1998, the cumulative Se load discharged to the SJR 

 7 Appendix B 
at Crows Landing/Patterson is 114,879 lbs Se (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). 

Of course, all sources, reservoirs, and discharges of Se are not known for the SJR system. 

 As described earlier, regulatory efforts through enactment of the TMML load allocation call for 

discharges of 1,001 to 3,088 lbs Se/year from the Grassland subarea, by the year 2010 (See Appendix 

C). 

Grassland Bypass Channel Project (Reuse of the San Luis Drain, WY 1997 to present) 

In 1990, the SJV Drainage Program considered re-routing drainage from the Grassland subarea 

through re-use of a portion of the SLD to avoid wetland contamination (i.e., drains to SLD to Mud 

Slough to SJR). Table B3 shows estimates by the SJV Drainage Program of potential drainage from

the zones of the Grassland subarea. They assumed concentrations of 2 μg Se/L in both drainage from

wetlands (Zone B) and in discharges from areas (Zone C). The discharge from the 72,000-acre Zone A 

was estimated at either 10,700 acre-feet containing a Se concentration of 150 μg Se/L or 21,000 acrefeet containing a Se concentration of 75 μg Se/L. The discharges from the entire Grasslands subarea 

was to be 4,524 lbs Se for year 2000 and 4,725 lbs Se for year 2040. These values are less than those 

measured for the recently initiated re-use of the SLD project described below (USBR et al., 1998 and 

1999) for discharge from Zone C (37,500 acre-feet of drainage containing 62.5 μg Se/L from

approximately 90,000 acres yielded 7,097 lbs Se in WY 1997, Table B8) and those measured 

historically (Tables B4 to B7). 

8

 Consideration of a project to re-open part of the SLD for use by the Grassland subarea was of 

enough concern to elicit a U.S. Congressional hearing in 1993 in Washington, D.C., as part of 

testimony on continuing agricultural drainage issues (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 a long-standing problem agricultural drainage problem in the SJV (U.S. House of Representatives, 

1993). On September 23, 1996 a cooperative project among agricultural, government, and 

environmental parties was initiated by the USBR (1995), which reopened the SLD on an interim fiveyear basis. The drain transports drainage to the SJR and thereby removes it from wetland channels. 

Named the Grassland Bypass Channel Project (GBCP), the project focuses on the use of a 28-mile 

portion of the SLD to provide drainage for approximately 97,400 acres in the Grassland subarea. The 

Grassland Bypass Channel Project is a regional effort to improve water quality by regulating Se loads. 
The goals include: 1) measuring and eventually reducing drainage loads through a regional program; 2) 

protecting riparian wildlife habitat by assuring the wetlands of an adequate clean-water supply; and 3) 

examining possible adverse effects that may result from the routing of drainage through the SLD and 

Mud Slough to the SJR. The GBCP contains commitments to meet and further define environmental 

concerns for wetlands and the SJR. A regional drainage agency that includes local water and drainage 

districts has been created and assigned responsibility for pollution. A federal/state interagency 

committee monitors flow, water-quality, sediment quality, biota and toxicity in the SLD, Mud Slough, 

Salt Slough, and the SJR (USBR et al., 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 (GAF, 1998a). 

 The Se load targets for the reuse of the SLD are defined only by the commitment that the input 

loads to the SJR “will not worsen” over historical loads (USBR, 1995). Appendix A (Figure A11) 

shows the monthly load targets adopted for the first two years of Grassland Bypass Channel Project. 

Compliance loads are measured at the discharge of the SLD into Mud Slough rather than at the SJR at 

Crows Landing, as previously regulated by the state (CCVRWQCB, 1996c). In September 1998, a 

waste discharge permit was issued for the GBCP by the state (CCVRWQCB, 1998a), which contained 

the negotiated load targets. Tables B8, B9, and B10 show the 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% 

reduction each year for the next three years. Also shown is the state’s prohibition of drainage 

discharge limitation for the SJR, which limits Se discharge to the SJR and tributaries to 8,000 lbs/year. 

If the annual target amount is exceeded by 20%, consideration would be given to shutting down the 

SLD and terminating the GBCP (USBR, 1995). The comparison of targets with measured loads shows 

that in neither year did the project meet the federal target, although loads in 1997 were lower than the 

state target. It is also notable that drain water discharged to the SJR through the SLD is more 

consistently concentrated than were the historic discharges to the wetlands channels system. The 

wastewater in the SLD is not diluted by wetlands flows, and loss of Se to sediment and biota, as 

occurred during transit through wetland channels (i.e., “in-transit loss”), may be reduced (USBR, 1995; 

Presser and Piper, 1998). Recent adoption by the state of a water-quality objective of less than 2 μg 

Se/L for the Grassland wetland channels as promulgated by USEPA (USEPA, 1992; CCVRWQCB, 

1996c; 1998a), has essentially removed these channels as alternative flow paths for drainage water, 

 9 Appendix B 
however. This regulation will make it difficult to re-use the wetland channels, for example, as 

alternative channels during flood runoff or in the event that WWD once again uses the SLD. 

 Tables B9 and B10 give the detailed monthly data for the GBCP including volumes and Se targets, 

loads, and concentrations (USBR et al., 1998 and 1999). The annual load of 7,104 for WY 1997 

includes 6,960 lbs Se that was discharged from the SLD and 137 lbs Se 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 the monthly and annual Se load targets by 437 lbs (6.6%) in the first year of the 

project. The annual load represents 0.073 lbs Se/acre or 0.189 lbs Se/acre-foot for the Grasslands Area 

of 97,400 acres. The average Se concentration in the discharge for WY 1997 was 62.5 μg Se/L and the 

total volume was 37,483 acre-feet. The annual load for the second year of the GBCP, WY 1998, was 

9,130 lbs Se. The annual Se load target was exceeded by 37% 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 upper watershed load was estimated at 487 lbs Se, 

with 350 lbs documented in overflow to wetland channels. The average Se concentration in the 

discharge for WY 1998 was 67 μg Se/L and the total volume was 45,858 acre-feet. The annual load 

represents 0.094 lbs Se/acre or 0.199 lbs Se/acre-foot for the Grasslands Area. 

 

Westlands Subarea in Combination with Grassland Subarea

An analysis by the USBR in 1983 showed a combined discharge for the SLU and Delta-Mendota 

Services Areas which includes the Grassland subarea. Taking the worst-case scenario for the year 

2020, the amount of drainage from the SLU Service Area is 135,240 acre-feet and from the DeltaMendota Service Area is 65,783 acre-feet. Using assigned concentrations of 50, 150, and 300 μg Se/L 

with these amounts of drainage, the range of Se discharged from SLU Service Area is from 18,393 to 

110,356 lbs Se/year and for the Delta-Mendota Service Area is from 8,946 to 53,679 lbs Se/year. The 

range of total discharge is from 27,339 to 164,035 lbs Se/year. 

Evidentiary hearings (WWD, 1996) also included a scenario in which the Grassland Area drainage 

being discharged to the SJR would be discharged to the SLD, along with the WWD discharges 

(although, under current agreements, the GBCP would terminate if WWD is given permission to use 

the SLD) (USBR, 1995). This additional drainage (30,000 to 40,000 acre-feet) is hypothesized to be of 

better quality than that of water discharged to Kesterson Reservoir. The additional load calculated 

using the measured average concentration (62.5 μg Se/L) for Grassland discharge for WY 1997 is 

10
5,100-6,800 lbs Se/year (Table B2). Thus, the range for a total annual load from WWD and the 

Grassland Area discharged under this scenario to the SLD is 13,518-15,273 lbs Se/year, if WWD 

drainage contains a concentration of 50 μg Se/L. The loads increase to 30,355 to 32,218 lbs Se/year if 

WWD drainage contains a concentration of 150 μg Se/L, and 55,610 to 57,637 lbs Se/year if WWD 

drainage contains a concentration of 300 μg Se/L. 

Projections from San Joaquin Valley Drainage Program Management Options

 The data for acreage and drainage volumes used by the SJV Drainage Program for planning 

purposes for each of the five subareas is given in Tables B11 through B17. Two possible alternative 

futures were defined by SJVDP: 1) no implementation of the SJV Drainage Program management plan, 

0.60 to 0.75 acre-feet/acre generated drainage, namely, without future and 2) with implementation of 

the SJV Drainage Program management plan, 0.40 acre-feet/acre generated drainage, namely, with 

future (SJV Drainage Program 1989 and 1990a). A third condition defined for use in our projections is 

called with targeted future. The targeted future condition applies a factor of 0.20 acre-feet/acre of 

generated drainage, exemplifying the lowest, although probably not realistic, irrigation water return. 

Like earlier plans, the SJV Drainage Program did not calculate concentrations of Se in drainage water, 

or Se loads directly, but rather focused on estimating the volume of drainage and the affected acreage 

for subareas. Assigning Se concentrations of 50, 150 and 300 μg Se/L to these volumes, gives the 

general magnitude of expected Se discharge or loading. 

Table B18 gives the details of specific loadings from each of the five subareas based on the 

estimates given by the SJV Drainage Program for year 2000 and assigned concentrations of 50, 150, 

and 300 μg Se/L. This summary gives ranges of acre-feet of drainage and potentially discharged 

annual loads of Se for the assigned concentrations. Figures B1a, b, and c depict the ranges of 

agricultural discharges for assigned concentrations of 50, 150, and 300 μg Se/L if all subareas are 

considered discharging to a valley-wide drain. Considered on a subarea basis, the Se loads are (Table 

B18): 

• Northern subarea. Discharge from the Northern subarea is to the SJR. The range of projections 

of annual Se loads for the Northern subarea is 925 to 3,536 lbs Se for an assigned concentration of 

50 μg Se/L; 2,774 to 10,608 lbs Se/year for an assigned concentration of 150 μg Se/L; and 5,549 to 

21,216 lbs Se/year for an assigned concentration of 300 μg Se/L. 

 11 Appendix B 
• Grassland subarea. Discharge from the Grassland subarea is to the SJR. The range of 

projections of annual Se loads for the Grassland subarea is 2,938 to 11,696 lbs Se/year for an 

assigned concentration of 50 μg Se/L; 8,813 to 35,088 lbs Se/year for an assigned concentration of 

150 μg Se/L; and 17,626 to 70,176 lbs Se/year for an assigned concentration of 300 μg Se/L. 

• Westlands subarea. WWD (i.e, encompassing the Westlands subarea) is currently asking to 

extend the SLD to the Bay-Delta as a drainage outlet. The range of projections of annual Se loads 

for the Westland subarea is 1,877 to 11,016 lbs Se/year for an assigned concentration of 50 μg 

Se/L; 5,630 to 33,048 lbs Se/year for an assigned concentration of 150 μg Se/L; and 11,261 to 

66,096 lbs Se/year for an assigned concentration of 300 μg Se/L.

• Tulare subarea. Tulare subarea currently discharges to privately owned evaporation ponds. The 

range of projections of annual Se loads for the Tulare subarea is 2,611 to 10,200 lbs Se/year for an 

assigned concentration of 50 μg Se/L; 7,834 to 30,600 lbs Se/year for an assigned concentration of 

150 μg Se/L; and 15,667 to 61,200 lbs Se/year for an assigned concentration of 300 μg Se/L Se.

• Kern subarea. Kern subarea currently discharges to privately owned evaporation ponds. The 

range of projections of annual Se loads for the Kern subarea is 1,088 to 6,256 lbs Se/year for an 

assigned concentration of 50 μg Se/L; 3,264 to 18,768 lbs Se/year for an assigned concentration of 

150 μg Se/L; and 6,528 to 37,536 lbs Se/year for an assigned concentration of 300 μg Se/L. 

 

Projections from Currently Available Data

Tables B1, B2, B9, B10, B19, B20, and B21 give the derivation and details of specific loads 

projected from each of the five subareas based on our compilation of currently available data on 

problem acreage, drainage volume, and Se concentration. These data have become available since the 

SJV Drainage Program was completed in 1990. Depending on the type of data available from each 

subarea, projections were made concerning concentration and load. Because of the limited data and 

broad range of management alternatives across the subareas, maximum and minimum Se 

concentrations are given to bracket possible load scenarios given a specific volume of drainage for 

each subarea. The projected concentration range is 5 to 10 μg Se/L for the Northern subarea, 68 to 152 

μg Se/L for Grassland subarea, 49 to 150 μg Se/L for Westlands subarea (note, no current data, only 

testimony on acreage is available), 1.7 to 9.8 μg Se/L for Tulare subarea, and 175 to 254 μg Se/L for 

12
Kern 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 SJR. The projected 

concentration range is 5 to 10 μg Se/L for the Northern subarea. The Northern subarea minimum

projection is based on a nominal 5 μg Se/L Se concentration applied to adhere to the USEPA 

promulgated Se standard for the SJR. Because management options were not recommended for the 

Northern subarea, the assumed drainage volume is that estimated by the SJV Drainage Program for 

year 2000 without implementation of the management plan alternatives (SJV Drainage Program, 

1990a) (Tables B13 through B17). The range of projected annual Se loads for the Northern 

subarea is 350 to 750 lbs Se/year, if a maximum concentration of 10 μg Se/L is applied to the same

drainage volume. 

• Grassland subarea. Discharge from the Grassland subarea is to the SJR. The projected 

concentration range is 68 to 152 μg Se/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 Se/year. 

The projected Grassland maximum load is 15,500 lbs Se/year, a load similar to that measured for 

the SJR at Crows Landing in an extremely wet year (i.e., WY 1998). The maximum load attempts 

to represent a load that includes upstream SJR loads of Se and recycled Se loads from the DeltaMendota Canal. 

• Westlands subarea. Westlands subarea (or WWD) currently recycles its drainage and therefore 

no discharge data is available. The projected concentration range is 49 to 150 μg Se/L for the 

Westlands subarea (note, no current data, only testimony on acreage is available). The WWD 

subarea minimum acre-feet discharge and load are for conditions presented as evidence for WWD 

(60,000 acre-feet at 49 μg Se/L Se, WWD, 1996) (Tables B1 and B2). The maximum load is based 

on a Se concentration of 150 μg Se/L (163 μg Se/L median and USBR conservative estimate of “at 

least 150 μg Se/L”) applied to 60,000 acre-feet. The projected range of annual Se loads for WWD 

is 8,000 to 24,480 lbs Se/year.

• Tulare subarea. Tulare subarea currently discharges to privately owned evaporation ponds. The 

Tulare subarea projections are based on measurements for volume and Se concentration from 1993 

 13 Appendix B 
to1997 (personal communication 1/98, Anthony Toto, CCVRWQCB). 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 Se loads. From the sparse data available from the 

Tulare subarea for 1993, 1995, and 1997, the projected concentration range is 1.7 to 9.8 μg Se/L. 

The range of projected annual loads for the Tulare subarea is 91 lbs to 519 lbs Se/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 Se load from this area is small relative to that projected from WWD and 

Grassland subareas, largely because the projected Se concentrations are 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 Se concentration from 1993 to1997 

(personal communication 1/98, Anthony Toto, CCVRWQCB). An average volume is used in the 

projections in conjunction with the minimum and maximum Se loads. From the sparse data 

available, the projected concentration range is 175 to 254 μg Se/L for Kern subarea. Projected 

annual Se 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 Se load from this area is small relative to that from WWD and 

Grassland subareas, largely because the projected volumes of drainage are low from the Kern 

subarea. 

 A compilation of our projections based on currently available data is given in Table 7. Sets of 

graphs in Figures B2 and B3 compare generalized projections from SJVDP volumes (Table B18) with 

those based on currently available data (Table 7). The ranges of drainage volume and annual Se loads 

are presented graphically for each assigned concentration, i.e., 50, 150, and 300 μg Se/L for each 

subarea (Figures B2a through e). The ranges of projected drainage volumes and annual Se loads are 

presented graphically for the minimum and maximum concentrations derived from current data 

(Figures B3a through e). In general, this graphical technique enables a prediction or projection of an 

14
annual Se 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 into an SLD extension. The graphical technique 

also shows patterns of Se concentration and load that are indicative of the geology, hydrology, and 

chosen management options for each subarea. 

Estimates of Capacity of Drainage Conveyance (i.e., proposed SLD extension)

As a final check of the magnitude of the load projections, the various design capacities of the SLD 

or a SLD extension are combined with assigned Se 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 SJR. The SLD design capacity is 

projected at 300 cfs (as suggested as early as 1955 and recently) (USBR, 1955; 1962; 1978; CSWRCB, 

1999a), which is equivalent to 216,810 acre-feet/year. At a concentration of 50 μg Se/L, the annual Se 

load is 29,486 lbs Se. Using an assigned concentration of 150 μg Se/L, the annual load to the BayDelta is 88,458 lbs Se. For a 300 μg Se/L discharge, the annual load is 176,917 lbs Se. Other 

historical estimates of annual discharge for the SLD (e.g. 144,200 acre-feet/year in early planning; 

150,000 estimated during 1975-1977 for 50-100 years of drainage; and 84,525 to 279,270 acre-feet 

estimated in 1983 for the period 1995-2095) also can be used to estimate loads by applying assigned 

concentrations to discharge capacity. An estimate of drainage available from the SJV for discharge to 

the San Francisco ocean outfall showed 375,000 acre-feet annual drainage discharge and a 400,000 –

500,000 acre-feet capacity of a drainage facility (Montgomery-Watson, 1993). All of these estimates 

show a need for a drain of greater than 200,000 acre-feet/year. 

 

Total flux from Agricultural Drainage Discharge (lbs Se/day)

It is also useful to present projected Se loading from the western SJV to the Bay-Delta in terms of 

rate of discharge (lbs Se/year and lbs/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 Se, 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 Se load. Table B23a shows that a projected 

 15 Appendix B 
Se discharge from the western SJV to a SLD extension to the Bay-Delta based on generalized SJV 

Drainage Program data (i.e., 314,000 acre-feet of problem water with an assigned concentration of 50 

μg Se/L, or 144,000-163,000 acre-feet of subsurface drainage with an assigned concentration of 150 μg 

Se/L) would be 2.4 to 3.8 ksts per year. The flux of Se discharge from the drain to the Bay-Delta is 

projected to range from 117 to 182 lbs Se/day. Tables B23b and B23c and Figures B4a and B4b show 

a projected Se rate of discharge (lbs Se/day) from each of the five designated subareas of the western 

SJV using the minimum and maximum scenarios defined earlier from currently available data (Figure 

B3). The range of Se flux from each subarea is: Northern, 0.95 to 1.9 lbs Se/day; Grassland, 19 to 42 

lbs Se/day; Westlands, 22 to 67 lbs Se/day; Tulare, 0.25 to 1.4 lbs Se/day; and Kern, 3.0 to 4.3 lbs 

Se/day. The total Se flux is 45 to 117 lbs Se/day under the assumed conditions. The Westlands and 

Grassland subareas discharge the largest proportion of the daily annual load (Figures B4a and B4b). 

The range of combined loads from the Grasslands and Westlands subareas is 0.86 to 2.29 ksts/year. 

For comparison, the current prohibition limitation for the Grassland subarea to the SJR is 8,000 

lbs/year or 0.46 ksts/year. 

16
Figure B1a

Figure B1b

Figure B1c

0 

2000 

4000 

6000 

8000 

10000 

12000 

lbs Se/year

0 20000 40000 60000 80000 

Acre-feet/year

Annual Se load projections, 50 ppb

Kern

Tulare

Westlands

Grassland

Northern

50 ppb line

0 

10000 

20000 

30000 

40000 

50000 

60000 

70000 

lbs Se/year

0 20000 40000 60000 80000 

Acre-feet/year

Annual Se load projections, 300 ppb

Northern

Kern

Tulare

Westlands

Grassland

300 ppb line

0 

5000 

10000 

15000 

20000 

25000 

30000 

35000 

lbs Se/year

0 20000 40000 60000 80000 

Acre-feet/year

Annual Se load projections, 150 ppb

Northern

Kern

Tulare

Westlands

Grassland

150 ppb line
Figure B2a

Figure B2b Figure B2c

Figure B2d Figure B2e

0 

2500 

5000 

Selenium (lbs)

0 2500 5000 7500 

Acre-feet

Kern Subarea

300 ppb

150 ppb

50 ppb

2,292 acre-feet

1,870 lbs

 935 lbs

 312 lbs

0 

20000 

40000 

Selenium (lbs)

0 15000 30000 45000 60000 

Acre-feet

Tulare Subarea

300 ppb

150 ppb

50 ppb

15,906 lbs

 7,953 lbs

 2,651 lbs

19,493 acre-feet

0 

20000 

40000 

60000 

Selenium (lbs)

0 15000 30000 45000 60000 75000 90000 

Acre-feet

Westlands Subarea

48,960 lbs

24,480 lbs

 8,160 lbs

60,000 acre-feet

300 ppb

150 ppb

50 ppb

0 

20000 

40000 

60000 

Selenium (lbs)

0 15000 30000 45000 60000 75000 90000 

Acre-feet

Grassland Subarea

300 ppb

150 ppb

50 ppb

 30,587 lbs

 15,293 lbs

 5,097 lbs

37,483 acre-feet

0 

250 

500 

750 

1000 

1250 

Selenium (lbs)

0 10000 20000 30000 40000 

Acre-feet

Northern Subarea

26,000 acre-feet

700 lbs

350 lbs

10 ppb

 5 ppb
Figure B3a

Figure B3c

Figure B3b

Figure B3d Figure B3e

0 

500 

1000 

1500 

2000 

Selenium (lbs)

0 10000 20000 30000 40000 50000 60000 

Acre-feet

Northern Subarea

26,000 acre-feet

10 ppb

5 ppb

350 lbs

700 lbs

0 

5000 

10000 

15000 

20000 

25000 

30000 

Selenium (lbs)

0 10000 20000 30000 40000 50000 60000 

Acre-feet

Grassland Subarea

37,483 acre-feet

152 ppb

15,500 lbs

 6,960 lbs 68 ppb

0 

500 

1000 

1500 

2000 

Selenium (lbs)

0 10000 20000 30000 40000 50000 60000 

Acre-feet

Tulare Subarea

19,493 acre-feet

9.8 ppb

 91 lbs 1.7 ppb

519 lbs

0 

5000 

10000 

15000 

20000 

25000 

30000 

Selenium (lbs)

0 20000 40000 60000 80000 

Acre-feet

Westlands Subarea

24,480 lbs

 8,000 lbs

60,000 acre-feet

150 ppb

49 ppb

0 

500 

1000 

1500 

2000 

Selenium (lbs)

0 2000 4000 6000 8000 10000 

Acre-feet

Kern Subarea

1,586 lbs

1,089 lbs 175 ppb

254 ppb

2,292 acre-feet

Figure B3b
 Figure B4a

 Figure B4b

Grassland (19 )

Northern (0.95 )

Tulare (0.25 )

Kern (3 )

Westlands (22 )

 Projected Annual Selenium - minimum

lbs per day

Total = 45.2 lbs Se / day

Grassland (42 )

Tulare (1.4 ) Northern (1.9 )

Kern (4.3 )

Westlands (67 )

Projected Annual Selenium - maximum

lbs per day

Total = 117 lbs Se / day
Table B1 Westlands Water District Historical Selenium Loading 

Use of San Luis Drain by Westlands Water District to discharge selenium to Kesterson Reservoir 

WWD planned drainage acreage/ total acreage 

Problem acreage with on-farm drains 

Problem acrefeet ppb Se lbs Se/tim

San Luis Drain discharge (measurement average 1983-1984) (CSWRCB, 1985; WWD, 1998) 

38,450

(total discharge for 65 months; January 1981 to May 1986) 

330-430

Estimated Westlands Water District annual discharge to San Luis Drain from January, 1981- September, 1985 (Se concentrations from use of drain in 1983-1984) (CSWRCB, 1985) 

5,000 7,000 

(*42,000) 

330-430 6,283-8,1

Projected Westlands Water District discharge to San Luis Drain by 1980 (based on 1965 management plans and Se concentrations from use of drain in 1983-1984) (WWD, 1996) 

300,000/600,000 (approximately 566,500 irrigated  acres) 

76,000 38,000/year 330-430 34,109-44

1986 Environmental Impact Statement (EIS) estimated San Luis Drain discharge (USBR, 1986): Total (January, 1981- September, 1985) Annual (total averaged over 57 months ) 

22,660 4,776/yea

1986 EIS estimated San Luis Drain discharge to Kesterson Reservoir (1981-1985) (USBR, 1986) 

17,400**

(1 kester

1986 EIS estimated San Luis Drain bed sediment accumulation (95,271 cubic yards) (USBR, 1986) 

5,280 

*WWD contends that the drainage from 5,000 subsurface-drained acres actually represents drainage from 42,000 acres because of upslop

downslope area (CSWRCB, 1985); ** The 17,400-lb amount is referred to as one kesterson (kst). The use of this unit provides perspectia hazard to wildlife when released directly to the wetland at Kesterson Reservoir (Presser and Piper, 1998). 
TABLE B2 Projections of annual selenium loading in the San Luis Drain using evidentiary evidence and selenium concentrations of 50, 

WWD drainage and 62.5 ppb for Grassland Area drainage if drainage to the San Luis Drain is to resume by Westlands Water District and Luis Drain is to resume by Westlands Water District and drainage by the Grassland Area Farmers to the San Luis Drain is to continue. Westlands Subarea or San Luis Unit 

Problem  acre-feet* 

Calculated Acre-feet/ acre 

Projectedppb Se 

Projected lbs Se/year 

Projectedppb Se 

Projected lbs Se/year 

Projppb 

Barcellos Judgment* not < 60,000 

not > 100,000 

50 8,160-13,600 150 24,480-40,800 300 

DEIS Planning Alternatives* 24,000 0.23 50 3,264 150 9,792 300 Initial hook-up of 7,600** acreage of on-farm drains 

 1,900-  2,300 

50 258-313 150 775-938 300 

Drainage of 200,000 acres of problem acreage** 

60,000 0.30 50 8,160 

(0.041lbs Se/acre or 0.136 lbs Se acre-foot) 

150 24,480

(0.122 lbs Se/acre  or 0.408 lbs Se acre-foot) 

300 

Additional drainage from** Grassland Area Farmers 

30,000- 40,000 

 62.5*** 5,100- 6,800 62.5*** 5,100- 6,800 62.5

Total for Westlands and Grassland (range) 

90,000- 100,000 

13,518-15,273 30,355-32,218 

 Evidence presented by Westlands Water District, 1*) Draft Environmental Impact Statement, December 20, 1991, San Luis Drainage P

 Project, California, in partial answer to the Barcellos Judgment of December 30, 1986 (USBR, 1992) and 2**) Statement Concerning C

 Westlands Water District Drainage Problem, submitted on the behalf of Westlands Water District, by William R. Johnston, April 4, 199measured in water year (WY) 1997. 
TABLE B3 Grassland Subarea discharge to the San Joaquin River for year 2000 and year 2040 using San Joaquin Valley Drainage 

 Program drainage volumes and selenium concentrations for Zones A, B, and C (SJVDP, 1989; 1990a). Grassland Subarea SJVDP 2000 

drained  acreage* 

SJVDP 2000 problem water acre-feet** 

SJVDP 2000 discharge to San Joaquin River(acre-feet)** 

Projected ppb Se** 

lbs Se/ acrefoot 

Projected lbs Se/year 

SJVDP 2040 discharge to San Joaquin River(acre-feet

Zone A 72,000 54,000 10,700 150 0.408 4,366 21,000 Zone B 14,000 10,600 7,000 2 0.0054 38 17,600 Zone C 30,000 22,000 22,000 2 0.0054 120 63,500 Total 116,000 86,600 39,700 4,524 102,100 * Preliminary Planning Alternatives, SJVDP, 1989, page 4-23 (assumption, drained acres will more than double by year 2000); ** SJVD

 and page 139. 
Table B4 Annual acre-feet, selenium concentrations, and selenium loads from the Grassland 

 Area Farmers Drainage Problem Area. Water-year acre-feet/year ppb Se (total) lbs Se/year lbs Se/acre-foot 1986 67,006 52.3 9,524 0.1421987 74,902 53.8 10,959 0.1461988 65,327 56.8 10,097 0.1541989 54,186 59.2 8,718 0.1611990 41,662 65.2 7,393 0.1771991 29,290 73.5 5,858 0.2001992 24,533 76.2 5,083 0.2071993 41,197 79.0 8,856 0.2151994 38,670 80.5 8,468 0.2191995 57,574 75.8 11,875 0.2061996 52,978 70 10,034 0.1891997* 37,483 62.5 7,097 0.186 1998* 9,118TOTAL 113,080

average 8,698 lbs/year 

DATA: CCVRWQCB, 1996b; c; 1998d; e; f; g; h; 2000,b; c; USBR et al., 1998, 1999. * measured at the SLD discharge to Mud Slough after the initiation of the Grassland Bypass Channel Project 
Table B5 Annual acre-feet, selenium concentrations, and selenium loads from Mud and Salt Sloughs. 

Water-year acre-feet/year ppb Se (total) lbs Se/year Mud Slough 

concentration range 

1986 284,316 8.6 6,643 2.3-22 1987 233,843 12.0 7,641 1.7-26 1988 230,454 13.0 8,132 1.4-18 1989 211,393 14.1 8,099 0.7-5.0 1990 194,656 14.6 7,719 0.6-8.1 1991 102,162 14.0 3,899 0.7-38 1992 85,428 12.6 2,919 0.8-48 1993 167,955 15.0 6,871 1.0-5.0 1994 183,546 16.0 7,980 0.5-22 1995 263,769 14.9 10,694 0.7-4.2 1996 267,344 13 9,697 -- 1997 288,253 10 7,722 5.0-80 1998 Not available Total 88,016 

average 7,335 lbs/year 

DATA: DATA: CCVRWQCB, 1996b; c; 1998d; e; f; g; h; 2000,b; c; USBR et al., 1998, 1999. 
Table B6 Annual acre-feet, selenium concentrations, and selenium loads measured at the San Joaquin River near Patterson/Crows Landin

Water-year (WY) million acre-feet/year ppb Se (total) lbs Se/year 

1986 2.67 1.6 11,305 1987 0.66 4.9 8,857 1988 0.55 6.2 9,330 1989 0.44 6.3 7,473 1990 0.40 5.6 6,125 1991 0.29 4.5 3,548 1992 0.30 3.7 3,064 1993 0.89 3.5 8,379 1994 0.56 4.8 7,270 1995 3.50 1.6 14,291 1996 1.44 3 10,686 1997 4.18 (range 986 to 73,458 daily) (3.73 USGS from 

GBCP data) 

1 8,667 (9,054 USGS from GBCP data

1998 5.13 (range 956-47,916 daily) (GBCP data) 15,501 (GBCP data) Total 114,496

average 8,807 lbs/year 

DATA: DATA: CCVRWQCB, 1996b; c; 1998d; e; f; g; h; 2000,b; c; USBR et al., 1998, 1999. 
Table B7 Annual acre-feet, selenium concentrations, and selenium loads measured at the San 

Joaquin River near Vernalis. Water-year million acre-feet/year ppb Se (total) lbs Se/year concentration range 1986 5.22 1.0 14,601 <0.1-1.4 (17?)1987 1.81 1.8 8,502 0.6-3.21988 1.17 2.7 8,427 0.8-4.01989 1.06 3.0 8,741 1.7-6.81990 0.92 3.0 7,472 0.8-9.61991 0.66 2.0 3,611 0.5-4.81992 0.70 1.9 3,558 0.4-4.41993 1.70 1.9 8,905 <0.4-6.11994 1.22 2.3 7,760 0.4-6.31995 6.30 1.0 17,238 0.5-3.51996 3.95 1.1 11,4311997 6.77 0.6 11,1901998 8.5 15,810Total 127,246

average 9,788 lbs/year 

DATA: DATA: CCVRWQCB, 1996b; c; 1998d; e; f; g; h; 2000,b; c; USBR et al., 1998, 1999. 
Table B8 San Luis Drain Re-use Project/Grassland Bypass Channel Project (1997-2001) 

Use of San Luis Drain by Grassland Area Farmers (Grassland subarea Zone A) to discharge selenium to the San Joaquin River 

problem acreage 

Measured problem acrefeet or discharge 

Measured ppb Se 

lbs Se/year Calc

lbs/albs/a

CCVRWQCB prohibition limitation of Se discharge to the San Joaquin River or tributaries from tile or open drainage systems (effective October 1, 1996; CVRWQCB, 1996a; d) 

8,000 

WY 1997-2001 San Luis Drain /Grassland Bypass Channel Project negotiated annual load target for discharge through the San Luis Drain to the San Joaquin River (USBR, 1995) 

93,400 5,661-6,660 0.06

WY 1997 San Luis Drain /Grassland Bypass Channel Project measured load **** discharged through the drain to the San Joaquin River (USBR et al., 1998) 

97,400 37,483 62.5 6,960 0.07

0.18

January 26, 1997 estimated load from Coast Range runoff discharged through the drain (Grassland Area Farmers, 1997) 

137 

WY 1998 San Luis Drain /Grassland Bypass Channel Project measured load discharged through the drain to the San Joaquin River (USBR et al., 1999) 

97,400 45,858 66.9 9,118 0.09

0.19

February, 1998 estimated load from Coast Range runoff discharged through the drain (Grassland Area Farmers, 1997) 

487 
Table B9 San Luis Drain Re-use Project/Grassland Bypass Channel Project WY 1997 Average Monthly Drainage Volumes and Selenium 

Concentrations, Annual Discharge, and Load Targets (USBR et al., 1998). WY 1997 Measured acre-feet (AF) Measured 

Se (ppb) (total) 

Calculated Se (lbs) 

Negotiated Se (lbs target) 

Incentive fee ($) 

Sept. 23-30,1996 [55 (est.)] * see Sept, 1997 October 1,274 60.8 (58.6) 202 348 0 November 1,566 58.3 252 348 0 December 1,943 51.5 285 389 0 January, 1997 3,696 59.5 599** 533 2,800 February 4,166 76.6 878** 866 700 March 4,867 84.2 1119 1066 700 April 4,446 105.5 1280 799 2,800 May 4,208 75.7 849 666 2,800 June 3,451 64.3 611 599 700 July 3,271 48.1 428 599 0 August 3,153 40.6 348 533 0 Sept, 1-30, 1997 1,442 25.3 109 350 0 Total (monthly) 37,483 6,960 7,096 (monthly) 10,500Total (yearly) 37,483 62.5 (average) 6,960 6,660 (yearly) 50,000 WY 1997 storm discharge (lower watershed, Agatha Canal) 

 137** 

Total (project plus storm discharge) 7,097 $60,500* not counted in total; ** 89 lbs Se in January and 48 lbs Se in February discharged to wetland sloughs (Agatha Canal) during SLD overf

 due to storms in January and February, 1998. 
Table B10 San Luis Drain Re-use Project/Grassland Bypass Channel Project WY 1998 Average Monthly Drainage Volumes and Seleniu

Concentrations, Annual Discharge, and Load Targets (USBR et al., 1999) WY 1998 Measured acre-feet (AF) Measured 

Se (ppb) (total) 

Calculated Se (lbs) 

Negotiated Se (lbs target) 

Incentive fees ($) 

October, 1997 1,753 51.9 248 348 0November 1,555 48.9 207 348 0December 1,403 48.7 178 389 0January, 1998 1,419 85.0 335 533 0February 6,980 52.5 965* 866 4,200**March 7,094 83.3 1600 1066 4,200**April 5,517 105.4 1554 (1560) 799 4,200**May 4,881 104.5 1371 666 4,200**June 3,629 82.1 807 599 4,200**July 4,564 49.7 615 599 1200August 3,876 47.5 500 533 0September 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) 150,000*WY 1998 storm discharge (lower watershed, Agatha Canal)) 350* Total (project plus storm discharge) 9,118 174,400 

(3,400 pa

*350 lbs Se discharged to wetland sloughs (Agatha Canal) during SLD overflow events due to storms in February, 1998; fees waived bec

above average rainfall for WY 1998. 
Table B11 Acreage used for planning purposes in 

1985-1990 by the SJVDP (SJVDP, 1989, Table 1-1) Subarea SJVDP

Acreage 

SJVDP irrigable* acreage 

SJVDP irrigated* acreage 

SJVDP drained acreage 

Northern 236,000 165,000 157,000 26,000Grassland* 707,000 345,000 311,000** 51,000Westlands 770,000 640,000 576,000 5,000 Tulare 883,000 562,000 506,000** 42,000Kern 1,210,000 762,000 686,000 11,000Total 3,806,000 2,474,000 2,235,000 135,000* A factor of 90 to 95% was used to calculate irrigated acres from irrigable acres (SJVDP, 1990a, Table 11; ** SJVDP, 1990a, Table 11, Grassland subarea 329,000 acres; Tulare subarea 551,000 acres. 
Table B12 The SJVDP 1990 and year 2000 irrigated acreage, abandoned acreage, problem acreage and cost for problem water reduction 

recommended SJVDP Management Plan (1990a). The “without future” (i.e., no implementation of a management plan) includes abandsalinization. 

Subarea SJVDP

1990 irrigated 

acreage** 

SJVDP 2000 irrigated acreage** without future

SJVDP 2000 abandoned acreage** without future

SJVDP 2000 problem acreage*** without future

SJVDP problem water generation acre-feet/acre   

SJVDP 2000 problem  acre-feet ** *** 

SJVDP 2040 problem  acre-feet ***** 

SJVDP annualicost/acrfor probwater reductio****** 

Northern 157,000 152,000 0 34,000 0.70-0.75 26,000 38,000 --- Grassland* 329,000 325,000 0 116,000 0,70-0.75 86,000 155,000 $107 Westlands 576,000 551,000 28,000 108,000 0.60 81,000 153,000 $136 Tulare 551,000 517,000 38,000 125,000 0.70-0.75 75,000 209,000 $104 Kern 686,000 665,000 18,000 61,000 0.71 46,000 111,000 $137 Total 2,299,000 2,210,000 84,000 444,000 314,000 666,000 * Grassland subarea total acreage is 707,000 with 329,000 irrigated acres (90% of irrigable lands) and the Grassland Area/Drainage Prob

approximately 100,000 acres; ** SJVDP Table 11; *** SJVDP Table 9;   SJVDP page 76;** *** SJVDP Table 10; ****** 50 year year 2000 problem acreage SJVDP pages 5, 143, 148, 153, and 156 (approximately $42, 000,000, page 5); cost/acre includes the cost of 
Table B13 The SJVDP 1990, 2000, and 2040 volumes of drainage with no drainage improvement (0.75 acre-feet/acre/year) or minimal 

improvement (0.55 acre-feet/acre/year) (SJVDP, 1990a). The conditions without implementation of SJVDP management plan is designa

as the “without future” alternative and includes abandonment of lands due to salinization. An additional calculation is made for Westlan “upslope” contributions to the tile drained acreage from non-tile drained acreage (CSWRCB, 1985). 

Subarea SJVDP 1990 

 tile-drained acres * 

factor AF/ acre/ year 

SJVDP 1990 drainage volumes (acrefeet)** 

SJVDP 2000 tile-drained  acres without  future*

factor AF/ acre/ year 

SJVDP 2000 drainage volumes (acrefeet) without  future** 

SJVDP 2040  tile-drained  acres without  future* 

factor AF/ acre/ year 

Northern 24,000 0.75 18,000 34,000 --*** 26,000 51,000 0.75 Grassland 50,000 0.75 38,000 85,000 -- 54,000 152,000 0.55 Westlands 5,000 0.75 4,000 50,000 -- 28,000 49,000 0.55 Westlands 42,000***** 0.75 31,500***** -- --Tulare 43,000 0.60 32,000 86,000 -- 47,000 94,000 0.55 Kern 11,000 0.75 8,000 14,000 -- 8,000 40,000 0.55 Total 133,000 100,000 269,000 -- 163,000 386,000 * SJVDP Table 11; ** SJVDP Table13; *** no factor given by SJVDP, Table 13;   In SJVDP Table 13 the values are 37,000 and 10** *** not included in total 
Table B14 Calculated volume of drainage using a drainage improvement factor of 0.40 acre-feet/acre/year (SJVDP, 1990a). The alterna

Implementation of the SJVDP management plan is designated by the SJVDP as the “with future” alternative. An additional calculation i

Westlands based on “upslope” contributions to the tile drained acreage from non-tile drained acreage (CSWRCB, 1985). 

Subarea SJVDP 1990 

 tile-drained acres** 

factor AF/ acre/ year***

Calculated 1990 drainage volumes (acre-feet) with future 

SJVDP2000  tile-drained acres with future** 

factor AF/ acre/ year *** 

Calculated 2000 drainage volumes (acre-feet) with future 

SJVDP2040  tile-drained acres with future** 

factor AF/ acre/ year *** 

Northern* 24,000 0.40 9,600 34,000 0.40 13,600 44,000 0.40 Grassland 50,000 0.40 20,000 108,000 0.40 43,200 192,000 0.40 Westlands 5,000 0.40 2,000 69,000 0.40 27,600 140,000 0.40 Westlands 42,000**** 0.40 16,800**** Tulare 43,000 0.40 17,200 96,000 0.40 38,400 277,000 0.40 Kern 11,000 0.40 4,400 53,000 0.40 21,200 106,000 0.40 Total 133,000 53,200 360,000 144,000 759,000 * No management plan recommended for Northern subarea; **SJVDP Table 27; *** factor applied from SJVDP Table 26; **** not incl
Table B15a Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Program problem wate

(“without future” alternative, 0.60 to 0.75 acre-feet/acre/year; SJVDP, 1990a) and a 50-ppb Se concentration in drainage discharge. Subarea SJVDP 2000 

problem acreage* 

SJVDP problem water generation acre-feet/acre/ year** 

SJVDP 2000 problem acre-feet *** 

Projected ppb Se 

Projected lbs Se/year 

Calculated lbs Se/acre 

Northern 34,000 0.70-0.75 26,000 50 3,536 0.1 Grassland 116,000 0,70-0.75 86,000 50 11,696 0.1 Westlands 108,000 0.70- 0.75 81,000 50 11,016 0.1 Tulare 125,000 0.60 75,000 50 10,200 0.08 Kern 61,000 0.70-0.75 46,000 50 6,256 0.1 Total 444,000 0.71 314,000 50 42,704 0.096 * SJVDP Table 9; ** SJVDP page 76 and *** SJVDP Table 10 Table B15b Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Program problem wat

(“without future” alternative, 0.60 to 0.75 acre-feet/acre/year; SJVDP, 1990a) and a 150-ppb Se concentration in drainage discharge. 

Subarea SJVDP 2000

problem acreage* 

SJVDP problem water generation acre-feet/acre/ year** 

SJVDP 2000 problem acre-feet*** 

Projected ppb Se 

Projected lbs Se/year 

Calculated lbs Se/acre 

Northern 34,000 0.70-0.75 26,000 150 10,608 0.31 Grassland 116,000 0,70-0.75 86,000 150 35,088 0.31 Westlands 108,000 0.70- 0.75 81,000 150 33,048 0.31 Tulare 125,000 0.60 75,000 150 30,600 0.24 Kern 61,000 0.70-0.75 46,000 150 18,768 0.31 Total 444,000 0.71 314,000 150 128,112 0.29 * SJVDP Table 9; ** SJVDP page 76 and *** SJVDP Table 10 Table B15c Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Program problem wat

(“without future” alternative, 0.60 to 0.75 acre-feet/acre/year; SJVDP, 1990a) and a 300-ppb Se concentration in drainage discharge. 

Subarea SJVDP 2000

problem acreage* 

SJVDP problem water generation acre-feet/acre/ year** 

SJVDP 2000 problem acre-feet*** 

Projected ppb Se 

Projected lbs Se/year 

Calculated lbs Se/acre 

Northern 34,000 0.70-0.75 26,000 300 21,216 0.31 Grassland 116,000 0,70-0.75 86,000 300 70,176 0.31 Westlands 108,000 0.70- 0.75 81,000 300 66,096 0.31 Tulare 125,000 0.60 75,000 300 61,200 0.24 Kern 61,000 0.70-0.75 46,000 300 37,536 0.31 Total 444,000 0.71 314,000 300 256,224 0.29 * SJVDP Table 9; ** SJVDP page 76 and *** SJVDP Table 10 
Table B16a Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Program subsurfac

drainage volumes (“without future” alternative, 0.60 to 0.75 acre-feet/acre/year; SJVDP, 1990a) and Se concentrations of 50, 150, anSubarea SJVDP 2000

drained acreage without future * 

SJVDP 2000 subsurface drainage volume (acre-feet) without future** 

Projected ppb Se 

Projected lbs Se/year 

Projected ppb Se 

Projected lbs Se/year 

Projected ppb Se 

Plb

Northern 34,000 26,000 50 3,536 150 10,608 300 2Grassland 85,000 54,000 50 7,344 150 22,032 300 4Westlands 50,000 28,000 50 3,808 150 11,424 300 2Tulare 86,000 47,000 50 6,392 150 19,176 300 3Kern 14,000 8,000 50 1,088 150 3,264 300 6Total 269,000 163,000 50 22,168 150 66,504 300 1* SJVDP Table 11; ** SJVDP Table 13. Table B16b Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Program subsurface 

drainage volumes (“with future” alternative, 0.40 acre-feet/acre/year; SJVDP, 1990a) and Se concentrations of 50, 150, and 300 ppb. 

Subarea SJVDP 2000

drained acreage with future * 

SJVDP 2000 subsurface drainage volume (acre-feet) with future** 

Projected ppb Se 

Projected lbs Se/year 

Projected ppb Se 

Projected lbs Se/year 

Projected ppb Se 

Plb

Northern 34,000 13,600 50 1,850 150 5,549 300 1Grassland 108,000 43,200 50 5,875 150 17,625 300 3Westlands 69,000 27,600 50 3,754 150 11,261 300 2Tulare 96,000 38,400 50 5,222 150 15,667 300 3Kern 53,000 21,200 50 2,883 150 8,650 300 1Total 360,000 144,000 50 19,584 150 58,752 300 1* SJVDP Table 11; ** SJVDP Table 13. Table B16c Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Program subsurface 

drainage volumes, our “with targeted future” alternative (0.20 acre-feet/acre/year; SJVDP, 1990a), and Se concentrations of 50, 150, 

Subarea SJVDP 2000

drained acreage with future * 

SJVDP 2000 subsurface drainage volume (acre-feet) with targeted future** 

Projected ppb Se 

Projected lbs Se/year 

Projected ppb Se 

Projected lbs Se/year 

Projected ppb Se 

Plb

Northern 34,000 6,800 50 925 150 2,774 300 5Grassland 108,000 21,600 50 2,938 150 8,813 300 1Westlands 69,000 13,800 50 1,877 150 5,630 300 1Tulare 96,000 19,200 50 2,611 150 7,834 300 1Kern 53,000 10,600 50 1,442 150 4,325 300 8Total 360,000 72,000 50 9,793 150 29,376 300 5* SJVDP Table 11; ** applied factor of 0.20 acre-feet/acre 
Table B17 Our projections of annual selenium loading for subareas for year 2000 using Se concentrations of 50 ppb, 150 ppb, and 300 p

 water “ without future” alternative, of drainage volumes in the “without future” alternative and in the “with future” alternative (SJVD

 future” alternative, we applied a factor of 0.2 acre-feet/acre/year. 

Subarea 1990

subsurface drainage acre-feet/ year 

ppb Se 

lbs Se/ year 

projected 2000 problem wateracre-feet/ year* 

ppb Se 

lbs Se/ year 

projected 2000 drainage acre-feet/yearwithout  future** 

ppb Se 

lbs Se/ year 

projected 2000 drainage acre-feet/yearwith  future*** 

ppb Se 

lbs Seyear 

Northern* 18,000 50 2,448 26,000 50 3,536 26,000 50 3,536 13,600 50 1,850 Grassland 38,000 50 5,168 86,000 50 11,696 54,000 50 7,344 43,200 50 5,875 Westlands 4,000 50 544 81,000 50 11,016 28,000 50 3,808 27,600 50 3,754 Tulare 32,000 50 4,352 75,000 50 10,200 47,000 50 6,392 38,400 50 5,222 Kern 8,000 50 1,088 46,000 50 6,256 8,000 50 1,088 21,200 50 2,883 Total 100,000 13,600 314,000 42,704 163,000 22,168 144,000 19,58Subarea 1990

subsurface drainage acre-feet/ year 

ppb Se 

lbs Se/ year 

projected 2000 problem wateracre-feet/ year* 

ppb Se 

lbs Se/ year 

projected 2000 drainage acre-feet/yearwithout  future** 

ppb Se 

lbs Se/ year 

projected 2000 drainage acre-feet/yearwith  future*** 

ppb Se 

lbs Seyear 

Northern* 18,000 150 7,344 26,000 150 10,608 26,000 150 10,608 13,600 150 5,549 Grassland 38,000 150 15,504 86,000 150 35,088 54,000 150 22,032 43,200 150 17,625 Westlands 4,000 150 1,632 81,000 150 33,048 28,000 150 11,424 27,600 150 11,260 Tulare 32,000 150 13,056 75,000 150 30,600 47,000 150 19,176 38,400 150 15,667 Kern 8,000 150 3,264 46,000 150 18,768 8,000 150 3,264 21,200 150 8,650 Total 100,000 40,800 314,000 128,112 163,000 66,504 144,000 58,75Subarea 1990

subsurface drainage acre-feet/ year 

ppb Se 

lbs Se/ year 

projected 2000 problem water acre-feet/ year* 

ppb Se 

lbs Se/ year 

projected 2000 drainage acre-feet/yearwithout  future** 

ppb Se 

lbs Se/ year 

projected 2000 drainage acre-feet/yearwith  future*** 

ppb Se 

lbs Seyear 

Northern* 18,000 300 14,688 26,000 300 21,216 26,000 300 21,216 13,600 300 11,098 Grassland 38,000 300 31,008 86,000 300 70.176 54,000 300 44,064 43,200 300 35,25Westlands 4,000 300 3,264 81,000 300 66,096 28,000 300 22,848 27,600 300 22,522 Tulare 32,000 300 26,112 75,000 300 61,200 47,000 300 38,352 38,400 300 31,334 Kern 8,000 300 6.528 46,000 300 37,536 8,000 300 6,528 21,200 300 17,299 Total 100,000 81,600 314,000 256,224 163,000 133,008 144,000 117,50*SJVDP Table 10; ** SJVDP Table 13; *** see calculation this report Table – (SJVDP Table 27 acreage with factor applied from SJVD

Table 15. 
Table B18 Summary of our projections of annual selenium loads for SJVDP subareas for year 2000. Scenarios 1, 2, 3: assigned selenium 

of 50, 150, 300 ppb Se and SJVDP estimates of drainage volume (SJVDP, 1990a). Subarea acre-feet/year

Assigned concentration 50 ppb (0.136 lbs Se/acre-foot) (lbs Se/year) 

Assigned concentration 150 ppb (0.408 lbs Se/acre-foot) (lbs Se/year) 

Assigned concentra300 ppb (0.817 lbs S(lbs Se/year) 

Northern 6,800 13,600 26,000 

925 1,850 3,536 

2,774 5,549 10,608 

5,549 11,098 21,216 

Grassland 21,600 43,200 54,000 86,000 

2,938 5,875 7,344 11,696 

8,813 17,625 22,032 35,088 

17,626 35,251 44,064 70,176 

Westlands 13,800 27,600 28,000 81,000 

1,877 3,754 3,808 11,016 

5,630 11,260 11,424 33,048 

11,261 22,522 22,848 66,096 

Tulare 19,200 8,400 47,000 75,000 

2,611 5,222 6,392 10,200 

7,834 15,667 19,176 30,600 

15,667 31,334 38,382 61,200 

Kern 8,000 10,600 21,200 46,000 

1,088 1,442 2,883 6,256 

3,264 4,325 8,650 18,768 

6,528 8,650 17,299 37,536 

Total drainage/year, all subareas Range 69,400 to 314,000 acre-feet Total lbs Se/year Minimum lbs, all subareas Minimum lbs without Northern Maximum lbs, all subareas Maximum lbs, without Northern

9,284 8,367 42,704 39,168 

27,847 25,073 128,112 117,504 

55,652 50,103 256,224 235,008 
Table B19 Tulare subarea 1988-1989 drainage discharges and selenium concentrations. 

Discharge to 21 privately owned evaporation basins 1988 and 1989* 

Drainage acre-feet/year 

ppb Se (measurement or range) 

lbs Se/year 

1988 TOTAL/YEAR TLDD (Total)  north  hacienda  south Westlake Meyer Stone Britz Others 

14,294 

2.6 -- 30 1-1.1 1 1.6-4.3 -- 9.6-757 

1989 TOTAL/YEAR TLDD (Total)  north  hacienda  south Westlake Meyer Stone Britz Others 

13,705 

2.0 --- 21 0.4-6.5 0.8 2.3-7.4 --- 1.0-62 

*Discharge data from CCVRWQCB, pers. com., Anthony Toto, 1998; Se concentration data from Water Quality in Evaporation Basins Used for the Disposal of Agricultural Subsurface Drainage Water in the San Joaquin Valley, California, 1988 and 1989 (CCVRWQCB, 1990a). 
Table B20 Tulare subarea 1993-1997 drainage discharges and selenium concentrations. 

Discharge to privately owned evaporation 

basins 1993-1997* 

Drainage 

acre-feet/year 

 ppb Se 

(measurement or range) 

lbs Se/year 

1993 TOTAL/YEAR 

TLDD** (Total) 

 north 

 hacienda 

 south 

Westlake 

Meyer 

Stone 

Britz 

17,899-18,955 

12,497 (net)***; 13,553 (gross) 

4,309 

-- 

 1,093 

-- 

1.9 avg 

 1.4 

 2.1 

 2.0 

 1.3 

-- 

 3.6 

124 

91-97 

65-71 

15 

-- 

10.7 

-- 

1994 TOTAL/YEAR 

TLDD** (Total) 

 north 

 hacienda 

 south 

Westlake 

Meyer 

Stone 

Britz 

19,468 

14,601 

1,432 

4,226 

8,943 

3,478 

-- 

 1,213 

 186 

1.8 

---- 

12.6 

1.2 

-- 

 3.7 

15-50 

7.0 

306 

11.6 

-- 

12.2 

7.6-25.3 

1995 TOTAL/YEAR 

TLDD** (Total) 

 north 

 hacienda 

 south 

Westlake 

Meyer 

Stone 

Britz 

20,403 

14,751 

1,373 

4,754 

8,624 

3,478 

 327 

 1,665 

 182 

2.5 

13.2 

12.0 

2.25 avg 

 0.76 

 2.4 

15-50 

494-519 

461 

 9.3 

171 

281 

 21 

 0.7 

10.9 

7.4-25 

1996 TOTAL/YEAR 

TLDD** (Total) 

 north 

 hacienda 

 south 

Westlake 

Meyer 

Stone 

Britz 

19,160 

13,676 

918 

4,515 

8,243 

5,152 

 332 

-- 

-- 

2.5 

--- 

8.3 

---- 

 0.99 

-- 

-- 

6.2 

186 

-- 

 0.894 

-- 

-- 

1997 TOTAL/ Water year

 TLDD** (Total) 

 north 

 hacienda 

 south 

Westlake 

Meyer 

Stone 

Britz 

20,005 

15,605 

1,199 

 5,238 

 9,168 

 4,400 

-- 

-- 

-- 

 2.1/1.8**** 

---/5.9 

13.6/6.0 

2.27 avg 

-- 

-- 

-- 

252-442 

240-430 

6.8-5.9 

84 

339-150 

12 

-- 

-- 

-- 

* 1993-1997data from CCVRWQCB, pers. com. Anthony Toto, 1998; ** Tulare Lake Drainage District*** net=gross 

minus interceptor seepage; **** two samplings for WY 1997, June and September, 1997.
Table B21 Kern subarea 1988-1997 drainage discharges and selenium concentrations. 

Kern Subarea Discharge to privately owned evaporation basins 1988, 1989, 1993-1997* 

Drainage acre-feet/year 

ppb Se lbs Se/year 

1988 TOTAL/YEAR Lost Hills Water District Rainbow Ranch Lost Hills Ranch 

2,452 142 

--- 2.4 

947 

1989 TOTAL/YEAR Lost Hills Water District Rainbow Ranch Loast Hills Ranch 

3,831 83-671 

212 2.1 

865-6,992 

1993 TOTAL/YEAR Lost Hills Water District Rainbow Ranch 

2,467 1,854  613 

220 190 

1,426 1109  317 

1994 TOTAL/YEAR Lost Hills Water District Rainbow Ranch 

2,318 1,739  579 

208 405 

1,586  948  638 

1995 TOTAL/YEAR Lost Hills Water District Rainbow Ranch 

2,237 1,549  688 

240 213 

1,410 1011  399 

1996 TOTAL/YEAR Lost Hills Water District Rainbow Ranch 

2,365 1,501  864 

238 185 

1,407  972  435 

1997 TOTAL/YEAR Lost Hills Water District Rainbow Ranch 

2,072 1,620  452 

195 187 

1,089  859  230 

* Data from CCVRWQCB, pers. com. Anthony Toto, 1998, except for selenium concentrations for 1988 and 1989 which are 

 from WaterQuality in Evaporation Basins Used for the Disposal of Agricultural Subsurface Drainage Water in the San  Joaquin Valley, California, 1988 and 1989 (CCVRWQCB, 1990). 
Table B22 Planned capacity of the San Luis Drain or Valley-Wide Drain. Loading scenarios use 

assigned selenium concentrations of 50 ppb, 150, ppb, and 300 ppb. San Luis Drain Design Capacity @ 50 ppb 

lbs Se/year 

@ 150 ppb lbs Se/year 

@ 300 ppb lbs Se/year 

300 cfs or 216,810 acre-feet/year (USBR, 1955) planned capacity Bakersfield to Mendota section 

29,486 88,458 176,917

450 cfs or 325,215 acre-feet/year (USBR, 1955) planned capacity Kesterson Reservoir to Bay/Delta section 

44,229 132,688 265,375

144,200 acre-feet/year (USBR, 1950’s, initially needed) 

19,611 58,834 117,667

after 50 years 154,100 acre-feet/year, maximum (range 3,100 to 154,100 acre-feet/year (USBR, 1978) 

20,958 62,873 125,746

after 25 years 201,025 acre-feet/year (range 84,525 to 279,270 acre-feet/year (USBR, 1983) 

27,339 82,018 164,036

Barcellos Judgment 60,000 to 100,000 acrefeet/year (USBR,1992) 8,160- 13,600 24,480- 40,800 48,960- 81,600 Westland Water District 60,000 acre-feet/year 8,160 24,480 48,960 375,000 acre-feet/year (400,000-500,000 acrefeet/year needed capacity) (San Francisco Ocean Out-fall, Montgomery Watson, 1993) 

51,000 153,000 306,000
Table B23a San Joaquin Valley Drainage Program generalized projected annual selenium discharge from the western San Joaquin Valle

extension to the Bay/Delta. A selenium concentration of 50 ppb Se was hypothesized to be attainable with treatment; a concentration of 

subsurface drainage. 

San Joaquin Valley acre-feet (all subareas) 

lbs Se/ year kestersons*/year 

(ksts/year) 

lbs Se/day Se Concentration 

ppb 

314,000 (problem water at 50 ppb Se) 

42,704 2.45 117 50 

144,000-163,000 (subsurface drainage at 150 ppb Se) 

58,752-66,504 3.4-3.8 161-182 150 

Table 23b Projected low-range annual selenium discharges from the western San Joaquin Valley to a San Luis Drain extension to the SaSan Joaquin Valley Subarea 

lbs Se/ year kestersons*/year 

(ksts/year) 

lbs Se/day Se Concentration 

ppb 

Northern 350 0.02 0.95 5 Grassland 6,960 0.40 19 68 Westlands 8,000 0.46 22 49 Tulare 91 0.005 0.25 1.7 Kern 1,089 0.062 3.0 175 TOTAL 16,490 0.95 45.2Table 23c Projected high-range annual selenium discharges from the western San Joaquin Valley to a San Luis Drain extension to the SaSan Joaquin Valley Subarea 

lbs Se/ year kestersons*/year 

(ksts/year) 

lbs Se/day Se Concentration 

ppb 

Northern 700 0.04 1.9 10 Grassland 15,500 0.89 42 152 Westlands 24,480 1.4 67 150 Tulare 519 0.03 1.4 9.8 Kern 1,586 0.09 4.3 254 TOTAL 42,785 2.46 117*one kesterson = 17,400 lbs Se 
APPENDIX C 

Agricultural Drainage Discharge to the San Joaquin River 

 
APPENDIX C 

Agricultural Drainage Discharge to the San Joaquin River 

CONTENTS 

Models of Discharge to the San Joaquin River 2 

Models that Target Load Reduction.....................................................................................................3 

Models that Maximize the Allowed Selenium Load by Targeting Concentration...............................6 

FIGURES 

C1. Number of selenium water quality exceedance months (U.S. EPA criteria) for the San Joaquin 

River at Crows Landing during WY 1986 through WY 1997. 

C2. Comparison of wet, dry, and critically dry years (TMDL model) for 5 μg/L, 4-day average, 1 out 

of 3 year exceedance inputs. 

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 inputs. 

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 inputs. 

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 inputs, b) 5 μg/L, monthly average, 1 out of 3 

year exceedance inputs, and c) 5 μg/L, 4-day average, 1 out of 5 month exceedance inputs. 

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 inputs, b) 5 μg/L, monthly average, 1 out 

of 3 year exceedance inputs, and c) 5 μg/L, 4-day average, 1 out of 5 month exceedance inputs. 

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 inputs, b) 5 μg/L, monthly average, 1 out 

of 3 year exceedance inputs, and c) 5 μg/L, 4-day average, 1 out of 5 month exceedance inputs. 

C8. TMML model projection at Crows Landing for 8 μg/L and 1 out of 3 year exceedance inputs. 

C9. Comparison of TMML model projections during a dry year at Crows Landing for a) 5 μg/L and 

4-day average inputs, and b) 5 μg/L and monthly mean inputs. 

C10. Comparison of TMML model projections during a wet year at Crows Landing for a) 5 μg/L, 

monthly average, and 1 out 3 years exceedance inputs, and b) 5 μg/L, 4-day average, and 1 out of 

3 year exceedance inputs. 

C11. Monthly selenium loads for a dynamic real time model during a wet year using a 5 μg/L input. 

TABLES 

 1 Appendix C 
C1. Modeled Selenium Load Allocation and Discharge to the San Joaquin River from the Grassland 

Drainage Problem Area. 

C2. Modeled (TMDL, Total Maximum Daily Load model) Annual Selenium Load Allowance to the 

San Joaquin River from the Grassland Area.

C3. Modeled (TMML model, Total Maximum Monthly Load model and DRT model, Dynamic RealTime model) Annual Selenium Load Allowance to the San Joaquin River from the Grassland 

Area. 

APPENDIX C 

Agricultural Drainage Discharge to the San Joaquin River 

Models of Discharge to the San Joaquin River 

In 1991 and 1992, the state acknowledged continuing elevated levels of Se in the SJR and parts 

of the Bay-Delta by declaring the lower 130-mile reach of the SJR a water-quality limited segment

(e.g., CCVRWQCB, 1994a; 1998b) and the Se levels in the bay of concern (CSFBRWQCB, 1992a). 

Discharge of Se to the SJR has continued based on an agreement to implement a regulatory control 

program for Se discharges started the year that Kesterson Reservoir was buried (CSWRCB, 1985 and 

1987). Figure C1 shows the number of months per year that the USEPA 5 μg Se/L Se standard was 

violated at the state compliance point for the SJR as a receiving water (i.e., SJR at Crows Landing) 

from 1986 to 1997. The number of violations is based on a mean monthly average of a varying number 

of collected grab samples (CCVRWQCB, 1998d,e,f,g,h,). In 1999, the state placed the SJR and the 

entire San Francisco Bay on the high priority list in the Consolidated Toxic Hot Spot Cleanup Plan 

(CSWRCB, 1999c). Besides the USEPA promulgated Se standard for the protection of aquatic life, an 

annual prohibition limitation of 8,000 lbs Se exists as part of the state San Joaquin and Sacramento 

River Basin Plan since 1996 and waste discharge requirement for Se discharge to the SJR since 1998. 

Violations of this prohibition recently have occurred at the SJR at Crows Landing from WY 1995 

through WY 1998 when 14,291 lbs Se, 10,868 lbs Se, 8,667 lbs Se, and 13,445 lbs Se were discharged 

annually during those years. 

2

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 the water-quality impaired water 

bodies like the lower reach of the SJR. The TMDL approach allows a state to implement water-quality 

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 Se, both the existing record and developed 

models for the SJR have important limitations (Presser and Piper, 1998). The existing record of waterquality conditions in the SJR is inadequate to ascertain if progress is being made towards either 

limiting loading of Se, meeting the water-quality objectives, or protecting the SJR (Westcot, et al., 

1996; Presser and Piper, 1998). The models are conservative-element dilution models that have not 

considered the potential for Se to accumulate in sediment or bioaccumulate in biota (Environmental 

Defense Fund, 1994; Karkoski, 1996). The assimilative capacity for the SJR in existing models is 

defined only by flow (i.e., dilution capacity). In one derivation of the 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 the implementation issues for the agricultural dischargers would remain 

the same (Environmental Defense Fund, 1994). Implementation issues may include an economic 

justification of continued impairment of the SJR’s beneficial uses required by anti-degradation policies 

(Code of Federal Regulations 40:131.12; Clean Water Act Section 303(d) as amended, 1987). 

Hydrologic-economic models for the SJV and information regarding the cost/benefit of agriculture in 

the SJV have been developed and compiled at various stages of planning for irrigation and drainage 

projects (e.g., SJV Interagency Drainage Program, 1979a; b; CDWR, 1982; Horner, 1986; Willey, 

1990; Dinar and Zilberman, 1991; Environmental Defense Fund, 1994; CCVRWQCB, 1996c). 

Monthly Se concentrations greater than 5 μg/L have not occurred further downstream in the SJR at 

Vernalis, the entrance to the Bay-Delta. 

Models that Target Load Reduction

Models were constructed in 1994 to target the load of Se that might be discharged to the SJR with 

the goal of meeting a federal 5 μg Se/L concentration standard and a state 8 μg Se/L concentration 

objective. USEPA rejected the 8 μg Se/L objective for the SJR in 1992 and promulgated a 5 μg Se/L 

standard for the SJR and a 2 μg Se/L standard for associated wetland channels (i.e., 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 in conjunction with the state (CCVRWQCB, 1994b; Environmental Defense Fund, 1994). 

The Environmental Defense Fund model was a test case for agricultural non-point source pollution 

 3 Appendix C 
control that applies 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). The modified version of the 

TMDL model for the SJR was adopted as part of a waste discharge permit for the Grassland subarea in 

1998 (CCVRWQCB, 1998a). 

The choice of a compliance site for the models and the waste discharge permit has critical 

implications for the perception of water quality in the SJR. Little fresh water flows into the SJR 

upstream of Crows Landing due to regulation of the SJR by Friant Dam. Most of the SJR is diverted 

south through the Friant-Kern Canal, leaving agricultural drainage as the majority of the flow in the 

SJR heading north in the 22 miles of river above confluence with the Merced River. A compliance site 

upstream of the Merced River would be the most precautionary. It would closely reflect the quality of 

the drainage water and be indicative of conditions in the upstream 22 miles. Compliance at the site 

below the confluence with the Merced River is influenced by the dilution water provided by the 

Merced River. This site is probably more indicative of downstream water quality. The current 

compliance point is the SJR downstream the Merced River at Crows Landing. It represents the 130-

mile reach of the lower SJR that is listed as impaired. The state permit for discharge to the SJR allows 

for a twelve-year compliance schedule. Full compliance for the SJR above and below the Merced 

River to a Se water-quality objective of 5 μg/L (4-day average) is scheduled for October 2010. 

 Variables considered in deriving a Se load allocation from the TMDL-type models are: 

• water-year type, 

• water-quality objective, 

• averaging period, 

• exceedance frequency, and 

• flow derivation. 

 Table C1 and Figures C2, C3 and C4 give a summary of volume of discharge and loads to compare 

example load allocations from the TMDL and the TMML models for different types of water years. 

Figure C2 shows the TMDL model loads for all water-year types (normal/wet, dry/below normal, and 

critically dry) for the case of a 5 μg Se/L standard, 4-day average, and a one-in-three-year violation 

rate. Figure C3 shows a comparison of the TMDL and TMML model loads for a wet-year allocation 

under the same conditions as above. Figure C4 shows a comparison of the TMDL and TMML model 

4
loads for a dry-year allocation under the same conditions as above. Tables C2 and C3 and Figures C5 

through C10 document in more detail the load allocations for the SJR calculated from several different 

combinations of model assumptions using a Se water-quality objective of 8 or 5 μg/L. These data are 

compiled from documentation for the TMDL and TMML models (CCVRWQCB, 1994b and 

Environmental Defense Fund, 1994). 

The base case for the SJR TMDL was a single design flow of approximately 92,000 acre-feet at 5 

μg Se/L. The model allocated a load of 1,248 lbs Se (Table C2) (Environmental Defense Fund, 1994). 

The quasi-static type TMDL model has three water-year classifications for the SJR (critically dry, 

dry/below normal, and above normal/wet; Table C2 and Figures C5, C6, and 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, C9, and C10). Figures C5 

through 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 wateryears are replaced by wet-year 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 through C10). The TMDL model allows 

annual discharges to the SJR at Crows Landing/Patterson of 1,394 to 4,458 lbs Se in dry years (i.e., 

critically dry, dry, and below normal years – Table C1) within the ranges of options and excursion 

frequencies. The TMML allows discharges of 1,240 to 1,809 lbs Se/year in dry years. In wet years the 

TMDL model allows loads of 3,165 to 6,547 lbs Se/year and the TMML model predicts loads of 3,760 

to 5,334 lbs Se/year. 

 The Clean Water Act requires a margin of safety be considered in regulatory load models based 

solely on dilution. The purpose is to take into account any lack of knowledge concerning the relation 

of effluent limitations and water quality (Environmental Defense Fund, 1994). Tables C1, C2, and C3 

also show Se loads used as a nominal 10% margin of safety to account for the uncertainties in the data 

and as estimated background loads from tributary rivers and wetlands. The margin of safety ranges 

from 123 to 448 lbs Se/year in dry years and 317 to 534 lbs Se/year in wet years. Background loads 

range from 91 to 273 lbs Se/year in dry years and 250 to 428 lbs Se/year in wet years. These loads 

were added to the modeled TMDL allowances for the dischargers, thereby increasing the modeled 

discharge to the SJR at Crows Landing (Tables C1, C2, and C3), but leaving in doubt protection of the 

SJR. 

 5 Appendix C 
Models that Maximize the Allowed Selenium Load by Targeting Concentration

 An alternative approach is to define a concentration target in a receiving water and manage Se 

discharges to maintain that target concentration under different flow conditions. Such a model, 

designed to manage loads using dynamic drainage effluent limits based on the real-time dilution capacity of the SJR, was recently suggested as a drainage management tool (Karkoski, 1996; CSWRCB, 

1999a). In this proposal, Se-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 to the 5 μg Se/L 

objective. The dynamic real-time (DRT) model, thus, uses timed-release of Se-laden drainage to take 

maximum advantage of the dilution capacity of the river at the given water-quality objective (e.g., the 

Se concentration in the SJR will be maintained at 5 μg Se/L at all times). Figure C11 shows an 

example from limited data of the DRT model loads for wet-year conditions using a 5 μg Se/L objective 

(Karkoski, 1996). Table C1 compares the loadings allowed by the DRT model to those allocated by 

the TMDL and TMML models, for a minimum, mean, and maximum amount of allowable loads of Se 

discharged per month in a wet year. Figure C11 shows that an order-of-magnitude higher loads occurs 

in some months than allowed by the TMDL or TMML models (e.g., 400 versus 4000 lbs Se) for some

months. The DRT approach uses short-term forecasts of flow and salt concentration. The loads 

discharged for a wet year range from 2,605 to 17,605 lbs Se/year, with a mean of 7,347 lbs Se/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 Se/year) and a dry year value of 4,631 lbs Se/year (SJV Drainage 

Implementation Program, 1999b). With real-time drainage management, ponds for flow regulation 

would be necessary in order to maximize release of Se loads during variable flow conditions in the 

river. The holding pond concept is reminiscent of planning for the SLD in the 1970’s when Kesterson 

Reservoir ponds were to be used as holding reservoirs to regulate flows until the SLD 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 the load model target was the intended use of the concentration-dependent water-quality 

standards defined by USEPA. The DRT approach uses a receiving water body’s capacity to provide 

6
dilution water to maximize disposal of Se. 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 longterm progress toward Se load reduction. The focus of the TMDL and TMML models is to reduce or 

minimize Se loads by establishing a load target. With real-time drainage management, the focus is 

shifted to a concentration target that, in essence, maximizes Se loads by adjusting the timing of 

discharges to coincide with dilution capacity. As a result the allowed Se load would increase over 

those allocated by the TMDL or TMML models. The DRT approach is best applied to maintaining the 

designated level of quality in the SJR as a receiving water. It is of less value in regulating the SJR as a 

source water for the Bay-Delta. 

Some additional practical considerations add complexity to applying the DRT concept. These 

include the fact that a regulatory authority for the responsibility of implementing real time regulation 

has not been identified. Uncertainty exists about the regulatory control program that would determine 

the target concentration. Different agencies and stakeholders have called for revisions of the Se 

objective upward from 5 μg Se/L, upward to 8 μg Se/L, or downward to 2 μg Se/L. The choice of a 

compliance point (SJR at Patterson or Crows Landing or SLD at Mud Slough) will have a strong 

influence on objectives, and therefore, it is also critical to determining the allowed load (as described 

above). Uncertainties about the use of the conveyance channel for the drainage (wetland channels or 

the SLD) could have implications for concentrations. Since agricultural drainage is regulated as nonpoint source pollution, a 5 μg Se/L effluent stream from the discharger has not been required in the 

past. It is unclear how this would be integrated into the regulatory control program. Finally, 

refinement of the assimilative capacity operations plan using real-time management does not include 

collecting data to assess whether re-defining the assimilative capacity of the SJR based on the 

bioaccumulative nature of Se is necessary (GAF, 1998a). Understanding the sources of Se and how Se 

moves through the agricultural discharge system becomes very 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 SJR 

has been to meet the salinity standard for the SJR at Vernalis (CSWRCB, 1994, 1997, and 1999a; EA 

Engineering, Science, and Technology, 1999). The state model predicted that controlled timing or 

wetland releases or a combination of drainage and wetland releases did not obtain 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 

 7 Appendix C 
of drainage release to the SJR also includes implementation of a system of storage including recycling 

facilities, evaporation ponds, and in-field subsurface storage (CSWRCB, 1997). Despite the several 

opportunities for manipulating the massively engineered CVP water supply, the ultimate alternative for 

salinity control seems to depend on managing the same lands that need drainage and that discharge Se, 

but the state plan does not include an analysis of Se impacts. 

8
0

1

2

3

4

5

6

7

8

9

10

11

12

NO. OF MONTHS

86 87 88 89 90 91 92 93 94 95 96 97

WATER YEAR

Exceedance months Se water quality

U.S. EPA criteria, SJR@Crows Landing

Figure C1
0

5000

10000

15000

20000

25000

30000

35000

SJR @ Crows L., (ac-ft)

0

100

200

300

400

500

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT Se (lbs) ACRE-FT Se (lbs) ACRE-FT Se (lbs) 

Comparison of Wet, Dry, Critically Dry

Years, 5 ppb Se, 4 Day average,1/3 yr

Normal/Wet

Dry/Below Normal

Critically dry

Figure C2
0

5000

10000

15000

20000

25000

30000

35000

SJR flow @ Crows L., (ac-ft)

0

50

100

150

200

250

300

350

400

450

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT Se (lbs) ACRE-FT Se (lbs) 

Comparison of TMDL & TMML - Wet Year

5 ppb Se, 4 day average, 1/3 year

Normal/Wet

Wet

Figure C3
0

5000

10000

15000

20000

25000

30000

SJR @ Crows L., (ac-ft)

0

100

200

300

400

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT Se (lbs) ACRE-FT Se (lbs) ACRE-FT Se (lbs)

Comparison of TMML & TMDL - Dry

5 ppb Se, 4 Day average, 1/3 yr

Dry

Critically Dry

Dry/Below Normal

Figure C4
0

5000

10000

15000

20000

25000

30000

SJR@Crows L., (ac-ft)

0

50

100

150

200

250

300

350

400

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT ACRE-FT ACRE-FT

Se (lbs) Se (lbs) Se (lbs)

TMDL-SJR@CL/CRITICALLY DRY YEARS

Goal - 5 ppb

4 day, 1/5 month

Annual Load

SJR @Crows Landing

=3,546 lbs Se

=260,859 Acre feet

Monthly Avg, 1/3 yr

Annual Load

SJR@Crows Landing

=1,994 lbs Se

=147,029 Acre feet

4 day, 1/3 yr

Annual Load

SJR@Crows Landing

=1,415 lbs Se

=104,030 Acre feet

Figure C5
0

10000

20000

30000

40000

SJR @ Crows L., (ac-ft)

0

100

200

300

400

500

600

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT ACRE-FT ACRE-FT Se (lbs) Se (lbs) Se (lbs)

TMDL-SJR@CL-DRY/BELOW NORMAL YEARS

Goal - 5 μg/L

4day,1/5 month

Annual Load

SJR @Crows Landing

=4,454 lbs Se

=328,002 Acre-ft

4day,1/3yr

Annual Load

SJR@CrowsLanding

=3,069 lbs Se

=225,995 Acre-ft

Monthly Avg., 1/3 yr

Annual Load

SJR @ Crows Landing

=3,666 lbs Se

=270,000 Acre-ft

Figure C6
0

10000

20000

30000

40000

50000

60000

SJR@Crows L., (ac-ft)

0

100

200

300

400

500

600

700

800

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT ACRE-FT ACRE-FT

Se (lbs) Se (lbs) Se (lbs)

TMDL-SJR@CL-ABOVE NORMAL/WET YRS

Goal - 5 μg/L

4day, 1/3 yr

Annual Load

SJR@ Crows Landing

=3,166 lbs Se

=233,186 Acre-feet

Monthly Avg., 1/3 yr

Annual Load

SJR @ Crows Landing

= 4,061 lbs Se

=299,049 Acre-feet

4day, 1/5 month

Annual Load

SJR@Crows Landing

=6,549 lbs Se

=481,934 Acre-feet

Figure C7
0

2000

4000

6000

8000

10000

12000

14000

16000

SJR flow @ Crows L., (ac-ft)

0

50

100

150

200

250

300

350

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT Se(lbs)

TMML - MODEL DATA - DRY YEAR

Mean Monthly Performance Goal - 8μg/L

1/3 years

 Annual Discharge

 SJR @ Crows Landing

= 2,896 lbs Se

Figure C8
0

2000

4000

6000

8000

10000

12000

14000

16000

SJR flow @ Crows L., (ac-ft)

0

50

100

150

200

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT Se (lbs) ACRE-FT Se(lbs)

TMML - MODEL DATA - DRY YEAR

Goal - 5 μg/L

Monthly Avg., 1/3 yrs

Annual Discharge

SJR @Crows Landing

=1,809 lbs Se

=133,210 AF

4 day average, 1/3 yrs

Annual Discharge

SJR @ Crows Landing

=1,240 lbs Se

=91,255 AF

Figure C9
0

10000

20000

30000

40000

SJR flow @ Crows L., (ac-ft)

0

100

200

300

400

500

Se, lbs

1011 12 1 2 3 4 5 6 7 8 9

MONTH

ACRE-FT Se(lbs) ACRE-FT Se (lbs)

TMML - MODEL DATA - WET YEAR

Goal - 5 μg/L

Monthly Avg., 1/3 yr

Annual Discharge

SJR @ Crows Landing

=5,334 lbs Se

=392,570 AF

4 day, 1/3 yr

Annual Discharge

SJR @ Crows Landing

= 3,760 lbs Se

=276,772 AF

Figure C10
0

1000

2000

3000

4000

5000

Se, (lbs)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

Minimum (2,605 lbs Se/yr) Mean (7,347 lbs Se/yr)

Maximum (17,605 lbs Se/yr)

Dynamic Real Time Model - WET

Real Time, Goal - 5 μg/L

Figure C11
Table C1 Modeled Selenium Load Allocation and Discharge to the San Joaquin River from the Grassland Drainage Problem Area 

Models Irrigated/

drained acres 

Range used to model Se discharge (San Joaquin River at Crows Landing) (acre-feet/year) 

Range of modeled Se load allocation (lbs Se/year) 

Range of Modeled Se background (lbs/Se/year) 

Range of modeled Se MOS (margin of safety) (uncertainty) (lbs Se/year) 

Total Maximum Daily Load (TMDL)* (5 ppb Se objective in San Joaquin River 4-day or monthly averaging period 1in 3 year or 1 in 5 month violation frequency) Critically Dry** Dry/Below Normal** Above Normal/Wet** 

93,390/ 49,273 

104,030-260,859 225,995-328,002 233,186-481,934 

1,163-3,060 2,504-3,737 2,598-5,463 

 91-129 257-273 250-428 

140-352 305-448 317-656 

Total Maximum Monthly Load (TMML)*** (5 ppb Se objective in San Joaquin River 4-day or monthly averaging period 1in 3 year violation frequency) Dry Wet 

90,620/ 44,860 

91,255-133,210 276,772-392,570 

1,001-1,514 3,088-4,451 

116-114 294-362 

123-179 381-534 

Dynamic Real Time (DRT) **** 5 ppb Se objective in San Joaquin River Wet 

2,605-17,605 (7,347 mean) 

* Environmental Defense Fund, 1994; CCVRWQCB, 1994b; **Critically Dry < 2.1MAF; dry 2.1-2.5 MAF; Below Normal 2.5-3.1 MAF; Above Normal 3.1-3.8 MAF; and Wet >3.8 MAF (CCVRW reference to San Joaquin River Index , threshold millions of acre-feet (CCVRWQCB, 1994b); *** Draft Submittal to USEPA from CCVRWQCB, 1996a;   Karkoski, 1996 (calculated effluent limits for wet years based on 22 year period of record). 
Table C2 Modeled (TMDL, Total Maximum Daily Load model) Annual Selenium Load Allowance to the San Joaquin River from the G

Selenium Performance Goal or Regulation Scenario 

Irrigated acreage/drained acreage** ** 

Modeled load allocation lbs Se/year 

Modeled background lbs Se/year 

Modeled MOS (Margin of Safety) (Uncertainty) lbs Se/year 

Modeled discharge to San Joaquin River at Crows Landing/ Patterson lbs Se/year 

TMDL Model* Single design flow  5 ppb Se 4-day average 1 in 3 yr violation frequency 93,390/49,273 1,248 TMDL Model 5 ppb Se 4-day average 1 in 3 yr violation frequency Critically Dry Dry/Below Normal Above Normal/Wet 

93,390/49,273 1,163 

2,504 2,598 

110 257 250 

140 305 317 

1,415 3,069 3,166 

TMDL Model 5 ppb Se monthly average 1 in 3 yr violation frequency Critically Dry Dry/Below Normal Above Normal/Wet 

93,390/49,273 1,676 

3,036 3,374 

119 265 280 

200 366 405 

1,994 3,666 4,061 

TMDL Model 5 ppb Se 4-day average 1 in 5 month violation frequency Critically Dry Dry/Below Normal Above Normal/Wet 

93,390/49,273 3,060 

3,737 5,463 

129 273 428 

352 448 656 

3,546 4,454 6,549 

* Developed by Environmental Defense Fund (EDF, 1994) and CCVRWQCB, 1994b) ** Draft submittal of TMML Model for Selenium in the San Joaquin River to USEPA (CCVRWQCB, 1996a) *** Modeled effluent load data from October, 1985 to December, 1988; modeled San Joaquin River flow at Crows Landing and Patterso

(Notes: Flow record for Crows Landing is from 1970-1972; the remainder of the data used in the model for Crows Landing was reconstruSJR at Patterson. Data was also “adjusted” for averaging period because record is incomplete, CCVRWQCB, 1994 b; Karkoski, 1996) 

  Environmental Defense Fund, 1994, Table II-4 Baseline Data for Pollution Allocation Subtotal (does not include 10,000 irrigated a

noted in Total) taken from water district data for various years (1987-1990) and CCVRWQCB data. 

 ** ***Critically Dry < 2.1MAF; dry 2.1-2.5 MAF; Below Normal 2.5-3.1 MAF; Above Normal 3.1-3.8 MAF; and Wet >3.8 MAF (CCV
Table C3 Modeled (TMML model, Total Maximum Monthly Load model and DRT model, Dynamic Real-Time model) Annual Selenium 

Joaquin River from the Grassland Area 

Selenium Performance Goal or Regulation Scenario 

Irrigated acreage/drained acreage**** 

Modeled load allocation lbs Se/year 

Modeled background lbs Se/year 

Modeled MOS (Margin of Safety) (Uncertainty) lbs/year 

Modeled discharge to San Joaquin River at Crows Landing/ Patterson lbs Se/year 

TMML Model*  8 ppb Se monthly mean 1 in 3 yr violation frequency critically dry/dry/below normal 

90,620/44,860

2,491 114 290 2,896 

TMML Model 5 ppb Se 4-day average 1 in 3 yr violation frequency critically dry/dry/below normal above normal/wet 

90,620/44,860

1,001 3,088 

116 294 

123 381 

1,240 3,760 

TMML Model 5 ppb Se monthly average 1 in 3 yr violation frequency critically dry/dry/below normal above normal/wet 

90,620/44,860

1,514 4,451 

114 362 

179 534 

1,809 5,334 

DRT Model** 5 ppb Se wet mean minimum maximum 

7,347 2,605 17,605 

* Draft submittal of TMML Model for Selenium in the San Joaquin River to USEPA (CCVRWQCB, 1996a); ** Karkoski, 1996; *** Modeled effluent load data from October, 1985 to December, 1988; model San Joaquin River flow at Crows Landing and Patterson 

(Note: flow record for Crows Landing is from 1970-1972. The remainder of the data used in the model for Crows Landing was reconstruat SJR at Patterson); ****CCVRWQCB, 1994b, Table 1. 
APPENDIX D 

Variability

 
APPENDIX D 

Variability 

CONTENTS 

Introduction 4

Time 5

Seasonal and inter-annual variability ...................................................................................................5 

Monthly, Daily and Hourly Measurements..........................................................................................6

Space 7

Prediction of Short-Term Selenium Reservoirs 9 

FIGURES 

D1. Monthly selenium concentration (μg Se/L) and volume (acre-feet) at site B (SLD 

outflow to Mud Slough) for WY 1997. 

D2. Monthly selenium load (lbs) and volume (acre-feet) at site B (SLD outflow to Mud Slough) 

for WY 1997. 

D3. Monthly salt concentration (mg/L) and volume (acre-feet) at site B (SLD outflow to Mud 

Slough) for WY 1997. 

D4. Monthly salt load (tons) and volume (acre-feet) at site B (SLD outflow to Mud Slough) for WY

1997. 

D5. Monthly selenium concentration (μg Se/L) and volume (acre-feet) at site B (SLD outflow to 

Mud Slough) for WY 1998. 

D6. Monthly selenium load (lbs) and volume (acre-feet) at site B (SLD outflow to Mud Slough) or 

WY 1998. 

D7. Monthly salt concentration (mg/L) and volume (acre-feet) at site B (SLD outflow to Mud 

Slough) for WY 1998. 

D8. Monthly salt load (tons) and volume (acre-feet) at site B (SLD outflow to Mud Slough) for WY

1998. 

D9. Continuous flow monitoring (cfs) at site B for WY 1997. 

D10. Continuous selenium concentration monitoring (μg Se/L) at site B for WY 1997. 

D11. Continuous specific conductance monitoring (μS/cm) at site B for WY 1997. 

D12. Calculated total dissolved solids (mg/L salt) at site B for WY 1997. 

D13. Continuous selenium load monitoring (lbs) at site B for WY 1997. 

D14. Calculated salt (tons/day) at site B for WY 1997. 

D15. Continuous flow monitoring (cfs) at site B for WY 1998. 

D16. Continuous selenium concentration monitoring (μg Se/L) at site B for WY 1998. 

D17. Continuous specific conductance monitoring (μS/cm) at site B for WY 1998. 

D18. Calculated total dissolved solids (mg/L salt) at site B for WY 1998. 

D19. Continuous selenium load monitoring (lbs) at site B for WY 1998. 

D20. Calculated salt (tons/day) at site B for WY 1998. 

2
D21. San Luis Drain Special Study. Hourly relations between electrical conductance (μmhos) and 

 selenium concentrations (μg Se/L) during 1 – 24 hour period (6/26/97). 

D22. Relation between selenium load (lbs) and selenium concentrations (μg Se/L) at Crows 

 Landing for WY 1997. 

D23. Relation between selenium load (lbs) and selenium concentrations (μg Se/L) at Crows 

 Landing for WY 1998. 

D24. Relation between salt load (tons) and salt concentration (mg/L) at Crows Landing for WY 

 1997. 

D25. Relation between salt load (tons) and salt concentration (mg/L) at Crows Landing for WY 

 1998. 

D26. Continuous flow monitoring (cfs) at Crows Landing for WY 1997. 

D27. Continuous selenium concentration monitoring (μg Se/L) at Crows Landing for WY 1997. 

D28. Continuous specific conductance monitoring (μS/cm) at Crows Landing for WY 1997. 

D29. Calculated total dissolved solids (mg/L salt) at Crows Landing for WY 1997. 

D30. Continuous selenium load monitoring (lbs) at Crows Landing for WY 1997. 

D31. Calculated salt (tons/day) at Crows Landing for WY 1997. 

D32. Continuous flow monitoring (cfs) at Crows Landing for WY 1998. 

D33. Continuous selenium concentration monitoring (μg Se/L) at Crows Landing for WY 1998. 

D34. Continuous specific conductance monitoring (μS/cm) at Crows Landing for WY 1998. 

D35. Calculated total dissolved solids (mg/L salt) at Crows Landing for WY 1998. 

D36. Continuous selenium load monitoring (lbs) at Crows Landing for WY 1998. 

D37. Calculated salt load (tons/day) at Crows Landing for WY 1998. 

D38. Percent selenium load (normalized to the selenium load at Vernalis) for Drainage Problem 

Area (DPA), Mud Slough + Salt Slough (MS+SS), and Crows Landing-Patterson (CL-PATT) for 

WY 1986 through WY 1997. 

D39. Percent salt load (normalized to the salt load at Vernalis) for Drainage Problem Area (DPA), 

Mud Slough + Salt Slough (MS+SS), and Crows Landing-Patterson (CL-PATT) for WY 1986 

through WY 1997. 

D40. Relation between total water applied (acre-feet) and drainage flow (acre-feet) for the Drainage 

 Problem Area (DPA) for WY 1986 through WY 1997. 

D41. Relation between total water applied (acre-feet), total dissolved solids (mg/L), and selenium 

 (μg Se/L) for the Drainage Problem Area (DPA) for WY 1986 through WY 1997. 

D42. Relation between total water applied (acre-feet), total dissolved solids loads (tons), and 

 selenium load (lbs) for the Drainage Problem Area (DPA) for WY 1986 through WY 1997. 

D43. Relation between drainage flow (acre-feet), selenium (μg Se/L), and total dissolved solids 

(mg/L) for the Drainage Problem Area (DPA) for WY 1986 through WY 1997. 

D44. Relation between drainage flow (acre-feet), selenium load (lbs), and total dissolved solids load 

(tons) for the Drainage Problem Area (DPA) for the WY 1986 through WY 1997. 

D45. Relation between 1) flow and selenium load and 2) between flow and selenium concentration 

at site B (SLD outflow to Mud Slough) for WY 1997. 

D46. Relation between 1) flow and selenium load and 2) between flow and selenium concentration 

at site B (SLD outflow to Mud Slough) for WY 1998. 

D47. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

and selenium concentration of drainage (μg Se/L) at site B for WY 1997. 

D48. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

 3 Appendix D 
and selenium load of drainage (lbs) at site B for WY 1997. 

D49. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

and selenium concentration of drainage (μg Se/L) at site B for WY 1998. 

D50. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

and selenium load of drainage (lbs) at site B for WY 1998. 

D51. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

and selenium concentration of drainage (μg Se/L) for base average WY 1986 through WY 

 1994. 

D52. Monthly relation between drainage discharge (acre-feet, irrigation + precipitation (acre-feet), 

 and selenium load of drainage (lbs) for base average WY 1986 through WY 1994. 

D53. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

 and salt concentration of drainage (mg Se/L) at site B for WY 1997. 

D54. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

 and salt load of drainage (tons) at site B for WY 1997. 

D55. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

 and salt concentration of drainage (mg Se/L) at site B for WY 1998. 

D56. Monthly relation between drainage discharge (acre-feet), irrigation + precipitation (acre-feet), 

 and salt load of drainage (tons) at site B for WY 1998. 

TABLES 

D1. Selenium load (lbs) from the Grassland Drainage Problem Area, Mud and Salt Sloughs, and 

the San Joaquin River at Patterson/Crows Landing as a percentage of selenium load at the San 

Joaquin River at Vernalis. 

D2. Salt load (TDS) from the Grassland Drainage Problem Area, Mud and Salt Sloughs, and the San 

Joaquin River at Patterson/Crows Landing as a percentage of salt load at the San Joaquin River 

at Vernalis. 

APPENDIX D 

Variability 

Introduction 

The above estimates of loadings contain some substantial uncertainties that have not been 

discussed. The most important of these are associated with the time dependence and the spatial 

dependence of Se loads or the ways those loads are determined. Given here are a series of graphs 

(Figures D1 through D56) based on available data that document the variability of agricultural 

drainage Se loads to the SJR and the SLD. Flow and concentration data also have been compiled and 

4
graphed as determinants of load. Because collection of data suitable for more detailed projections is 

essential in the future, suggestions for monitoring also are given. 

Discharge data from the Grassland Area (or historically the Drainage Problem Area) represent 

drainage from the source area (i.e., farmland sumps or agricultural drainage canals). Discharge was 

measured at the SLD outflow to Mud Slough (i.e., site B). Downstream sites from the SLD discharge 

are the combined discharge of Mud Slough and Salt Slough (MS and SS), the SJR at Crows 

Landing/Patterson below the confluence with the Merced River (CL/PATT, approximately 50 miles 

downstream from the farm agricultural discharge sumps), and the SJR at Vernalis (VERN, 

approximately 130 miles downstream from the agricultural discharge). 

Time 

Seasonal and inter-annual variability

The salt imbalance in the SJV is also a driving force for management activities. Selenium loads 

are compared to salt loads to elucidate the behavior of a conservative element, represented by salt (i.e., 

total dissolved solids or specific conductance as a surrogate for salt concentrations), to that of the nonconservative element, Se. Salt concentrations were calculated from specific conductance by using the 

equation: 

specific conductance X 0.65 = mg/L total dissolved solids (TDS) or salt 

A salt or total dissolved solid (TDS) load (in tons) is calculated using the equation: 

[salt or TDS concentration (ppm) X volume of drainage (acre-feet)] X 0.00136 = salt or TDS load 

(tons), 

where 0.00136 tons salt or TDS per acre-foot is equal to a concentration of one part per million (ppm) 

salt or TDS. Pounds can be converted to tons using the conversion factor: tons = lbs 

÷ 2,000. Conversion factors used for salt and Se are compiled in Table 4. 

 5 Appendix D 
Monthly, Daily and Hourly Measurements

The Grassland Bypass Channel Project (GBCP) Monitoring Plan provides for more frequent 

measurements of flow and Se and salt concentrations in the SLD (USBR et. al., 1996). The Grassland 

Area or Drainage Problem Area discharge was measured at the SLD outflow to Mud Slough (i.e., site 

B) for WY 1997 and 1998 (see also Appendix A, Table A7 and A8) (USBR et al., 1998 and 1999). 

Figures D1 through D8 show the variation for WY 1997 and WY 1998 in monthly SLD discharge 

(averages of daily flow measurements), monthly Se concentrations (averages of daily measurements), 

monthly salt concentrations [averages of daily specific conductance converted to TDS or salt 

concentration], and calculated monthly Se and salt loads. With initiation of the GBCP, drainage 

management is aimed at meeting monthly Se load targets listed in Appendix A, Tables A7 and A8 and 

shown in Appendix B, Figure B1, which are based on the seasonal nature of drainage generation. 

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-feet; Se 

concentration 25 to 105 μg Se/L; salt concentration 2,175 to 3,255 mg/L, Se 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 

acre-feet; Se concentration 43 to 105 μg Se/L; salt concentration 2,391 to 3,704 mg/L, Se load 178 to 

1,598 lbs, and salt load 5,563 to 31,182 tons. 

 Figures D9 through D20 show the daily variation for WY 1997 and WY 1998 in SLD flow (based 

on 20-minute interval measurements), Se concentrations, TDS or salt concentrations (based on specific 

conductance measurements), Se loads, and salt loads (USBR et al., 1998 and 1999). Ranges of daily 

variation for WY 1997 are: flow 21 to 181 acre-feet; Se concentration 15 to 116 μg Se/L; and salt 

concentration 1,703 to 3,671 mg/L. Daily loads vary from 1.1 to 54 lbs Se and 66 to 860 tons salt. 

Ranges of daily variation for WY 1998 are: flow 20 to 288 acre-feet; Se concentration 20 to 128 μg 

Se/L; and salt concentration 4,114 to 2,230 mg/L. Daily loads vary from 2.7 to 69 lbs Se and 83 to 

1,218 tons salt. 

 Figure D21 shows the hourly variation in Se concentration and conductivity for the SLD discharge 

for 6/26/97 (Rudy Schnagl, CCVRWQCB, personal communication, 6/1/98). Ranges of hourly 

variations are: Se concentration 47 to 78 μg Se/L; and conductivity 4,280 to 4,675 μmhos/cm

(equivalent to 2,782 to 3,039 mg/L TDS).

6

Figures D22 and D23 compare monthly Se load and concentration data for the SJR at Crows 

Landing downstream of the SLD discharge for WY 1997 and 1998 (USBR et al., 1998 and 1999). In 
WY 1997 Se concentrations were lower compared to those of WY 1998 because flow in the SJR below 

the Merced River in WY 1998 was sustained at a higher level for a longer period than 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 Se load of 

9,054 lbs for WY 1997 and 15,884 lbs for WY 1998, but only violation of the 5 μg Se/L objective in 

WY 1997, not in WY 1998 at the SJR below the Merced River. Figures D24 and D25 compare salt 

load and concentration data for the SJR at Crows Landing for WY 1997 and 1998. Salt load and 

concentration patterns generally follow those for Se load and concentration in WY 1997, but the salt 

concentration pattern deviates from that of Se concentration in WY 1998. Ranges of monthly variation 

for WY 1997 are: flow 28,761 to 1,212,948 acre-feet; Se concentration, 0.36 to 6.8 μg Se/L; salt 

concentration 109 to 952 mg/L; Se load, 149 to 1,533 lbs; and salt load, 24,563 to 242,735 tons. 

Ranges of monthly variation for WY 1998 are: flow 40,200 to 998,158 acre-feet; Se concentration, 

0.69 to 2.6 μg Se/L; salt concentration 108 to 934 mg/L; Se load, 262 to 3,133 lbs; and salt load, 

37,006 to 284,356 tons. 

Daily measurements also were taken during WY 1997 and 1998 for the SJR at Crows Landing 

(USBR et al., 1998 and 1999). Figures D26 through D31 show the WY-1997 daily variation of flow, 

Se and salt concentrations, and calculated daily Se and salt loads. Ranges of daily variation for WY

1997 are: flow 413 to 37,100 cfs or 818 to 73,458 acre-feet; Se concentration 0.1 to 9.7 μg Se/L; salt 

concentration 82 to 1,165 mg/L; Se load 1.3 to 183 lbs; and salt load 500 to 15,956 tons. Figures D32 

through D37 show the WY1998 daily variation of flow, Se and salt concentrations, and calculated 

daily Se and salt loads. Ranges of daily variation for WY 1998 are: flow 483 to 24,200 cfs or 956 to 

47,916 acre-feet; Se concentration 0.5 to 4.1 μg Se/L; salt concentration 79 to 1,165 mg/L; Se load 3.4 

to 183 lbs; and salt load 809 to 15,482 tons. 

Space 

Given in Tables D1 and D2 for WY 1986 to 1997 are the percentages of the input Se (nonconservative element) and salt (conservative element) loads to the discharged load of Se and salt for 

the SJR at Vernalis, the entrance to the Bay-Delta (CCVRWQCB, 1996a; b; 1998d; e; f; g; h). These 

data show that 162% to 72% of the Se load to the SJR is discharged above or at the Merced River 

inflow to the SJR which would include the loads from both slough and river sources (i.e., the SJR is the 

 7 Appendix D 
only outlet from the SJV). The Merced River inflow to the SJR is approximately 60 miles above 

Vernalis, which is the entrance of the SJR to the Bay-Delta. Between the Merced River confluence 

and Vernalis, the Tuolumne and Stanislaus Rivers flow into the SJR. Approximately 68% to 87% of 

the salt load to the SJR is discharged above or at the Merced River inflow to the SJR. Figure D38

shows the percent of the Se load from the Drainage Problem Area, combined Mud and Salt Sloughs, 

and Crows Landing/Patterson normalized to the Se load at the SJR at Vernalis. Figure D39 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 SJR at Vernalis. The pattern of Se’s nonconservative behavior is different from that of the conservative salt. The Se loads measured as the 

input to the system (i.e., primary drainage canals, Drainage Problem Area) are perpetually different 

from those measured as the outputs from the system (i.e., downstream in wetland sloughs or the SJR). 

Downstream Se loads show both decreases (measured at Salt and Mud Sloughs) and increases (SJR at 

Crows Landing and Vernalis) (see Appendix B, Tables B4 to B7). In the absence of the SLD extension 

to the Bay-Delta, which would provide a single source of Se at a single discharge point, loads 

discharged from the SJR at Vernalis to the Delta are not likely to equal loads discharged into the river 

from the drainage source area. 

Selenium is persistently discharged from the Grassland area to the SJR, but is dependent on the 

monitoring site location within the Grassland area (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 in these graphs for WY 1986 to WY 1998 generally can be related to physical variables that 

affected drainage conditions (e.g., drought 1987 through 1992, California Coast Range flooding in 

1995, and Sierra Nevada flooding in 1997; also see Appendix A, Figure A10, SJV annual rainfall for 

CIMIS #124). Ranges of yearly variation for WY 1986 to 1997 for the DPA are: flow, 24,533 to 

67,006 acre-feet; Se concentration 52 to 80 μg Se/L; Se 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-feet; Se concentration 10 to 

16 μg Se/L; Se 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 

Crows Landing/Patterson are: flow, 0.29 to 4.18 million acre-feet/year; Se concentration 1 to 6.3 μg 

Se/L; and Se load 3,064 to 14,291 lbs/year. Ranges of yearly variation for Vernalis are: flow, 0.66 to 

6.77 million acre-feet/year; Se concentration 0.6 to 3.0 μg Se/L; and Se load 3,611 to 17,238 lbs/year. 

8
Except for WY 1990, data from 1986 to 1995 showed Se input loads (upstream drainage canals, 

Drainage Problem Area, Appendix B, Table B4) higher than output loads (downstream of Mud and 

Salt Sloughs, Appendix B, Table B5). Comprehensive monitoring data are not available to determine 

the Se “loss” (i.e., that amount of load unaccounted for) after transit through the Grasslands wetlands 

(estimated annual maximum potential attenuation of 50%). 

 Loads further downstream in the SJR at Patterson/Crows (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 (i.e., Drainage Problem Area). The 

increases may be due to other sources of Se entering the SJR or errors introduced through limitations 

of the data as noted above. During WY 1986 to WY 1998, the loads in the SJR at Patterson/Crows 

range from 3,064 to 15,884 lbs Se with the maximum occurring in WY 1998 (Appendix B, Table B6). 

The Se loads for the SJR at Vernalis from WY 1986 to WY 1997 range from 3,558 to 17,238 lbs, with 

the two highest values occurring in 1986 and 1995 (Appendix B, Table B7). In the referenced data, 

two values have been calculated for the SJR at Crows Landing for WY 1998 (15,501 lbs and 13,445 

lbs) depending on sets of flow data. For WY 1998 for the SJR at Vernalis, the reported value is 

15,810 lbs Se/year which is less than or similar to the value measured for the SJR at Crows Landing. 

A state prohibition limitation for drainage over 8,000 lbs Se from the Grassland Area was enacted in 

1996. 

Prediction of Short-Term Selenium Reservoirs 

Data from WY 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 (CCVRWQCB, 1996a;b; 

1998d; e; f; g; h; GAF, 1998b). Measurements for the drainage problem area are referred to agricultural 

drainage canals for WY 1986 to 1996 and site B (SLD discharge into Mud Slough) for WY 1997 and 

WY 1998. Figures D40 through D44 show, using data from WY 1986 to 1997, general relations 

among annualized amounts of: 

• irrigation water applied to the drainage source area; 

• the flow generated from the drainage source area (i.e., discharge); 

• the concentration of Se in the generated discharge; and 

• the loads of salt and Se generated from the drainage source area. 

 9 Appendix D 
This series of figures show some of the variables that affect load generation, but not the fundamental 

processes controlling the distribution and transport of Se and salt. Based on annualized data, Figure 

D40 shows that as total water (applied irrigation water plus precipitation) increases, flow from the 

Drainage Problem Area increases. Figure D41 shows that as total applied water increases, Se and salt 

concentrations in the discharge decreases. Figure D42 shows that as total applied water increases, Se 

and salt loads from the Drainage Problem Area increase. Figure D43 shows that as flow from the 

Drainage Problem Area increases, Se and salt concentrations decreases. Figure D44 shows that as flow 

from the Drainage Problem Area increases, Se load increases. 

 Based on monthly and daily data these annual relations are not valid. Figures D45 and D46 show 

the relation among flow, concentration, and load using daily measurements for WY 1997 and 1998 at 

the SLD discharge to Mud Slough (site B) (USBR et al., 1998; 1999). In WY 1997 Se load and 

concentration increase with flow. In WY 1998 however, concentration and load decrease at flows 

greater than approximately 100 cubic feet per second, thus showing some drainage relief through 

dilution at the higher flows during storms in February 1998. These data have been generalized in 

Figure 6 to help denote the characteristics of source water versus receiving water. 

Figures D47 through D56 are a series of graphs that depict the relation between load, 

concentration, applied water, and flow or discharge at site B in the SLD on a monthly basis for the 

Grassland Area. Figures D47 through D50 are WY-1997 and -1998 summaries using monthly 

averages of flow (i.e., discharge), Se load, and Se concentration along with amounts of applied water 

(irrigation and precipitation). Figures D51 and D52 show a monthly average of WY 1986 through 

1994 (the base year average used for generating the GBCP load targets, see Appendix B, Figure B1) 

for the same parameters. For comparison, Figures D53 through D56 are summaries of salt load and 

salt concentration data for the SLD discharge shown in a similar series of graphs for that of Se 

discharge in WY 1997 and 1998. Patterns of loading to the SLD are similar through the series of 

graphs, showing peak Se loads and concentrations during the months of March or April. Maximum

application of water occurred in June, July, and August. Winter rainfall peaks can be seen especially in 

WY 1998 during February. 

10
Figure D1 Figure D2

Figure D3 Figure D4

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

Acre-feet

0 

200 

400 

600 

800 

1000 

1200 

1400 

1600 

Se, (lbs)

101112 1 2 3 4 5 6 7 8 9

MONTH

Acre-ft Se load, lbs

SITE B - Acre - feet vs Se LOAD

WY 1997

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

Acre-feet

0 

4000 

8000 

12000 

16000 

20000 

24000 

28000 

32000 

Salt LOAD (tons)

10 12 2 4 6 8

MONTH

Acre-ft Salt load, tons

SITE B - Acre - feet vs SALT LOAD

WY 1997

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

Acre-feet

0 

20 

40 

60 

80 

100 

120 

Se, ppb

101112 1 2 3 4 5 6 7 8 9

MONTH

Acre-ft Se, ppb

SITE B - Acre - feet vs Se CONC

WY 1997

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

Acre-feet

0 

400 

800 

1200 

1600 

2000 

2400 

2800 

3200 

3600 

Salt CONC, (mg/L)

101112 1 2 3 4 5 6 7 8 9

MONTH

Acre-ft Salt, mg/L

SITE B - Acre - feet vs Salt CONC

WY 1997
Figure D5 Figure D6

Figure D7 Figure D8

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

Acre-feet

0 

200 

400 

600 

800 

1000 

1200 

1400 

1600 

Se, lbs

101112 1 2 3 4 5 6 7 8 9

MONTH

Acre-ft Se load, lbs

SITE B - Acre - feet vs Se LOAD

WY 1998

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

Acre-feet

0 

20 

40 

60 

80 

100 

120 

Se, ppb

101112 1 2 3 4 5 6 7 8 9

MONTH

Acre-ft Se, ppb

SITE B - Acre - feet vs Se CONC

WY 1998

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

Acre-feet

0 

4000 

8000 

12000 

16000 

20000 

24000 

28000 

32000 

Salt LOAD, tons

10 12 2 4 6 8

MONTH

Acre-ft Salt load, tons

SITE B - Acre - feet vs SALT LOAD

WY 1998

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

Acre-feet

0 

400 

800 

1200 

1600 

2000 

2400 

2800 

3200 

3600 

Salt CONC, (mg/L)

101112 1 2 3 4 5 6 7 8 9

MONTH

Acre-ft Salt, mg/L

SITE B - Acre - feet vs SALT CONC

WY 1998
Figure D9 Figure D10

Figure D11 Figure D12

Figure D13 Figure D14

0 

20 

40 

60 

80 

100 

120 

140 

160 

FLOW (cfs)

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

SITE B - CONTINUOUS MONITORING - FLOW

10/1/96 to 9/30/97

0 

20 

40 

60 

80 

100 

120 

140 

Se CONCENTRATION, (μg/L)

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

SITE B-CONTINUOUS MONITORING-Se CONC

10/1/96 to 9/30/97

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

SPECIFIC CONDUCTANCE (μS/cm)

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

SITE B-CONTINUOUS MONITORING-SP COND

10/1/96 to 9/30/97

0 

500 

1000 

1500 

2000 

2500 

3000 

3500 

4000 

4500 

mg/L salt (calculated)

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

SITE B - TDS (calculated)

10/1/96 to 9/30/97

0 

10 

20 

30 

40 

50 

60 

70 

Se LOAD (lbs)

10/01/96 12/18/9603/06/97 05/23/97 08/09/97

DATE

SITE B-CONTINUOUS MONITORING-Se LOAD

10/1/96 to 9/30/97

0 

200 

400 

600 

800 

1000 

1200 

salt (tons/day), calculated

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

SITE B - SALT (calculated)

10/1/96 to 9/30/97
Figure D15 Figure D16

Figure D17 Figure D18

Figure D19 Figure D20

0 

20 

40 

60 

80 

100 

120 

140 

160 

FLOW (cfs)

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

SITE B - CONTINUOUS MONITORING - FLOW

10/1/97 to 9/30/98

0 

20 

40 

60 

80 

100 

120 

140 

Se CONCENTRATION, (μg/L)

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

SITE B-CONTINUOUS MONITORING-Se CONC

10/1/97 to 9/30/98

0 

1000 

2000 

3000 

4000 

5000 

6000 

7000 

SPECIFIC CONDUCTANCE (μS/cm)

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

SITE B-CONTINUOUS MONITORING-SP COND

10/1/97 to 9/30/98

0 

500 

1000 

1500 

2000 

2500 

3000 

3500 

4000 

4500 

mg/L salt (calculated)

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

SITE B - TDS (calculated)

10/1/97 to 9/30/98

0 

10 

20 

30 

40 

50 

60 

70 

Se LOAD (lbs)

10/01/97 12/18/9703/06/98 05/23/98 08/09/98

DATE

SITE B-CONTINUOUS MONITORING-Se LOAD

10/1/97 to 9/30/98

0 

200 

400 

600 

800 

1000 

1200 

salt (tons/day), calculated

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

SITE B - SALT (calculated)

10/1/97 to 9/30/98
4200 

4300 

4400 

4500 

4600 

4700 

Lab EC (μmhos)

45 

50 

55 

60 

65 

70 

75 

80 

Se (μg/L)

0 2 4 6 8 10 12 14 16 18 20 22

Time

Lab EC (μmhos) Se (μg/L)

SPECIAL STUDY - SAN LUIS DRAIN

Hourly Data - 6/26/97

Figure D21
Figure D22 Figure D23

Figure D24 Figure D25

0 

400 

800 

1200 

1600 

2000 

2400 

2800 

3200 

Se, lbs

0 

1 

2 

3 

4 

5 

6 

7 

Se, ppb

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

Se load, lbs Se, ppb

Crows Landing - Se LOAD vs Se CONC

WY 1997

0 

400 

800 

1200 

1600 

2000 

2400 

2800 

3200 

Se, lbs

0 

1 

2 

3 

4 

5 

6 

7 

Se, ppb

10 11 12 1 2 3 4 5 6 7 8 9

MONTH

Se load, lbs Se, ppb

Crows Landing - Se LOAD vs Se CONC

WY 1998

0 

50000 

100000 

150000 

200000 

250000 

300000 

350000 

Salt (tons)

0 

200 

400 

600 

800 

1000 

Salt (mg/L)

10 12 2 4 6 8

MONTH

Salt load, tons Salt, mg/L

Crows Landing - Salt LOAD vs Salt CONC

WY 1998

0 

50000 

100000 

150000 

200000 

250000 

300000 

350000 

Salt, (tons)

0 

200 

400 

600 

800 

1000 

Salt, (mg/L)

10 12 2 4 6 8

MONTH

Salt load, tons Salt, mg/L

Crows Landing - Salt LOAD vs Salt CONC

WY 1997
Figure D26 Figure D27

Figure D28 Figure D29

Figure D30 Figure D31

0 

10000 

20000 

30000 

40000 

FLOW (cfs)

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

Crows Landing, Cont. Monitoring, FLOW

10/1/96 to 9/30/97

0 

2 

4 

6 

8 

10 

Se CONCENTRATION, (μg/L) 10/01/96 12/18/9603/06/97 05/23/97 08/09/97

DATE

Crows Landing, Cont. Monitoring, Se

10/1/96 to 9/30/97

0 

200 

400 

600 

800 

1000 

1200 

1400 

1600 

1800 

Specific Conductance, μS/cm

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

Crows Landing, Cont. Monitor., S. Cond

10/1/96 to 9/30/97

0 

200 

400 

600 

800 

1000 

1200 

mg/L salt, (calculated)

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

Crows Landing - TDS (calculated)

10/1/96 to 9/30/97

0 

2000 

4000 

6000 

8000 

10000 

12000 

14000 

16000 

tons/day salt, (calculated)

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

Crows Landing - Salt (calculated)

10/1/96 to 9/30/97

0 

50 

100 

150 

200 

Se LOAD (lbs)

10/01/9612/18/9603/06/9705/23/9708/09/97

DATE

Crows Landing, Cont. Monitoring, LOAD

10/1/96 to 9/30/97
Figure D32 Figure D33

Figure D34 Figure D35

Figure D36 Figure D37

0 

10000 

20000 

30000 

40000 

FLOW (cfs)

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

Crows Landing, Cont. Monitoring, FLOW

10/1/97 TO 9/30/98

0 

2 

4 

6 

8 

10 

Se CONCENTRATION, (μg/L) 10/01/97 12/18/9703/06/98 05/23/98 08/09/98

DATE

Crows Landing, Cont. Monitoring, Se

10/1/97 to 9/30/98

0 

50 

100 

150 

200 

Se LOAD, (lbs)

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

Crows Landing, Cont. Monitoring, LOAD

10/1/97 TO 9/30/98

0 

200 

400 

600 

800 

1000 

1200 

1400 

1600 

1800 

Specific Conductance, μS/cm

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

Crows Landing, Cont. Monitor., S. Cond

10/1/97 to 9/30/98

0 

200 

400 

600 

800 

1000 

1200 

mg/L salt, (calculated)

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

Crows Landing - TDS (calculated)

10/1/97 to 9/30/98

0 

2000 

4000 

6000 

8000 

10000 

12000 

14000 

16000 

tons/day salt, (calculated)

10/01/9712/18/9703/06/9805/23/9808/09/98

DATE

Crows Landing - Salt (calculated)

10/1/97 to 9/30/98
0 

50 

100 

150 

200 

% (various locations/VERNALIS)

86 87 88 89 90 91 92 93 94 95 96 97 98a98b

YEAR

DPA/V MS+SS/V CL-PATT/V

% Se load DPA, MS+SS, CL-PATT

normalized to Se load at VERNALIS

FigureD38
0 

20 

40 

60 

80 

100 

% (various locations/VERNALIS)

86 87 88 89 90 91 92 93 94 95 96 97

YEAR

DPA/V MS+SS/V CL-PATT/V

% Salt Load DPA, MS+SS, CL-PATT

normalized to salt load at VERNALIS

Figure D39
Figure D40 Figure D41

Figure D42 Figure D43

Figure D44

0 

400 

800 

1200 

1600 

2000 

2400 

2800 

3200 

TDS (mg/L)

0 

10 

20 

30 

40 

50 

60 

70 

80 

Se (μg/L)

180000 220000 260000 300000 340000 

TOTAL WATER (acre-feet)

TDS(mg/L) Se(μg/L)

TOTAL WATER vs TDS, Se CONCENTRATION

DPA

0 

20000 

40000 

60000 

80000 

FLOW (acre-ft)

180000 220000 260000 300000 340000 

TOTAL WATER (acre-ft)

FLOW

TOTAL WATER vs FLOW

DPA

0 

40000 

80000 

120000 

160000 

200000 

240000 

TDS (tons)

0 

2000 

4000 

6000 

8000 

10000 

12000 

Se (lbs)

180000 230000 280000 330000 

TOTAL WATER (acre-feet)

TDS(tons) Se (lbs)

TOTAL WATER vs TDS, Se LOADS

DPA

0 

400 

800 

1200 

1600 

2000 

2400 

2800 

3200 

TDS (mg/L)

0 

10 

20 

30 

40 

50 

60 

70 

80 

Se (μg/L)

20000 40000 60000 80000 

FLOW, acre-feet

TDS(mg/L) Se(μg/L)

FLOW vs Se, TDS

DPA

0 

40000 

80000 

120000 

160000 

200000 

240000 

TDS (tons)

0 

2000 

4000 

6000 

8000 

10000 

12000 

Se (lbs)

20000 40000 60000 80000 

FLOW acre-feet

TDS(tons) Se (lbs)

FLOW vs Se load, TDS load

DPA
0 

20 

40 

60 

80 

100 

120 

140 

Se (μg/L), Se load (lbs)

10 30 50 70 90 110 130 

Flow (cfs)

Se (μg/L) Se (lbs)/day

Flow vs Se load, Se concentration

1997

Figure D45
0 

20 

40 

60 

80 

100 

120 

140 

Se (μg/L), Se load (lbs)

10 30 50 70 90 110 130 150 

Flow (cfs)

Se, μg/L Se, lbs/day

Flow vs Se load, Se concentration

1998

Figure D46
Figure D47 Figure D48

Figure D49 Figure D50

Figure D51 Figure D52

0 

10000 

20000 

30000 

40000 

50000 

acre-feet (average)

0 

20 

40 

60 

80 

100 

120 

ppb Se (average)

101112 1 2 3 4 5 6 7 8 9

MONTH

DISCHARGE PPT+IRR ppb Se

BASE AVERAGE WY 1986-1994

0 

10000 

20000 

30000 

40000 

50000 

acre-feet (average)

0 

200 

400 

600 

800 

1000 

1200 

1400 

1600 

1800 

2000 

Se lbs (average)

10 12 2 4 6 8

MONTH

DISCHARGE PPT+IRR Se lbs

BASE AVERAGE WY 1986-1994

0 

10000 

20000 

30000 

40000 

50000 

acre-feet

0 

20 

40 

60 

80 

100 

120 

ppb Se

101112 1 2 3 4 5 6 7 8 9

MONTH

DISCHARGE PPT+IRR ppb Se

SITE B-DISCHARGE,PPT+IRR, ppb Se

WY 1997

0 

10000 

20000 

30000 

40000 

50000 

acre-feet

0 

200 

400 

600 

800 

1000 

1200 

1400 

1600 

1800 

2000 

Se, lbs

10 12 2 4 6 8

MONTH

DISCHARGE PPT+IRR Se lbs

SITE B-DISCHARGE,PPT+IRR,Se lbs

WY 1997

0 

10000 

20000 

30000 

40000 

50000 

acre-feet

0 

20 

40 

60 

80 

100 

120 

ppb Se

101112 1 2 3 4 5 6 7 8 9

MONTH

DISCHARGE PPT+IRR ppb Se

SITE B-DISCHARGE,PPT+IRR,ppb Se

WY 1998

0 

10000 

20000 

30000 

40000 

50000 

acre-feet

0 

500 

1000 

1500 

2000 

Se lbs

10 12 2 4 6 8

MONTH

DISCHARGE PPT+IRR Se lbs

SITE B-DISCHARGE,PPT+IRR,Se lbs

WY 1998
Figure D53 Figure D54

Figure D55 Figure D56

0 

10000 

20000 

30000 

40000 

50000 

acre-feet

0 

400 

800 

1200 

1600 

2000 

2400 

2800 

3200 

3600 

Salt, mg/L

10 12 2 4 6 8

MONTH

DISCHARGE PPT+IRR Salt, mg/L

SITE B-DISCHARGE,PPT+IRR, Salt ppm

WY 1997

0 

10000 

20000 

30000 

40000 

50000 

acre-feet

0 

5000 

10000 

15000 

20000 

25000 

30000 

35000 

Salt, tons

10 12 2 4 6 8

MONTH

DISCHARGE PPT+IRR Salt load, tons

SITE B-DISCHARGE,PPT+IRR,Salt tons

WY 1997

0 

10000 

20000 

30000 

40000 

50000 

acre-feet

0 

400 

800 

1200 

1600 

2000 

2400 

2800 

3200 

3600 

Salt, mg/L

10 12 2 4 6 8

MONTH

DISCHARGE PPT+IRR Salt, mg/L

SITE B-DISCHARGE,PPT+IRR, Salt ppm

WY 1998

0 

10000 

20000 

30000 

40000 

50000 

acre-feet

0 

5000 

10000 

15000 

20000 

25000 

30000 

35000 

Salt, tons

10 12 2 4 6 8

MONTH

DISCHARGE PPT+IRR Salt load, tons

SITE B-DISCHARGE,PPT+IRR,Salt tons

WY 1998
TABLE D1 Selenium load (lbs) from the Grassland Drainage Problem Area, Mud and Salt Sloughs, 

and the San Joaquin River at Patterson/Crows as a percentage of selenium load at the San Joaquin River at Vernalis. Selenium (lbs/year) DPA/ Vernalis (%) Mud and Salt/Vernalis (%) Patterson (Crows)/Vernalis (%) 1986 65 46 721987 126 88 1011988 120 96 1101989 100 93 851990 99 103 821991 162 108 981992 143 82 861993 99 77 921994 109 102 941995 69 62 831996 88 83 941997 62 69 77
TABLE D2 Salt load (TDS) from the Grassland Drainage Problem Area, Mud and Salt Sloughs, 

and the San Joaquin River at Patterson/Crows as a percentage of salt load at the San Joaquin River at Vernalis. Salt (tons/year) DPA/ Vernalis (%) Mud and Salt/Vernalis (%) Patterson (Crows)/Vernalis (%) 1986 17 39 781987 27 48 791988 28 54 861989 28 54 751990 25 56 791991 27 46 871992 24 43 851993 21 38 781994 24 54 841995 17 35 871996 17 40 681997 10 32 74
APPENDIX E 

Sediment Quality and Quantity Tables 

 
APPENDIX E 

Sediment Quality and Quantity Tables 

TABLES 

E1. Quantity of bed sediment and suspended sediment and concentrations and loads of selenium in bed 

sediment of the San Luis Drain (constructed concrete channel). 

E2. Concentration of selenium in bed sediment , suspended sediment, and plankton in natural channels 

1 Appendix E 
APPENDIX E

Sediment Quality and Quantity Tables 

TABLE E1 Quantity of bed sediment and suspended sediment and concentrations and loads of selenium in bed sedimen(constructed concrete channel). Sediment in agricultural drainage canal (constructed concrete channel) 

tons (dry weight) 

cubic yards (dry weight) 

lbs Se ppm range/ 

average (dry weight) 

mg/L suspsedim(avg

San Luis Drain (1986, USBR) 28-mile segment 85-mile segment (1984) 

 80,583 211,000 5,280 5 - 190/84 

San Luis Drain (1984-1993) compilation of five surveys (Presser et al., 1996) 

1.4 - 210/55 

San Luis Drain (1987) (USBR et al., 1998; 1999; 2000) 28-mile segment 85-mile segment 

 58,094  ---- 

San Luis Drain 1994 (Presser et al., 1996 ; Presser and Piper, 1998) 8/94 9/94 

3.2 - 110/43 11 - 94/44 

San Luis Drain 1995 (Presser and Piper, 1998) 28-mile segment 85-mile segment 55,788 

177,900 

 4,500* 14,400*

San Luis Drain 1997 (USBR et al., 1998; 1999; 2000) 28-mile segment 60,593 2.9 - 100/30 

(whole core average except 0.1 value) 

San Luis Drain WY 1997 (USBR et al., 1998) (estimated from suspended solids) 

465 tons deposited/year 

@1.8gm/cc 308 cy @2.6 gm/cc 213 cy 

no dataavailable 

102 

* Calculated using an average concentration of selenium in SLD bed sediment of 44 ppm Se (see 1994 data). 

2 
TABLE E2 Concentration of selenium in bed sediment, suspended sediment, and plankton in natural channels. 

Sediment in natural channels subjected to intermittent agricultural 

drainage discharge from Grassland Drainage Problem Area 1) 1950’sSept., 1996 from Agatha Canal and Camp 13 Slough; 2) October, 1996-

continuing from SLD. All sites are downstream of discharge except as 

noted. 

Bed Sediment 

ppm Se (value 

or range) 

(dry weight) 

Suspended 

Sediment 

ppm Se (value 

or range) 

(dry weight) 

Plankton 

ppm Se (value 

or range) 

(dry weight) 

Agatha Canal, CDFG, 1988 1.0 1.4 3.8

Camp 13 Slough, CDFG 1987 

1988 

1989 

0.79 

0.71-1.4 

0.89 

1.6-2.6 

3.2 

0.54-3.6 

3.2 

East Big Lake (1992-1993, USFWS; Henderson et al., 1995) impoundment 1.0-1.8

Mud Slough, CDFG 200m downstream of SLD (inactive)* 

1987 

1988 

1989 

0.32-1.3 

0.31-1.8 

1.1 

2.1 

1.2-6.7 

2.4 

0.19-3.4 

3.8 

Mud Slough (1992-1993, USFWS; Henderson et al., 1995) 

600 yards upstream of SLD discharge 

immediately downstream (120 m) of SLD (inactive)* 

6.6 miles downstream of SLD (inactive) 

0.15-0.75 

(average of 

all sites) 

Mud Slough (1993-Sept.,1996; USBR, 1995) 

upstream of SLD discharge 

immediately downstream of SLD (inactive)* 

6.6 miles downstream of SLD (inactive) 

<0.1-0.3 

<0.1-0.4 

<0.1-0.7 

Mud Slough (WY 1997; USBR et al., 1998) 

upstream of SLD discharge 

immediately downstream of SLD discharge 

6.6 miles downstream of SLD discharge 

0.10-0.44 

0.10-0.76 

0.70-1.9 

Mud Slough seasonal backwater (low flow depositional area) (1993-1996; 

USBR, 1995) 0.3-0.6 

Mud Slough seasonal backwater (low flow depositional area) (March, 

1997; USBR et al., 1998) 0.4-1.5 

Salt Slough, CDFG near hwy 165 

1987 

1988 

1989 

0.31-1.3 

1.1-1.4 

1.5 

1.4 

1.2-2.6 

2.0 

0.17-4.2 

5.0 

Salt Slough (1992-1993, USFWS; Henderson et al., 1995) 0.2-0.45

Salt Slough (1993-Sept., 1996; USBR, 1995) 0.2-1.3

Salt Slough (WY 1997; USBR et al., 1997) 0.12-0.94

San Joaquin River, CDFG at Lander Ave. (upstream of discharge) 

1987 

1988 

1989 

0.01 

0.04-<0.18 

<0.18 

0.98 

1.0-1.8 

2.0 

<0.08-0.16 

0.23 

San Joaquin River (CDFG) at or below Merced River 

1987 

1988 

1989 

0.19-0.75 

(<0.18) 0.28-0.56 

0.18 

1.7 

1.3-2.2 

1.9 

0.33-2.0 

2.5 

San Joaquin River (CDFG) at Vernalis (Airport Blvd.; Maze Blvd; all

below Stanislaus River) 

1987 

1988 

1989 

0.25-1.2 

<0.18-5.2 

-- 

1.2 

0.91-2.4 

1.4 

0.11-2.1 

1.2 

Note: The San Luis Drain was not in use from July 1,1986 to September 23, 1996. References: CDFG = White et al., 1987; 

1988;1989; Urquhart and Regalado, 1991; Henderson et al., 1995; USBR, 1995; USBR et al., 1998. 

3 Appendix E 
APPENDIX F 

Supplemental Spreadsheets 

 
APPENDIX F 

Supplemental Spreadsheets 

TABLES 

F1. This scenario assumes that all freshwater exports are from the Sacramento River and that all SJR 

inflow enters the Bay-Delta. Sac R inflow is outflow index minus SJR discharge. Se concentration in the SJR 

is maintained at 2 μg Se/L. A total of 32,935 lbs of Se is released annually. Flow data are from 1997. 

F2. This scenario assumes that all freshwater exports are from the Sacramento River and that all SJR 

inflow enters the Bay-Delta. Sac R inflow is outflow index minus SJR discharge. Se concentration in the SJR is 

maintained at 1 μg Se/L. A total of 16,468 lbs of Se is released annually. Flow data are from 1997. 

F3. Calculation of particulate Se concentrations (μg Se/g) from inputs of the Sacramento River (Sac 

R), the San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and the oil refineries under 

different load scenarios. Forecasts are for a wet year during the high flow season. 

F4. Calculation of particulate Se concentrations (μg Se/g) from inputs of the Sacramento River (Sac 

R), the San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and the oil refineries under 

different load scenarios. Forecasts are for a wet year during the low flow season. 

F5. Calculation of particulate Se concentrations (μg Se/g) from inputs of the Sacramento River (Sac 

R), the San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and the oil refineries under 

different load scenarios. Forecasts are for a critically dry year during the low flow season. 

F6. Bioaccumulation of Se by a generic bivalve under various scenarios. Forecasts are for a wet year 

during the high flow season. 

F7. Bioaccumulation of Se by a generic bivalve under various scenarios. Forecasts are for a wet year 

during the low flow season. 

F8. Bioaccumulation of Se by a generic bivalve under various scenarios. Forecasts are for a critically 

dry year during the low flow season. 

F9. Bioaccumulation of Se by a generic bivalve under various scenarios. Forecasts are for a targeted 

SJR load of approximately 7,000 lbs Se annually (3,400 or 3,590 lbs Se per six months). 

1 Appendix F 
Table F1. This scenario assumes that all freshwater exports are from the Sacramento River and that all SJR inflow 

enters the Bay-Delta. Sac R inflow is outflow index minus SJR discharge. Se concentration in the SJR is 

maintained at 2 ug Se/L. A total of 32,935 lbs of Se is released annually. Flow data are from 1997.

Volume Volume Volume Concentration Load Load Contribution Volumes Concentration Concentration at

Avg cfs MAF billion L ug Se/L billion ug lbs Se Sum Sum FW Endmember Carquinez Strait

Month billion ug billion liters ug Se/L at 20 psu

January

Total OF 256565

Sac R. 224096 13.31 16412.84 0.04 657 1,448

SJR 32469 1.93 2378.04 2 4756 10,492

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

5,464 18,792 0.29 0.15

February

Total OF 119090

Sac R. 86950 5.16 6368.24 0.04 255 562

SJR 32140 1.91 2353.94 2 4708 10,386

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

5,014 8,723 0.57 0.29

March

Total OF 33831

Sac R. 20944 1.24 1533.94 0.04 61 135

SJR 12887 0.77 943.85 2 1888 4,164

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

2,000 2,479 0.81 0.40

April

Total OF 13734

Sac R. 9811 0.58 718.56 0.04 29 63

SJR 3923 0.23 287.32 2 575 1,268

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

655 1,007 0.65 0.33

May

Total OF 12261

Sac R. 7210 0.43 528.06 0.04 21 47

SJR 5051 0.30 369.94 2 740 1,632

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

812 899 0.90 0.45

June

Total OF 8762

Sac R. 5550 0.33 406.48 0.04 16 36

SJR 3212 0.19 235.25 2 470 1,038

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

538 643 0.84 0.42
July

Total OF 9350

Sac R. 7326 0.44 536.56 0.04 21 47

SJR 2024 0.12 148.24

2 296 654

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

369 686 0.54 0.27

August

Total OF 9031

Sac R. 7378 0.44 540.37 0.04 22 48

SJR 1653 0.10 121.07

2 242 534

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

315 662 0.48 0.24

September

Total OF 4555

Sac R. 2633 0.16 192.84 0.04

8 17

SJR 1922 0.11 140.77

2 282 621

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

341 335 1.02 0.51

October

Total OF 4571

Sac R. 2237 0.13 163.84 0.04

7 14

SJR 2334 0.14 170.94

2 342 754

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

400 336 1.19 0.60

November

Total OF 6270

Sac R. 4095 0.24 299.92 0.04 12 26

SJR 2175 0.13 159.30

2 319 703

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

382 460 0.83 0.41

December

Total OF 18914

Sac R. 16780 1.00 1228.97 0.04 49 108

SJR 2134 0.13 156.29

2 313 690

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

413 1,386 0.30 0.15

Total Selenium Exported from SJR (lbs) 32,935
Table F2. This scenario assumes that all freshwater exports are from the Sacramento River and that all SJR inflow 

enters the Bay-Delta. Sac R inflow is outflow index minus SJR discharge. Se concentration in SJR is 

maintained at 1 ug Se/L. A total of 16,468 lbs of Se is released annually. Flow data are from 1997.

Volume Volume Volume Concentration Load Load Contribution Volumes Concentration Concentration at

Avg cfs MAF billion L ug Se/L billion ug lbs Se Sum Sum FW Endmember Carquinez Strait

Month billion ug billion liters ug Se/L at 20 psu

January

Total OF 256565

Sac R. 224096 13.31 16412.84 0.04 657 1,448

SJR 32469 1.93 2378.04 1 2378 5,246

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

3,086 18,792 0.16 0.08

February

Total OF 119090

Sac R. 86950 5.16 6368.24 0.04 255 562

SJR 32140 1.91 2353.94 1 2354 5,193

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

2,660 8,723 0.30 0.15

March

Total OF 33831

Sac R. 20944 1.24 1533.94 0.04 61 135

SJR 12887 0.77 943.85 1 944 2,082

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

1,057 2,479 0.43 0.21

April

Total OF 13734

Sac R. 9811 0.58 718.56 0.04 29 63

SJR 3923 0.23 287.32 1 287 634

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

367 1,007 0.36 0.18

May

Total OF 12261

Sac R. 7210 0.43 528.06 0.04 21 47

SJR 5051 0.30 369.94 1 370 816

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

442 899 0.49 0.25

June

Total OF 8762

Sac R. 5550 0.33 406.48 0.04 16 36

SJR 3212 0.19 235.25 1 235 519

SLD 0.00 0.00 62.5 0 0

Refineries 0.00 1.03 50 51 113

303 643 0.47 0.24
July

Total OF 9350

Sac R. 7326 0.44 536.56 0.04 21 47

SJR 2024 0.12 148.24

1 148 327

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

221 686 0.32 0.16

August

Total OF 9031

Sac R. 7378 0.44 540.37 0.04 22 48

SJR 1653 0.10 121.07

1 121 267

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

194 662 0.29 0.15

September

Total OF 4555

Sac R. 2633 0.16 192.84 0.04

8 17

SJR 1922 0.11 140.77

1 141 311

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

200 335 0.60 0.30

October

Total OF 4571

Sac R. 2237 0.13 163.84 0.04

7 14

SJR 2334 0.14 170.94

1 171 377

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

229 336 0.68 0.34

November

Total OF 6270

Sac R. 4095 0.24 299.92 0.04 12 26

SJR 2175 0.13 159.30

1 159 351

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

223 460 0.48 0.24

December

Total OF 18914

Sac R. 16780 1.00 1228.97 0.04 49 108

SJR 2134 0.13 156.29

1 156 345

SLD 0.00 0.00 62.5

00

Refineries 0.00 1.03 50 51 113

257 1,386 0.19 0.09

Total Selenium Exported from SJR (lbs) 16,468
Table F3. Calculation of particulate Se concentrations (ug Se/g) from inputs of the Sacramento River (Sac R),

the San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and the oil refineries under

different load scenarios. Forecasts are for a wet year during the high flow season.

Volume Load Concentration Concentration Concentration at Particulate Concentration 

MAF lbs Se per ug Se/L FW Endmember Carquinez Strait Kd = 1,000 Kd=3,000 Kd = 10,000

 6 months in source ug Se/L at 20 psu FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait

 ug Se/g

1. San Luis Drain Scenarios: Wet year (1997 data); High Flow Season

a) SLD at half capacity (150 cfs), 50 ppb Se (6,800 lbs in six months); SJR reaches the Bay-Delta.

Sac R. 17 1,850 0.04

SJR 2 5,440 1

SLD 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

b) SLD at full capacity (300cfs), 62.5 ppb Se (18,700 lbs in six months); SJR reaches Bay-Delta.

Sac R. 17 1,850 0.04

SJR 2 5,440 1

SLD 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

c) SLD at full capacity (300 cfs), 150 ppb Se (44,880 lbs in six months); SJR reaches Bay-Delta.

Sac R. 17 1,850 0.04

SJR 2 5,440 1

SLD 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

d) SLD at full capacity (300cfs), 300 ppb Se (89,760 lbs in six months); SJR reaches Bay

Sac R. 17 1,850 0.04

SJR 2 5,440 1

SLD 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

Targeted SJR load 7,180 lbs annually; 3,590 lbs in six months; full conveyance to the Bay-Delta.

Sac R. 17 1,850 0.04

SJR 1.1 3,590 1.2

SLD 0 0 0

Refineries 0.005 680 50

0.12 0.06 0.120 0.060 0.360 0.180 1.200 0.600

A "restoration scenario" for the SJR; (No SLD extension, refinery cleanup).

Sac R. 17 1,850 0.04

SJR 2.25 3,060 0.5

SLD 0 0 0

Refineries 0.005 680 50

0.11 0.05 0.110 0.050 0.330 0.150 1.100 0.500
Table F4. Calculation of particulate Se concentrations (ug Se/g) from inputs of the Sacramento River (Sac R),

the San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and the oil refineries under 

different load scenarios. Forecasts are for a wet year during the low flow season.

Volume Load Concentration Concentration Concentration at Particulate Concentration 

MAF lbs Se per ug Se/L FW Endmember Carquinez Strait Kd = 1,000 Kd=3,000 Kd = 10,000

6 months in source ug Se/L at 20 psu FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait

 ug Se/g

2. San Luis Drain Scenarios: Wet Year (1997 data); Low Flow Season

a) SLD at half capacity (150 cfs), 50 ppb Se (6,800 lbs in six months); little SJR reaches Bay-Delta.

Sac R. 2.3 250 0.04

SJR 0.001 3 2

SLD 0.05 6,800 50

Refineries 0.005 680 50

1.21 0.6 1.210 0.600 3.630 1.800 12.100 6.000

b) SLD at full capacity (300cfs), 62.5 ppb Se (18,700 lbs in six months); little SJR reaches Bay-Delta.

Sac R. 2.3 250 0.04

SJR 0.001 5 2

SLD 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

c) SLD at full capacity (300 cfs), 150 ppb (44,880 lbs in six months); little SJR reaches Bay-Delta.

Sac R. 2.3 250 0.04

SJR 0.001 5 2

SLD 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

d) SLD at full capacity (300 cfs), 300 ppb Se ( 89,760 lbs in six months); little SJR reaches Bay-Delta.

Sac R. 2.3 250 0.04

SJR 0.001 5 2

SLD 0.11 89,760 300

Refineries 0.005 680 50

13.80 6.9 13.800 6.900 41.400 20.700 138.000 69.000

Targeted SJR load of 6,800 lbs annually; 3,400 lbs in six months; full conveyance to the Bay-Delta.

Sac R. 2.3 250 0.04

SJR 0.5 3,400 2.5

SLD 0 0 0

Refineries 0.005 680 50

0.57 0.28 0.570 0.280 1.710 0.840 5.700 2.800

A "restoration scenario" for the SJR (No SLD extension, refinery cleanup). 

Sac R. 2.3 250 0.04

SJR 0.75 1,020 0.5

SLD 0 0 0

Refineries 0.005 680 50

0.23 0.12 0.230 0.120 0.690 0.360 2.300 1.200
Table F5. Calculation of particulate Se concentrations (ug Se/g) from inputs of the Sacramento River (Sac R),

the San Joaquin River (SJR), a proposed San Luis Drain (SLD) extension, and the oil refineries under 

different load scenarios. Forecasts are for a critically dry year during the low flow season.

Volume Load Concentration Concentration Concentration at Particulate Concentration 

MAF lbs Se per ug Se/L FW Endmember Carquinez Strait Kd = 1,000 Kd=3,000 Kd = 10,000

6 months in source ug Se/L at 20 psu FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait

 ug Se/g

3. San Luis Drain Scenarios: Critically Dry Year (1994 data); Low Flow Season

a) SLD at half capacity (150 cfs), 50 ppb Se (6,800 lbs in six months); little SJR reaches Bay-Delta.

Sac R. 1.3 141 0.04

SJR 0.0005 3 2

SLD 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

b) SLD at full capacity (350 cfs), 62.5 ppb Se (18,700 lbs Se in six months); little SJR reaches Bay-Delta.

Sac R. 1.3 141 0.04

SJR 0.0005 3 2

SLD 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

c) SLD at full capacity (300 cfs), 150 ppb Se (44,880 lbs in six months); little SJR reaches Bay-Delta.

Sac R. 1.3 141 0.04

SJR 0.001 5 2

SLD 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

d) SLD at full capacity (300 cfs), 300 ppb Se (89,760 lbs in six months); little SJR reaches Bay-Delta.

Sac R. 1.3 141 0.04

SJR 0.0005 3 2

SLD 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

Targeted SJR load of 7,180 lbs annually (3,590 lbs in six months); full conveyance to Bay-Delta.

Sac R. 2.3 250 0.04

SJR 0.5 3,400 2.5

SLD 0 0 0

Refineries 0.005 680 50

0.86 0.43 0.860 0.430 2.580 1.290 8.600 4.300

A "restoration scenario" for the SJR (No SLD extension, refinery cleanup). 

Sac R. 1.6 174 0.04

SJR 0.28 381 0.5

SLD 0 0 0

Refineries 0.005 680 50

0.24 0.12 0.240 0.120 0.720 0.360 2.400 1.200
Table F6. Bioaccumulation of Se by a generic bivalve under various scenarios.

AE1=0.35 AE2=0.55 AE3=0.63 AE4=0.8 Ke=0.03 IR=0.2

AE = assimilation efficiency; Kd = distribution (partitioning) coefficient; Ke = rate constant of loss; IR = ingestion rate

1A 1B 2A 2B 3A 3B

Kd = 1,000 Kd=3,000 Kd = 10,000

FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait

All values in the table below are ug Se/g dry weight. 

Scenario: Wet year (1997 data); High flow season

SLD at half capacity (150 cfs), 50 ppb Se (6,800 lbs in six months); SJR reaches Bay-Delta.

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

SLD at full capacity (300 cfs), 62.5 ppb Se (18,700 lbs Se in six months); SJR reaches Bay-Delta

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

SLD at full capacity (300 cfs); 150 ppb Se (44,880 lbs in six months); SJR reaches Bay

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

Prior to refinery cleanup (No SLD 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
Table F7. Bioaccumulation of Se by a generic bivalve under various scenarios.

AE1=0.35 AE2=0.55 AE3=0.63 AE4=0.8 Ke=0.03 IR=0.2

AE = assimilation efficiency; Kd = distribution (partitioning) coefficient; Ke = rate constant of loss; IR = ingestion rate 

1A 1B 2A 2B 3A 3B

Kd = 1,000 Kd=3,000 Kd = 10,000

FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait

All values in the table below are ug Se/g dry weight. 

Scenario: Wet Year (1997 data); Low flow season

SLD at half capacity (150 cfs), 50 ppb Se (6,800 lbs in six months); little SJR reaches Bay-Delta.

Particles 1.2 0.6 3.6 1.8 12.1 6.0

AE1 3.5 1.8

AE2 16.6 8.3

AE3 63.5 47.3

AE4 80.7 60.0

SLD at full capacity (300 cfs), 62.5 ppb Se (18,700 lbs Se in six months); little SJR reaches Bay-Delta

Particles 3.0 1.5 9.0 4.5 29.9 14.9

AE1 8.7 4.3

AE2 41.1 20.5

AE3 157.0 117.34

AE4 199.3 149.00

SLD at full capacity (300 cfs), 150 ppb Se (44,880 lbs in six months); little SJR reaches Bay-Delta

Particles 7.0 3.5 20.9 10.5 69.7 34.9

AE1 20.3 10.2

AE2 95.8 48.0

AE3 365.9 274.84

AE4 464.7 349.00

Prior to refinery cleanup (No SLD extension)

Particles 0.390 0.200 1.170 0.600 3.900 2.000

AE1 1.71 0.88

AE2 8.04 4.13

AE3 30.71 15.75

AE4 39.00 20.00
Table F8. Bioaccumulation of Se by a generic bivalve under various scenarios.

AE1=0.35 AE2=0.55 AE3=0.63 AE4=0.8 Ke=0.03 IR=0.2

AE = assimilation efficiency; Kd = distribution (partitioning) coefficient; Ke = rate constant of loss; IR = ingestion rate

1A 1B 2A 2B 3A 3B

Kd = 1,000 Kd=3,000 Kd = 10,000

FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait

All values in the table below are ug Se/g dry weight. 

Scenario: Critically Dry Year; Low flow season

SLD at half capacity (150 cfs), 50 ppb Se (6,800 lbs in six months); little SJR reaches Bay-Delta.

Particles 2.1 1.0 6.2 3.1 20.7 10.3

AE1 6.1 2.9

AE2 28.4 14.2

AE3 108.7 81.1

AE4 138.0 103.0

SLD at full capacity (300 cfs), 62.5 ppb Se (18,700 lbs Se in six months); little SJR reaches Bay-Delta.

Particles 5.1 2.5 15.2 7.6 50.7 25.4

AE1 14.9 7.3

AE2 69.7 34.8

AE3 266.2 200.03

AE4 338.0 254.00

SLD at full capacity (300 cfs), 150 ppb Se (44,880 lbs in six months); little SJR reaches Bay-Delta.

Particles 11.9 5.9 35.6 17.8 119.0 59.0

AE1 34.7 17.2

AE2 163.2 81.6

AE3 624.8 464.6

AE4 793.3 590.0

Prior to refinery cleanup (No SLD extension).

Particles 0.530 0.270 1.590 0.810 5.300 2.700

AE1 2.32 1.18

AE2 10.93 5.57

AE3 41.74 21.26

AE4 53.00 27.00
Table F9. Bioaccumulation of Se by a generic bivalve under various scenarios.

AE1=0.35 AE2=0.55 AE3=0.63 AE4=0.8 Ke=0.03 IR=0.2

AE = assimilation efficiency; Kd = distribution (partitioning) coefficient; Ke = rate constant of loss; IR = ingestion rate

1A 1B 2A 2B 3A 3B

Kd = 1,000 Kd=3,000 Kd = 10,000

FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait

All values in the table below are ug Se/g dry weight. 

Targeted SJR Load of approximately 7,000 lbs Se annually (3,400 or 3,590 lbs Se in six months)

Critically Dry Year; Low Flow Season

Particles 0.86 0.43 2.58 1.29 8.60 4.30

AE1 2.5 1.3

AE2 11.8 5.9

AE3 45.2 33.9

AE4 57.3 43.0

Wet Year; Low Flow Season

Particles 0.57 0.28 1.71 0.84 5.70 2.80

AE1 1.7 0.8

AE2 7.8 3.9

AE3 29.9 22.05

AE4 38.0 28.00

Wet Year; High Flow Season

Particles 0.12 0.06 0.36 0.18 1.20 0.60

AE1 0.4 0.2

AE2 1.7 0.8

AE3 6.3 4.7

AE4 8.0 6.0