## 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 (Regio n 9, Water Division) and Joint Funding Agreements w i th Contra Costa County and Contra Costa Water District. The contents of this document do not necessarily reflect the view s 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 nam e s in this report is for identification purposes only and does not
constitute endorsem e nt 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 ......................................................................................2 5 Drainage management

............................................................................................................ .........27 Forecasting loads of selenium : general cons ideratons ....................................................................28
How to determine load

.......................................................................................................... ..........30 Characteristics of ag ricultural subareas

....................................................................................... ...32 Develop m ent of forecast s

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

....................................... . 38 Forecasting selenium loadings using data from individual subarea s

............................................. .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
Su mm a ry

........................................................................................................................ ................ . 44 Inputs of Selenium from Oil Refineries

......................................................................................... ... . 45 Inputs of Selenium from the Sacra m ento River

................................................................................ .46 Summary

........................................................................................................................ .....................47
HYDRAULIC CONNECTIONS AND CONVEYANCE OF SELENIUM TO THE BAY-DELTA 47
CONCENTRATIONS OF SELENIUM IN THE BAY-DELTA 4 9

Interpreting Effects of Source W ater Se Loads on Receiving W ater Se Concentration s

.................. . 49 Existing Concentrations in the Bay-Delt a

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

.............................................................................................................. ..............51 Concentrations observed in the Bay-Delta ......................................................................................5 2 iiiCHEMICAL 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 Sele nium in the Bay-Delta .............................................................................59

Particulate selenium in the San Joaquin Rive r

............................................................................... .59
Particulate seleni um in the Delta

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

..................................................... . 61
Sedi m entary selenium in Suisun Bay and San Pablo Bay

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

.............................................. . 63
Su mm a ry

........................................................................................................................ ................ . 64
BIOACCUMULATION OF SELENIUM BY INVERTEBRATES 64 Processes

..................................................................................................................... . ..................... . 64
Selenium in Invertebra tes from the Bay-Delt a

.................................................................................. . 65
Su mm ary of Selenium in Invertebrates from the Bay-Delt a

............................................................. . 68 Modeling Selenium Bioaccumulation in the Bay-Delta: DynBaM ....................................................69
BIOACCUMULATION OF SELENIUM BY PREDATORS 71 Dietary Exposur e

.............................................................................................................. . ................ . 71 Existing Selenium Concentrations in Tissues of Birds and Fish in the Bay-Delt a

........................... . 73
EFFECTS OF SELENIUM ON WILDLIFE 76 Relating Selenium Concentrations in F ood (Prey) to Effects in Predator s

....................................... . 78

Fis h

.......................................................................................................................... . ...................... . 78
Bird s

......................................................................................................................... . ..................... . 78 Relating Selenium Concentrations in Tissue to Effects in Predator s

................................................ .79

Fis h

.......................................................................................................................... . ...................... 79
Bird s

......................................................................................................................... . ..................... .81 Comparison to Selenium Hazard Index

............................................................................................ ..83
FORECASTS 85 Forecasts of Co m posite Input Loads and Volu m es to the Bay-Delta

............................................... . 85
Forecasts of W aterborne Selenium Concentrations

.......................................................................... .89 ivCalculating co m posite selenium input (or freshwater end m e m ber) concentration s

...................... .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 sele nium concentration s

............................................................................... . 94 Su mm a ry of forecast s

.......................................................................................................... . .......... . 96 Forecasts of Speciation and Transformation

..................................................................................... .98 Defining speciation, transfor mation, and bioavailability ................................................................99 Comparison to Bay-Delta conditions prior to refinery cleanup ....................................................101
Forecasts of Particulate S e lenium Concentration s

.......................................................................... . 101
Sedi m ent quality guideline s

................................................................................................... . ..... . 101
Particulate selenium concentrations (all concentrations are in μ g Se/g dry weight, dw)

............ . 102
Cu m ulative su mm a ry

............................................................................................................ . ...... . 104 Other possible scenario s

...................................................................................................... . ........ . 106
Forecasts of Bioaccu m ulation in Consu m er Organis m s

................................................................. . 107 Calculating bioaccu m ulation in a generic bivalve ( m odeling)

.................................................... . 107 Comparing model predictions to Bay-Delta conditions prior to refinery cleanup ........................109 Bivalves as food for predators

................................................................................................ . .... . 109
Generic bivalve selenium concentrat i ons (i.e., conta m ination 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
CONC L USIONS 117

Cu m ulative I m pacts on the Bay-Delta

........................................................................................... . . 117 Extent and Sustainability of Agricultural Discharge from the San Joaquin Valle y

........................ . 120
I m plications and Monitoring Need s

............................................................................................. . .. . 122

ACKNOW LE DGM E N T S 127
R E F E R E NC E S 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 Invent ory 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 D 1

- 26 APPENDIX E Sediment Quality and Quantity Tables E1-3 APPENDIX F Supple m ental 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 wa ters) 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 disc harges from the five subareas of the western San Joaquin Valley using current available data. Di scharges 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.

vi9. The balance between water diversions (e.g., pum ping 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., pum ping 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 Sacram ento River are diluted by concentrations in the Pacific Ocean as indicated by salinities (practical-salinity units, psu). The

exam ple m i xing profile shows the selenium concentration in a hypothetical average freshwater endm em ber as it is diluted by concentrations in the Pacific Ocean. This endm em ber was calculated f r om loads and volum es in the Sacram ento River at 20 m illion acre-f eet (MAF) per year plus refinery inputs of approxim a tely 4,000 lbs Se per y ear (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,

com p aring 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,

com p aring high and low flow seasons in 1986 (9/86) and in 1995-96 (10/96). 14. Frequency distributions of selenium concentrations in (a) 129 com posite sam p les of C. fluminea collected between January 1985 and October 1986; and (b) 62 com posite sam p les 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 com posite sam p les of P. amurensis from 1995 through 1997 as a function of Delta outflow. Flows are averaged on a m onthly basis. 16. Selenium concentrations in replicate com posite sam p les of P. amurensis at 22 locations in the BayDelta during October 1996. Bivalve selenium concentrations are given in μ g Se/g dry weight. 17. Selenium concentrations in fish sam p les coll ected from the North Bay during 1986. Data from California Departm e nt of Fish and Gam e Selenium Verification Study (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). 18. Average selenium concentrations in bird liver sam p les collected from Suisun Bay and San Pablo Bay from 1986 to 1990. Data from Califor nia Departm e nt of Fish and Gam e Selenium Verification Study (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). Species m a rked with an asterisk were collected in Suisun Marsh. 19 . Forecasts of com posite freshwater endm em ber selenium concentrations for a series of concentration m a nagem e nt scenarios for the San Jo aquin River in low flow seasons of both wet and dry years. 20. Forecasts of m onthly com posite freshwater endm em ber selenium concentrations under three discharge scenarios (San Joaquin River at 1 and 2 μ g Se/L; San Luis Drain at 62.5 μ g Se/L) contrasted to input concentrations and loads of selenium

. 21. Dilution of selenium through the estuary as a functi on of salinity (practical-salinity units, psu) in October 1997 (wet year). Carquinez Strait is assum e d to be about half seawater salinity (17.5 practical-salinity units). The com posite freshwater endm em ber selenium concentrations are forecast for the SJR at 1 and 2 μ g Se/L and for a SLD extension at 62.5 μ g Se/L. 22. Forecasts of seasonal com posite freshwater endm em ber 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 m onths. The SJR forecast releases 3,500 lbs Se per six m onths.

vii23. Calculation of eight com posite freshwater endm em ber selenium concentrations as derived from different com b inations of total input load and total river inflow. River inflows are the com posited

m a ss of water that reaches the estuary in a six-m onth period. The range of inflows and input loads are typical of different clim ate regim e s (wet year or dry year) during the six-m onth dry season. 24. Suspended particulate selenium concentrations as a function of total dissolved selenium concentrations. Lines describing predicted par ticulate concentrations using Kd’s of 1 X 10 3 and 1 X 10 4 are superim posed 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 superim posed on the projections. 26. Relation between bivalve selenium concentrations and selenium concentrations in surf scoter liver. Data from California Departm e nt of Fish and Gam e Selenium Verification Study (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). 27. Relation between bivalve selenium concentrations and selenium concentrations in sturgeon flesh. Data from California Departm e nt of Fish and Gam e Selenium Verification Study (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). 28. Relation between bivalve selenium concentrations and selenium concentrations in sturgeon liver. Data from California Departm e nt of Fish and Gam e Selenium Verification Study (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991).



### TABLES 1 . Chronology of authorizing, planning, regulatory a nd evidentiary events for construction of a valleywide drain or San Luis Drain. 2 . Chronology of investigative and regulatory ev ents for the San Francisco Bay-Delta Estuary concerning selenium

. 3. Measured and estim ated selenium concentrations in shallow ground water and subsurface drainage in W e stlands W a ter 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 m illion acre-feet (MAF) and selenium loads from the upstream drainage source (Drainage Problem Area or Grassland Bypass Cha nnel Project site B) and downstream sites for Mud and Salt Sloughs, and the San Joaquin River at Crows Landing (state com p liance 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 assum e d 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 im plem entation of recom m e nded plan) and with future (i.e., im plem entation of recom m e nded 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, estim ating the lowest, although probably not realistic, irrigation water return. The year 2000 projection for problem wateris calculated here applying a factor of 0.4 acrefeet per acre per year; this projection was not part of the SJV Drainage Program consideration.

viii7 . Our calculations of selenium concentrations in discharge from SJV Drainage Program subareas based on evidence presented by W e stlands W a ter District or currently available ranges of

m easurem ents for drainage volum e (acre-feet) and selenium load (i.e. m easured values after the SJV Drainage Program database m easurem ents in 1986-1989; see footnotes for source), except for Northern subarea where there is no recom m e nded m a nagem e nt plan by the SJV Drainage Program (1990a) (see footnote). Only one set of values for the W e stlands W a ter District drainage volum e and selenium load was presented in evidence (see m i nim u m ) . Since no updated m easurem ents are available for W e stlands W a ter District, the condition for the m a xim u m load was calculated using an assigned* concentration of 150 ppb to the volum e of drainage presented in evidence. 8 . Projections of selenium loads from the we stern San Joaquin Valley under different drainage scenarios. A kesterson (kst) is 17,400 lbs of Se, the cum u lative load that caused visible ecological dam a ge when released to a wetland (Kesterson National W ildlife Refuge, California). 9 . Load of Se discharged if a constant concentration is m a intained in the SJR and conveyed to the Delta under high (3.0 MAF per year) and low (1.1 MAF per year) flow regim e s. Approxim a tely 220,000 acre-feet represent the annual volum e of flow from a proposed San Luis Drain extension at

m a xim u m capacity or a sm all 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 perm itting was required by 1998. 11 . Partitioning between dissolved Se and particulate or sedim e nt Se in ecosystem s f o r which reliable analytical data is available. 12 . Selenium concentrations in fish ( μ g Se/g dry weight) from the Bay-Delta (North Bay including Suisun, San Pablo, Grizzly and Honker Bays) a nd Hum boldt Bay (Selenium Verification Study, W h ite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). 13. Exam ples of thresholds for Se effects (health, repr oductive, teratogenesis, or survival) in fish based concentrations of Se in food; the exam ple of m a ssive poisoning at Kesterson Reservoir, California also applies to aquatic birds. Selenium concentrations in the m o st abundant benthic prey (food) organism in the Bay-Delta are given for com p arison. 14. Exam ples of thresholds for Se effects (health, repr oductive, 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 com p arison. 15 . Exam ples 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 speci es from Kesterson Reservoir and the Bay-Delta are given for com p arison. 22. Selenium loads em ployed in forecasts of Se im pacts. Loads were calculated for a six-m onth season. Annual loads would be two tim es higher if Se discharge is continuous (i.e., at a constant rate). Agricultural inputs fall into three groups depending on m a nagem e nt 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. Com p arison of Se hazard in the Bay-Delta and other environm ents. Values are Se concentrations in μ g Se/g dry wt. Hazard ratings for each set of concentrations are stated within each cell (as defined by Lem l y, 1995 and 1996b). The individual scores and total score are com p ared to listed evaluation criteria to determ ine a hazard rating (high, m oderate, low, m i nim a l, or none identified) (Lem ly, 1995). For the Bay-Delta, bird egg concentr ations are converted from bird liver. Data

ixsources are Lem l y, 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 com posite freshwater (FW ) endm em ber concentration of Se ( μ g Se/L) from inputs of the Sacram ento River (Sac R), the San Joaquin River (SJR), and oil refineries under conditions sim u lating those prior to refinery cleanup. Forecas ts contrast wet and dry years: and high and low flow seasons. Load is expressed in lbs Se per six m onths. 19. Calculation of a com posite freshwater (FW ) endm em ber concentration of Se ( μ g Se/L) from inputs of the Sacram ento 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 m onths. Forecasts 1a through 1d use a SLD extension and assum e a 2 MAF SJR inflow reaches the Bay-Delta. The final forecast

assum e s no SLD extension and a SJR inflow of 1.1 MAF. 20. Calculation of a com posite freshwater (FW ) endm em ber concentration of Se ( μ g Se/L) from inputs of the Sacram ento 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 m onths. Forecasts 2a through 2d use a SLD extension and assum e little SJR inflow reaches the Bay-Delta. The final forecast assum e s no SLD extension and a 0.5 MAF SJR inflow. 21. Calculation of a com posite freshwater (FW ) endm em ber concentration of Se ( μ g Se/L) from inputs of the Sacram ento 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 m onths. Forecasts 3a through 3d use a SLD extension and assum e little SJR inflow reaches the Bay-Delta. The final forecast assum e s no SLD extension and a 0.5 MAF SJR inflow. 22. Calculation of a com posite freshwater (FW ) endm em ber concentration of Se from inputs of the Sacram ento River (Sac R), the San Joaquin River (SJR), and oil refineries under a “restoration” scenario. Se load is lbs Se per six m onths. A ssum e greater SJR inflows enter the Bay-Delta to aid fish m i gration and the SJR input is held constant at 0.5 μ g Se/L. High flow season conveys 75% of the SJR annual flow; low flow season, 25%. 23. Sum m a ry of forecasts of Se concentrations in a com posite freshwater endm ember entering the BayDelta under different conditions. Load is expressed in lbs per six m onths. SLD loads are for the SLD only; targeted load and “restoration” scenario is for the SJR only. C F is a com posite concentration in all sources of freshwater at the h ead of the estuary (i.e. near the discharge point of a proposed SLD extension); C E is a com posite concentration at 17.5 practical-salinity units (psu), usually near Carquinez Strait during the low flow season. 24. Sum m a ry of forecasts of Se concentrations in pa rticulate m a terial under different conditions. Load is expressed in lbs Se per six m onths. 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 10 4

, typical of suspended sedim e nt; C2 is the concentration forecast at a Kd of 3X10 3 , typical of shallow-water bed sedim e nt; C3 is the low reactivity concentration f o recast at a Kd of 10 3 . 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 clim ate regim e s;
• in different seasons; and

x• for alternative speciation and biogeochem i cal behavior patterns. The scenarios considered are:

• a SLD extension discharge of 18,700 lbs per six m onths (full capacity, 62.5 μ g Se/L);

• a SJR discharge of a targeted load of 3,590 lbs per six m onths for a wet year (1.2 μ g Se/L) and 3,400 lbs per six m onths for a dry year (2.5 μ g Se/L). Forecasts are com p ared to conditions prior to refinery cleanup. 26 . Laboratory-derived physiological constants for Se bioaccum u lation by several species of bivalve and com posite values for a generic bivalve (data from Luom a 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 elem en tal Se (constants from Luom a et al., 1992 and Reinfelder et al., 1997). 28 . Sum m a ry of forecasts of Se concentrations in a generic bivalve under different conditions. Load is expressed in lbs per six m onths. 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 10 4 , typical of suspended sedim e nt; C2 is the concentration forecast at a Kd of 3X10 3 , typical of shallow-water bed sedim e nt; C3 is the low reactivity concentration forecast at a Kd of 10 3 . Four assim ilation efficiencies have been assum e d 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 bioaccum u lated by a generic bivalve at the head of the Bay-Delta estuary:

• in years with different clim ate regim e s;
• in different seasons; and

• for alternative speciation and biogeochem i cal behavior patterns. The scenarios considered are:

• a SLD extension discharge of 18,700 lbs per six m onths (full capacity, 62.5 μ g Se/L);

• a SJR discharge of a targeted load of 3,590 lbs per six m onths for a wet year (1.2 μ g Se/L) and 3,400 lbs per six m onths for a dry year (2.5 μ g Se/L). Forecasts are com p ared to conditions prior to refinery cleanup. 30. Regression equations for bivalves versus bivalve predators. Data from Selenium Verification Study (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991) 31. Data em ployed in regression of Se concentrations in bivalves versus Se concentrations in bivalve predators. Means from different years are a ggregated; 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 (W hite et al., 1987*; 1988*; 1989*; Urquhart and Regalado, 1991*; Johns et al., 1988*; Luom a and Linville, 1997****; Linville and Luom a, in press ). Selenium as ppm is equivalent to m i cr ogram s 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 m onths (37,400 lbs Se per year) and 2) the SJR scenario is for a targeted load of 3,500 lbs per six m onths (7,000 lbs per year) (SJR conditions defined earlier). All forecasts are for six m onths of discharge during the low flow season of a critically dry year. Forecast concentrations are com p ared to average Se concentrations in these organism s (Corbicula flum inea in 1988-1990; Potam o corbula am urensis, 1995-1996; surf scoter, greater and lesser scaup,

xiand 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, com posite freshwater endm em ber Se concentrations, particulate Se concentrations, Se bioaccum u lation by bivalves, Se bioaccum u lation 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 m i xing; and the low flow season of a dry year. Conditions prior to refinery cleanup are given for com p arison. 

### CONVERSION FACTORS By weight: m i crogram per gram is equivalent to parts per m illion (ppm ) 1 m i crogram ( μ g/g) = 10 -6 gram (g) For concentration of dissolved solids less than approxim a tely 7,000 m g /L: Milligram per liter (m g/L) is equivalent to parts per m illion Microgram per liter ( μ g/L) is equivalent to parts per billion (ppb) 1,000 m i crogram per liter ( μ g/L) = 1 m illigram per liter (m g/L) See also Table 4 (in text) which is duplicated below. Selenium (Se) Salt or Total Dissolved Solids (TDS) 1 ppb Se =1 μ g Se/ L 1 p p m TDS = 1 m g salt/L 1 gal l on = 3.785 Li t e rs 1 gal l on = 3.785 Li t e rs 1 acre-foot = 325,900 gallons = 1,233,532 liters 1 acre-foot = 325,900 gallons = 1,233,532 liters

1,233,532 μ gram s Se/ acre-foot at

1 ppb Se 1.23 gram s Se/ acre-foot at 1 ppb Se 1, 234 gram s salt/acre-foot at 1 ppm salt 454 gram s = 1 l b 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 l b s = 1 t on 1 ppm salt = 0.00136 tons salt/acre-foot VOLUME 1 cubi c foot per second (cfs) = 1.98 acre-feet / d ay For those who prefer to use the International System of Units (SI), the conversion factors f

o r term s used in this report are listed below. Mu ltip l y B y To o b t ain Acre 4,047 square m e t e r (m 2 ) A c r e 0

. 4 0 4 7 hect a r e ( h a ) acre-foot 1,233 cubi c m e t e r (m 3 ) cubi c foot per second (cfs) 0. 02832 cubi c m e t e rs per second (m 3 /s)

xii

### ABBREVIATIONS
AF Acre-foot AE Assim ilation Efficiency BAF Bioaccum u lation Factor BSAF Biota to Sedim e nt Accum u lation Factor Bay-Delta San Francisco Bay-Delta Estuary CALFED A cooperative, interagency effort of fifteen federal and state agencies with

m a nagem e nt and regulatory responsibilities for the Bay-Delta CCtF Clifton Court Forebay CCVRW QCB Calif ornia Central Valley Regional W a ter Quality Control Board CDFG California Departm e nt of Fish and Gam e CDW R California Departm e nt of W a ter Resources CSFBRW QCB Calif ornia San Francisco Bay Regional W a ter Quality Control Board CSW RCB California State W a ter Resources Control Board CVP Central Valley Project dw dry weight DynBaM Dynam i c Multi-path Bioaccum u lation Model FR Feeding Rate GBCP Grassland Bypass Channel Project K d Distribution (partitioning) coef f i cient kst kesterson unit (equals 17,400 lbs Se) MAF Million Acre-Feet NMFS National Marine Fisheries Service psu practical-salinity unit Sac R Sacram ento River SJR San Joaquin River SJV San Joaquin Valley SJVDP San Joaquin Valley Drainage Program SLD San Luis Drain SLU San Luis Unit SW P State W a ter Project TMDL Total Maxim u m Daily Load TMML Total Maxim u m Monthly Load USBR United States Bureau of Reclam ation USEPA United States Environm ental Protection Agency USFW S United States Fish and W ildlife Service USGS United States Geological Survey WWD We s t l a n d s Wa t e r D i s t r i c t W Y W a ter Year (A water year begins on October 1 st )

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 stat e agencies m a y be required to evaluate proposals and discharge perm its that could significantly change se lenium (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 m a y include discharge requirem e nts 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 agreem ent to allow the existing por tion 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 refinem e nts to prom ulgated Se criteria for the protection of aquatic life for the estuary. Understanding the biotransfer of Se is essential to evaluating the fate and im pact of proposed changes in Se discharges to the Bay-Delta. However, past m onitoring program s have not addressed the specific protocols necessary for an elem ent that bioaccu m u lates. Confusion about Se threats in the past
have stem m e d from failure to consider the full com p lexity of the processes that result in Se toxicity. Past studies show that predators are m o re at risk from Se contam ination than their prey, m a king it
difficult to use traditional m e thods to predict risk from environm ental concentrations alone. In this report, we em ploy a novel procedure to m odel the fate of Se under different, potentially realistic load
scenarios from the SJV. For each potential load, we progressively forecast the resulting environm ental concentrations, speciation, transform a tion to particulate form , bioaccum u lation 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 dir ectly into the North Bay via a conveyance such as
the SLD. Our approach uses 1) existing knowledge concerning the biogeochem i cal reactions of Se (e.g., 1speciation, partitioning between dissolved and particul ate form s, and bivalve assim ilation efficiency) and 2) site-specific data m a inly from 1986 to 1996 on clam s and bottom

- feeding fish and birds. Forecasts of Se loading from oil refineries and agricultural drainage from the SJV enable the
calculation of a com posite freshwater endm em ber Se concentration at the head of the estuary and at Carquinez Strait as a foundation for m odeling. Our analysis of effects also takes into account the m ode of conveyance for agricultural drainage (i.e., the SL D or SJR). The effects of variable flows on a
seasonal or m onthly basis from the Sacram ento River and SJR are also considered.
The results of our forecasts for external SJV watershed sources of Se m i rror predictions m a de since 1955 of a worsening salt (and by inference, Se) buildup exacerbated by the arid clim ate and irrigation for agricultural use. W e show that the reservoir of Se in the SJV is sufficient to provide loading at an annual rate of approxim a tely 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 m a y 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 treatm e nt 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. Com ponents of this valley-wide load include five source subareas (i.e., Grassland, W e stlands, Tulare, Kern, and Northern) based on water and drainage

m a nagem e nt. Loads vary per subarea m a inly because of proxim ity of the subarea to geologic sources and irrigation history. Loads from the Sacram ento River, depending on flow conditions, range from 0.8 to 10 lbs Se per day. A consistent picture of ecological risk em erges for the Bay-Delta based on concurrent lines of evidence. The threat to the estuary is greatest during low flows and dry years. W h ere Se undergoes reactions typical of low flow or longer residen ce tim e, highly problem atic bioaccum u lation in prey (food) is forecast to result. The Bay-Delta predat ors—surf scoter, greater and lesser scaup, and white sturgeon—appear to be m o st at risk because they feed on filter-feeding bivalves. Recent findings add
Sacram ento splittail to that list. During the low flow season of dry years, the lower range of proposed protective guidelines for waterborne, particulate, di etary, and predator tissue Se is exceeded under the

m o st likely forecast of Se inputs from a proposed SLD extension. Also under low flow conditions, the
2upper range of guidelines (i.e., high certainty of advers e effects) is exceeded in all instances except at the lowest load considered. High flows afford som e protection in the forecast SJR scenarios under certain conditions. However, m eeting a com b ined goal of releasing a specific load during m a xim u m flows and keeping Se concentrations below a certain objective to protect against bioaccum ulation m a y not always be attainable. Managem e nt of the SJR on a constant concentration basis could also create problem atic bioaccum u lation during a wet year, esp ecially 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 contam ination was sufficient to threaten reproduction in key species within the Bay-Delta ecosystem s and hum an health advisories were posted based on Se concentrations in livers of diving ducks. During this tim e, Se concentrations in the Bay-Delta were well below the

m o st stringent water quality criteria. Enhanced biogeochem i cal transf orm a tions to bioavailable particulate Se and efficient uptake by bivalves and th en predators characterized the system . If these biogeochem i cal conditions continue to prevail, the forecasts suggest the risk of adverse effects will be
difficult to elim inate under an out-of-valley resolution to the Se problem

. The forecasts for Se loading present a new t ool to evaluate ecological effects based upon the m a jor processes leading from loads through consum er organism s to predators. It is a feasible approach for site-specific analysis and could provide a fram ew ork for developing new protective criteria. W e conclude that credible protective criteria should be based on 1) contam inant concentrations in sources, such as particulate m a terial, that m o st inf l uence bioavailability and 2) concentrations in m e dia and organism s relevant to vulnerable food webs. Existing criteria for water, particulate m a terial, and tissue of prey and predators should be used in com b ination to evaluate risk or hazard. Bivalves appear to be
the m o st sensitive indicator of Se contam ination in the Bay-Delta.



### INTRODUCTION The sources and biogeochem i stry of Se com b ine to m a ke contam ination with this elem ent an ecological issue of widespread concern [Treleas e and Beath, 1949; National Research Council, 1976; 1989, U.S. Environm ental Protection Agency (U SEPA), 1980; 1987; 1992; 1998; W ilber, 1983; also

see com p ilations in Frankenberger and Benson, 1994; Lem l y, 1995; Frankenberger and Engberg, 1998; Skorupa, 1998a; Seiler et al., 1999; Ham ilton, 1999; Eisler, 2000; Ham ilton, 2000a]. Selenium is especially enriched in organic-rich shales that are source rocks for oil, coal, and phosphate ores (Figure 1) (Cum bie and Van Horn, 1978; Presser, 1999; Piper et al., 2000). Release of Se to aquatic system s is 3a result of weathering and anthropogenic activities such as refining, power production, and m i ning.
Selenium is also enriched in the soils and runoff derived from these source sedim e ntary shales in m a ny

sem i -arid regions exploited for irrigated agriculture, such as in the SJV, California (Presser, 1994a; b; Seiler et al., 1999). Salinization of som e of these soils is accom p anied by Se contam ination that
increases the com p lexity of problem s associated with continued exploitation of such lands (SJV Drainage Program , 1990a; Dinar and Zilberm a n, 1991). Irrigation, leaching, and generation of subsurface drainage leads to surface and ground wate rs being contam inated (Presser and Ohlendorf, 1987). Treatm e nt technologies for Se have utilized both chem ical and biological processes to rem ove Se from the water colum n, but with little operational success or cost-effectiveness (SJV Drainage Program , 1990a; Hanna et al., 1990; SJV Drainage Im plem entation Program , 1998; 1999a). Use of large-scale biological treatm e nt technologies (e .g. wetlands or evaporation ponds) has generated serious ecological problem s and hazardous Se wastes for disposal (Presser and Piper, 1998; Skorupa, 1998a; Ham ilton, 2000b). Selenium rem oval is further ham p ered by the failure of traditional chem ical

m e thods to reduce Se to levels acceptable for rem e diation and, in arid regions, by the problem of disposal of associated salts (SJV Drainage Progr am , 1990a). Rem e diation has not been established other than that dependent on dilution in a larger body of water (SJV Drainage Im plem entation Program , 1998; U.S. Departm e nt of the Interior’s National Irrigation W a ter Quality Program , 2000). Managem e nt plans for the western SJV that incl ude drainage storage and reduction through source control have been developed, but system atic and com p rehensive im plem entation has not taken place (SJV Drainage Program , 1990a; SJVDP, 1991; SJ V Drainage Im plem entation Program , 1998;
Environm ental Defense Fund, 1994). The biogeochem i cal cycling of Se and its role as an essential nutrient lead to the dom inance of biological reactions over therm odynam i c reactions in aquatic system s (Shrift, 1964; Stadtm an, 1974; National Research Council, 1976; Measures a nd Burton, 1978; Cutter and Bruland, 1984; Lem l y, 1985; Presser and Ohlendorf, 1987; Orem land et al ., 1989; Luom a et al., 1992; Maier and Knight, 1994; Presser, 1994a; Lem l y, 1997b; W a ng et al., 1996; Luom a and Fisher, 1997; Dowdle and
Orem land, 1999; Reinfelder et al., 1998). The fate and adverse ecological effects of Se discharges are
determ ined by a sequence of linked processes that connect loads, concentrations, speciation, bioavailability, trophic transfer, and effects on pr edators (Luom a et al., 1992; Luom a, 1996; W a ng et al., 1996; Reinfelder et al., 1997; 1998; Luom a and Fisher, 1997) (Figure 2). Pathway
bioaccum u lation m odels allow consideration of 1) biotransfer from different types of
4suspended/particulate m a tter (e.g., phytoplankton, se ston, and benthos); 2) biotransform ation to different speciation regim e s (selenate, selenite, or gano-Se, elem ental Se); 3) bioaccum u lation via the lower trophic food web; and 4) uptake of food by predat or species. Because Se concentrations can be

m a gnified 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 m o st vulnerable to adverse effects from Se

contam ination. Aquatic species potentially at ri sk from Se contam ination (Figure 1) include
charism a tic birds (e.g., ducks, shorebirds, and grebes ) and fish (e.g., sturgeon, carp, trout, and sunfish) (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991; Luom a et al., 1992; Lem l y, 1993a; 1998a; b; Skorupa, 1998a). Herps (frogs and snakes ) also m a y be at risk from Se [Skorupa, 1998b;
U.S. Fish and W ildlife Service (USFW S) and Na tional Marine Fisheries Service (NMFS), 1998 and

am ended, 2000), as m a y Sacram ento splittail (Stewart, et al., in preparation). Analysis of one of the above sets of processes, in isolation, is inadequate to characterize Se problem s (Luom a and Fisher, 1997). If correlations m a de am ong factors or processes skip links, then
serious uncertainties will result. Failure to consider the f u ll sequence of interacting processes is a

m a jor cause of controversy surrounding m a ny interpretations of Se effects on the environm ent (e.g., O’Toole and Raisbeck, 1998; Ham ilton and Lem l y, 1999; Chapm a n, 1999; Lem l y, 1999a; Skorupa, 1998a; 1999). In view of advances in the understanding of Se environm ental chem istry, the USEPA has recently called for a re-definition of the Se crite ria for the protection of aquatic life (USEPA, 1998; Renner, 1998).
Selenium contam ination of aquatic ecosystem s is of special concern in large areas of California, and
other sem i -arid regions of western North Am erica (Presser, 1994a; b; Seiler et al., 1999). Selenium issues are of particular concern in the SJR basin (F igure 3) and in the Bay-Delta (Figure 4). Here, Se issues are intricately interwoven with issues of water m a nagem e nt, urbanization, irrigated agriculture, and protection of fish and wildlife resources [Conom os, 1979; Conom os et al., 1985; Cloern and Nichols, 1985; Nichols et al., 1986; California State W a ter Resources Control Board (CSW RCB), 1994; 1999a; USFW S, 1995; Hollibaugh, 1996; Presse r and Piper, 1998; CALFED, 1998a; b; 1999a; b; c; d; Thom pson et al., 2000]. The SJV has also su ffered m a jor losses of crucial habitat for m i gratory birds (Gilm er at al., 1982; Vencil, 1986). The goal of this paper is to introduce a com p rehensive approach to forecast the ecological effects of Se under an array of scenarios that could result from different resolutions of water and waste

m a nagem e nt issues. W e concentrate on analysis of Se inputs based on engineering solutions that 5would convey Se-laden salts from the western SJV to the Bay-Delta via a proposed extension of the San Luis Drain (SLD) (Barcellos, 1986; W a nger, 1994; CSW RCB, 1996b; c; 1999a; d; Stevens and Bensing, 1994; Contra Costa County, 1997; San Joaqui n River Exchange Contractors W a ter Authority, 1999; Trinity County, 1999; U.S. House of Representa tives, 1999; Hug, 2000). W e 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. W e present a history of the disc ussions surrounding the construction of the drain and use of the SJR to convey Se outside the SJV. W e fo recast loads, concentrations, fate, and effects of Se
on anim als in the estuarine food web that could result from projected Se discharges. Our approach involves using existing knowle dge, that includes em pirical observations from the Bay-Delta and m odels, to convert proposed m a ss em issions to concentrations in receiving waters under
several scenarios. Bioaccum u lation in lower trophic level consum er organism s (bivalves) is projected
from a likely range of concentration, partiti oning, and speciation scenarios using pathway
bioaccum u lation m odels. Com p arisons of Se concentrations in Bay-Delta clam s are m a de 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
estim ate of potential adverse effects of Se m a ss em issions. The specific inform ation—bioaccum ulation of Se by clam s and biotransfer of Se to fish and waterfowl—could be applied to evaluate proposals for disposal of Se from the SJV that include discharg e to aquatic system s (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
im portant as the specifics of the discussion as applied to the Bay-Delta. The general process of a
linked bioaccum u lation m odel using a bioindicator organism to assess potential adverse im pacts on predators can be applied to other ecosystem s subjected to Se loading and can help in the developm ent of national or site-specific Se criteria for aquatic protection.

Generic Selenium Issues Existing knowledge concerning the biogeochem i stry of Se allows the following generalizations:
1. Geologic sources of Se are widespread (Figure 1).
2. Exploitation of energy sources (oil and coal), m i ning of phosphate ore, irrigation of areas underlain by organic-rich m a rine shales, and irriga tion of lands where alluvium is derived from
6such shales, m obilize geologic Se and ultim ately result in the contam ination problem s found today (see exam ples in Figure 1).
3. Linked biological and geochem i cal reactions aff ect the form of Se (Figure 2). Geochem i cal
form (speciation) determ ines how readily the elem ent enters aquatic food webs, initiates food web transfer, and cycles through particulate m a tter, sedim e nts, consum er organism s, and predators.
4. Hydrologic connections also determ ine the effects of Se. Com p artm entalized ecological system s can interact at critical hydrologic junctures such as in estuaries. Seem ingly harm less concentrations of Se in a riverine system m a y becom e problem atic in downstream
im poundm ents, m a rshes, or wetlands, where cycling and bioaccum u lation are accentuated (Luom a et al., 1992; Skorupa, 1998a; Lem l y, 1999b). The geographic scale of Se issues can extend beyond local conditions and therefore, an analysis of downstream effects needs to
f

o llow.
5. Traditional toxicity tests are problem atic because they determ ine toxicity only via direct waterborne exposures. Direct transfer of Se from solu tion to anim als such as fish and bivalves is a

sm all proportion of exposures. Bioaccum u lation and uptake via food is the m o st im portant route of Se transfer to upper trophic level speci es (Figure 2) (Ohlendorf et al., 1986; Saiki and Lowe, 1987; Presser and Ohlendorf, 1987; Lem l y, 1985; Luom a et al., 1992; Presser et al., 1994).
6. Selenium efficiently bioaccum u lates through aqua tic food webs, and strongly biom agnifies into

m a ny com ponents of the food web (Saiki, 1986; Presser and Ohlendorf, 1987; Luom a et al., 1992; Maier and Knight, 1994). Invertebrates m a y be the best indicator for m onitoring predator exposure. Consum er species like bivalves integrate the influences of environm ental concentrations, speciation, and transform a tions of Se and are practical to sam p le. Predators, on the other hand, are m obile and im practical to sam p le in large num bers on a routine basis. A predator’s choice of food, which varies widely am ong species, could result in som e trophic pathways being m o re efficient accum u lators of Se than others (Lem ly, 1982; 1985; Luom a, et al., 1992; Luom a and Fisher, 1997; Skorupa, 1998a; CH2M HILL, 1996; 1999a).
7. Charism a tic species (birds and fish) are the first to express the effects of Se contam ination due
to this efficient bioaccum l ation in the food web and their sensitivity to exposure to Se (Ohlendorf, 1989; Ohlendorf et al., 1989a; Ham ilton et al., 1990; Lem l y, 1996b ; c; Skorupa,
71998a; 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
environ m ent was at Kesterson National W ildlife R e fuge 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, ma ss 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; Santol o et al., 1999). Reproductive damage and teratogenesis can occur at low concentrations [low micrograms per liter ( μ g/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 base d 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 expos ure of surrogate species. Uncertainty also 8exists for criteria derived using lim ited field data on food chain exposure, because few studies
were available at the tim e of prom ulgation (U SEPA, 1992; 1998). The toxicity-testing database
does not consider bioaccum u lation, although bioaccum u lation from food determ ines the ecological effects of Se. A Se criterion deri ved prim arily from food web exposure would be

m o re relevant to field conditions in aquatic system s. 11. Effects of Se on hum an health are of concern. State hum an health advisories have restricted

consum ption of edible fish and birds and elim inated consum ption for children and pregnant

wom e n when Se concentrations exceed a certain criterion [California Departm e nt of Fish and
Gam e (CDFG), 1985; 1986; 1988, all on-going; 1987; Fan et al., 1988; SJV Drainage Program , 1989; 1990b]. 12. No satisfactory chem ical, physical or biological treatm e nt technology yet exists to rem ove Se

contam ination from irrigation drainage waters (Hanna et al., 1990; Hansen et al., 1998; SJV Drainage Im plem entation Program , 1999a; b; c; d) . Treatm e nt technologies that work on sm all
effluent stream s are inefficient and expensiv e to em ploy on large volum es of contam inated water (SJV Drainage Program , 1990a; SJV Drai nage Im plem entation Program , 1998; National Irrigation Drainage Program , 2000). Treatm e nt t echnologies still being tested are flow-through wetlands and biological precipitation (Hansen, et al., 1998; SJV Drainage Im plem entation Program , 1999a), even though large-scale biological treatm e nts have generated serious ecological problem s (Presser and Piper, 1998; Skor upa, 1998a). A m a nagem e nt plan specific to
the arid western SJV has dem onstrated through in-depth studies that com p rehensive and system atic im plem entation of com ponents, such as source control and land fallowing, can
reduce the am ount 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 com p lex, hydrologic system that extends
from the riparian wetlands of the Sacram ento River and SJR through the Bay-Delta to the Pacific Ocean (Presser and Piper, 1998) (Figures 3 and 4). This natural system provides the fram ework for the Central Valley Project (CVP) which is a m a ssive e ngineered com p lex of dam s , off-stream storage reservoirs, pum ping facilities, irrigation and drinki ng water supply canals, and agricultural irrigation drainage canals [U.S. Bureau of Reclam ation (US BR), 1984a]. Figure 5 presents a detailed schem a tic
9of the hydrologic connections of the SJV (Figure 3) to the Bay-Delta (Figure 4) including the
Sacram ento River and SJR. The sustainability of the balance and quality of water in this system are crucial to the welf are of Calif ornia, especially to the arid SJV.
Selenium issues are of special concern within the Bay-Delta ecosystem because:
1. Selenium contam ination exists under present conditions in the Bay-Delta from known sources of Se within the estuary and in watersheds draining to the estuary. W a tershed sources are
linked to SJV farm land activities where irrigation of salinized soils has led to proposed

m a nagem e nt alternatives to sustain agriculture by draining salts and Se collected as subsurface drainage to the Bay-Delta via the SJR or SLD [e.g., CSW RCB, 1985; SJV Drainage Program , 1990a; Presser and Ohlendorf, 1987; Presser and Piper, 1998; Skorupa, 1998a; California Central Valley Regional W a ter Quality Control Board (CCVRW QCB), 1998a; b; USFW S and NMFS, 1998 and am ended 2000). Proposals for c onstruction of a collector drain and an extension of the existing SLD to rem ove salts and Se from the SJV have been under
consideration f o r approxim a tely 50 years (Table 1). W a ter quality in the SJR has degraded significantly since the 1940’s because of disposal of agricultural wastewater from the SJV (CCVRW QCB, 1995). Even though the SJR is a source water for the Bay-Delta, selenium
sources and contam ination within the North Ba y (i.e., Suisun Bay and San Pablo Bay) have been linked in the past m a inly to oil refineries discharging waste from processing Se-enriched
crude oil from the SJV and adjacent Coast Ranges (e.g., W h ite et al., 1987; 1988; 1989; Cutter, 1989; Johns, et al., 1988; Cutter and San Die go-McGlone, 1990; Urquhart and Regalado, 1991; San Francisco Estuary Project, 1991; 1992; L uom a, et al., 1992; Brown and Luom a, 1995a;
Luom a and Linville, 1997; Linville and Luom a, in press; USFW S and NMFS, 1998 and

am ended, 2000).
2. Selenium contam ination docum ented from 1982 to the m i d-1990’s was sufficient to threaten reproduction (> 10 μ g Se/g in tissue) in key species within the Bay-Delta estuary ecosystem s (Table 2) [W hite et al., 1987; 1988; 1989; Urquha rt and Regalado, 1991; San Francisco Estuary Project, 1991; 1992; Harvey et al., 1992; Californi a San Francisco Bay Regional W a ter Quality Control Board (CSFBRW QCB), 1992a; b; 1993; Brown and Luom a, 1995a; Linville and
Luom a, in press]. The m o st severely threatened species appear to include, but are not restricted to white sturgeon ( Acipenser transmontaus ), Sacram ento splittail ( Pogonichthys macrolepidotas ), starry flounder ( Platichthys stellatus ), Dungeness crab ( Cancer magister ), 10surf scoter ( Melanitta perspicillata)
, greater scaup ( Aythya marilla)
, and lesser scaup (Aythya affinis ) (Ohlendorf et al., 1986; W h ite et al., 1987; 1988; 1989; Ohlendorf et al., 1989b; c; Urquhart and Regalado, 1991; Luom a et al., 1992; USFW S, 1995; Hothem et al., 1998). In 1989-1990 in the North Bay, average Se concentrations in surf scoter liver sam p les exceeded the threshold level for avian reproductive toxicity (Heinz, 1996) by eight-fold and in sturgeon
flesh sam p les exceeded the threshold for effects in fish (Lem ly, 1998b) by two-fold. Currently, populations and catches per unit effort (where applicable) of all the predator species m e ntioned
above are in decline. A num ber of causative factors m a y be involved (CALFED, 1998a; b; 1999a; b; c; d; USFW S and NMFS, 1998 and am ended, 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. Som e food webs in the Bay-Delta m a y be particularly vulnerable to m oderate Se

contam ination. Analyses in 1982-1996 showed that the anim als with the highest Se tissue
concentrations from the North Bay (i.e., Suis un Bay, Carquinez Strait, and San Pablo Bay) ingested bivalves ( Corbicula fluminea prior to 1986 and Potamocorbula amurensis in subsequent sam p lings) as a m a jor com ponent of their diet. Selenium concentrations in the predom inant bivalve in the Bay-Delta were higher in the m i d-1990’s (Linville and Luom a, in press) than in 1977 through 1990 (W hite et al., 1987; 1988; 1989; Cutter, 1989; Johns et al., 1988; Urquhart and Regalado, 1991), partly because a new species ( P. amurensis ) had becom e predom inant in the Bay-Delta. The specific bioaccum u lation pathway from sedim e nt and benthic/suspended biom ass to bivalves to pr edators (bottom feeding fish, diving ducks, and Dungeness crab) m a y be the m o st im portant route of Se transfer to the upper trophic levels in the estuary. Levels in P. amurensis reached 20 μ g Se/g dry weight (dw) in the North Bay in October 1996, exceeding two-fold the toxicity threshold in food for predators (> 10 μ g 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

contam ination from a suite of chem icals (e .g., m e rcury, diazinon, PCBs, dioxin, PAHs, and Se) (CCVRW QCB, 1994a; 1998b; CSW RCB, 1999b; c). State or federal criteria have been exceeded in these listed waterbodies, causing adverse aquatic life and hum an health im pacts (e.g., Fairey et al., 1997; Davis et al., 1997; Dubr ovsky et al., 1998). Portions of the SJR are

11designated 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 am ount and quality of the wetlands in the Bay-Delta leaves in doubt the future status of

m a ny wildlife populations (Harvey et al., 1992; CALFED, 1998a; b; San Francisco Estuary Project, 1999); Se contam ination affects the quality of the already lim ited acreage of wetlands and other crucial habitat (CALFED, 1998a; b and 1999a; b; c; d). A recovery plan was deem ed necessary for Sacram ento/San Joaquin Delta native fishes (USFW S, 1995). The plan includes designation of critical habitat (i.e., slight changes in habitat condition m a y cause large changes in population status) for Delta sm elt ( Hypomesus transpacificus ), a threatened species (58 Federal Register 12854). Critical habitat for the threatened Sacram ento splittail ( Pogonichthys macrolepidotas) (64 Federal Register 5963) is not currently designated.
6. Environm ental safeguards were enacted after the ecological disaster at Kesterson National
W ildlife Refuge, but m a ny m a y be inadequate for the specific problem s of the Bay-Delta. For

exam ple: a) The USEPA criterion for the protection of aquatic life (5 μ g Se/L) is not in effect for upstream inflows to the Bay-Delta (i.e., the SJR and its tributary sloughs) due to state postponem e nts of com p liance until 2010 (USEPA, 1992; CCVRW QCB, 1996d). Selenium concentrations in the river have exceeded USEPA criteria (50% of the tim e for the period 1987 to 1997 at Crows Landing, Figures 3 and 5) si nce the discovery of Se effects at the
Kesterson National W ildlife Refuge (CCVRW QCB, 1996a; b; 1998f). Load lim its enacted by the state in 1996 were exceeded in 1996 through 1998. Im pacts from Se on the SJR have not been directly evaluated partly because no program system atically collects biological, water quality, and flow data (Presser et al., 1996; Presser and Piper, 1998). An aquatic
hazard assessm ent of a tributary slough receiving the greatest im pact from agricultural drainage found the Se hazard as “high” (Lem ly, 1995; 1996a; USBR et al., 1998; 1999). Replacem ent 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 fi sh in the SJR and adjacent sloughs are now
dom inated by introduced species having broad environm ental tolerances (USBR et al., 1998; 1999). The role of Se in these changes is not proven, but effects on native fish

12populations are docum ented elsewhere (e.g., Lem l y, 1997b; Ham ilton, 1998; 999; and
Ham ilton et al., 2000a). b) Refinery inputs to the Bay-Delta have declined since 1998. State waste discharge perm its
lim it oil refinery effluents based on Se loads. Effluents, however, m a y reach a daily

m a xim u m of 50 μ g/L Se, which is ten tim es above the prom ulgated USEPA criterion (CSFBRW QCB, 1992b; USEPA, 1987 and 1992). It is expected that food web

contam ination attributable to the ref i neries will decline; dilution of the ef f l uent discharges by low Se inflows is critical. In 1995, deform ed em bryos were found in 30% of m a llard ( Anas platyrhynchos ) nests and in 10% of Am erican coot ( Fulica americana ) nests at a

m a rsh used for Se rem e diation in the Nort h Bay receiving a refinery effluent of 20 μ g Se/L (without dilution) (Skorupa, 1998a). c) Selenium concentrations were below all prom ulgated water quality protection guidelines (2
to 5 μ g Se/L) in both the Delta and the Bay in all surveys of the Bay-Delta from 1982 to the

m i d-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 som e species
and a concern to hum an health if those species were consum ed (CDFG, 1988 and on-going; Fan et al., 1988; SJV Drainage Progr am , 1990b; CSFBRW QCB, 1992a; b).

13 d) A biological opinion and form al cons ultation by the USFW S and NMFS (1998 and

am ended, 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 sm elt ( Hypomesus transpacificus ), Sacram ento splittail ( Pogonichthys macrolepidotus ), steelhead trout ( Oncorhynchus mykiss ) and chinook salm on ( Oncorhynchus tshawytsch ], birds [California light-footed rail ( Rallus longirostris levipe) , California clapper rail ( Rallus longirostris
obseletus ), Calif ornia least tern ( Sterna antillarum browni ), and m a rbled m u rrelet ( Brachyramphus marmoratus )] and am phibians/reptiles [ g iant 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

recom m e nd a 2 μ g 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 perm its for Se discharges to private evaporation ponds used for agricultural drainage disposal are lim ited only to a Se hazardous waste criterion of 1,000 μ g Se/L (California Code of Regulations, 1979 and as am ended). These ponds, in the Tulare basin of the southern SJV, are located in part of the Paci fic Flyway heavily used by m i gratory birds. A state health hazard warning for consum ption of Am erican coot was posted for a 16-pond area in 1987 (CDFG, 1987; SJV Drainage Program , 1989; 1990b). A 10-50% rate of

em bryo teratogenesis was docum ented during the period 1987 to 1990 (Skorupa, 1998a; b).
An attem p t to regulate evaporation ponds on the basis of field observations of bird im pacts was not adopted in lieu of altering drainage evaporation ponds to lim it bird-use (i.e., “birdfree” ponds) and provision of com p ensatory and alternative wetland habitat (CSW RCB, 1996a). Deform ed 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 (CCVRW QCB, 1994a; 1996a) anti-degradation policies

m a y apply to the im paired water quality segm ent of the SJR or the groundwater aquifers of the SJV. In addition to the degradation of the SJR noted above, m obilization of Se by irrigation and contam ination of ground water have resulted in concentrations of Se greater than 1,000 μ g/L Se (a hazardous waste; Californi a Code of Regulations, 1979 and as

am ended) in som e aquifer locations of the SJV (Deverel et al., 1984).
8. Hum a n health advisories against consum ing Se-contam inated edible tissue of f

i sh [ b luegill ( Lepomis macrochirus ) and largem outh bass ( Micropterus salmodes )] and birds (ducks and coots) are presently posted for the SJV (C DFG, 1985 and on-going; 1986 and on-going; Fan et al., 1988; SJV Drainage Program , 1990b). Advisori es also exist for eating birds (scoter and scaup) from the Bay-Delta (CDFG, 1988 and on-goi ng). The advisories are issued when Se
concentrations in flesh reach or exceed 2 μ g/g wet weight [6-12 μ g/g dw, assum i ng 65-85%

m o isture] (SJV Drainage Program , 1990b; Saiki et al., 1991) and restrict hum an consum ption to not exceed 112 gram s of flesh per one- or two-week period or 20 gram s of fish or bird m u scle per day in addition to the regular daily intake (Fan et al., 1988). Children and pregnant wom e n are advised not to consum e any gam e from the posted areas.
9. Im portant gaps also occur in existing knowledge (Luom a and Fisher, 1997; Clem ents, 2000). Most Se studies have taken place in wetlands and in freshwater reservoirs. There is a deficit of 14knowledge about the fate and effects of Se in estuarine environm ents sim ilar to the Bay-Delta,
and im portant data gaps exist for specific regions of the Bay-Delta. Many of the processes and

m echanism s that determ ine Se im pacts m a y be known generically, but are less well known in the Bay-Delta. On the other hand, knowledge of som e of the m o st com p lex processes— influences of speciation, m echanism s of bi oaccum u lation, food web transfer, and effects on predators—is probably better known for Se than for m a ny other contam inants. In this paper we prim arily:

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

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

m a nagem e nt alternatives proposed historically;

• detail the state of knowledge of the processes that determ ine the fate and effects of Se released to the Bay-Delta;

• sum m a rize existing knowledge concerning Se contam ination in the Bay-Delta ecosystem ;

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

• forecast concentrations, form , bioaccum u lation, tr ophic transfer, and effects of Se on predators for several load scenarios; and

• define research needs and actions that m i ght help narrow the uncertainties about proposed discharges of Se to aquatic ecosystem s. 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 (s ee specific listing in next section). Forecasts of
the ef f

ects of such changes are essential to a holistic, successf ul restoration or rehabilitation ofthe BayDelta. Scientific data and m odels 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 f u ture. The SJR is the only current m eans (i.e., the only natural channel) by which Se and salts can be rem oved 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

15discharges to the SJR will be m a nifested in these downstream receiving waters (i.e., south Delta, Suisun Bay, Carquinez Strait, San Pablo Bay) to the ex tent that those waters are m a naged so that they
reach the downstream estuary ecosystem s. Existing policies for the western SJV are probably not sustainable [W anger, 1994; Stevens and Bensing, 1994; CSW RCB, 1997 and 1999a; d; W e stlands W a ter District (W W D ), 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 Im plem entation Progr am , 1998); disposal sites of sufficient scale for collected drainage (e.g. at Kesterson National W ildlife 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, environm ental im pact reports prepared, and engineering studies of the problem m a de (Table 1) [e.g., USBR, 1962; Calif ornia Departm e nt of W a ter Resources (CDW R), 1965a; b; 1969, and 1974; USBR, 1978; SJV Interage ncy Drainage Program , 1979a; b; Brown and Caldwell, 1986; SJV Drainage Program , 1990a; SJV Drainage Im plem entation Program , 1998). As
discussed later in m o re detail (also see Appendix A ) , m a ny studies of Se contam ination have provided insufficiently holistic evaluations of the problem

. These studies do not adequately account for linked
factors that determ ine effects of Se on the aquatic food web and higher trophic levels.
Salinization and Se contam ination issues in the western SJV ultim ately stem f

r om the geologic setting, an im balance in the hydrologic cycle, and clay layers im peding drainage (SJV Interagency Drainage Program , 1979a; CH2M HILL, 1988; SJV Drainage Program , 1989; 1990a). High evaporation rates in the sem i -arid clim ate 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). W h ere drainage has been halted, Se is accum u lating in the internal reservoir of ground water in the SJV (SJV Drainage Program , 1990a; SJV Drai nage Im plem entation Program , 1998; W W D, 1996; 1998). The accum u lation of salts and contam inants in ground water will, eventually, im pede beneficial use of this resource (CSW RCB, 1985; 1987; 1994; 1999a; d; CCVRW QCB, 1988; 1996a; 1998b).
W h ere drainage water is being collected, its disposal results in increases in Se contam ination of surface water resources, with possible effects on ecological integrity (see m a ndated environm ental reviews for proposed SLD in 1965, 1975, 1977, 1979, 1981, 1984, 1985, 1987, 1991, 1994, and 1999, Table 1). 16No f easible engineering solutions yet exist f o r treati ng irrigation drainage to rem ove Se fromthe watercolum n, at least not at the scale necessary to alle viate the problem of waste disposal (Hanna, et al., 1990; SJV Drainage Program , 1990a; SJV Drai nage Im plem entation Program , 1999a). In August 1999, the California State W a ter Resources Control Board (CSW RCB, 1999d) held an agricultural drainage discharge workshop in which it was decided to go forward with a m e m o randum of understanding that would begin perm it applications and environm ental docum entation for a m a ster drain (i.e., an extension of the SLD) to rem ove salts from the western SJV. As in earlier proposals, the final point of discharge of this drain was the Bay-De lta. This action was an ef f

o rt to seek relief f

o r California farm ers. Environm ental groups rem a in opposed to studying the drain as an alternative
solution to source control im plem ented through a num ber of m easures including water conservation, drainage reuse, and land retirem ent (i.e., cessation of irrigation in areas of elevated Se concentrations in shallow ground water). Nevertheless, during the ne xt few years, federal and state agencies m a y be required to evaluate proposals and discharge perm its 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-m ile 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 rem oving salts
from the valley. The SLD would convey subsurf ace 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 f e deral agreem ent and state perm it to allow an existing 28-m ile section of the SLD to convey subsurface agricultural drainage to the SJR. Load targets and m a nagem e nt alternatives are under negotiation. A net increase or an increase during som e m onths (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 som e types of river discharge and

m a nagem e nt scenarios.

• In response to state regulated salinity objectiv es and USEPA’s regulation of non-point source pollution through TMDLs (Total Maxim u m Daily Loads), real-tim e dilution of salt, Se, boron or dissolved oxygen could occur in portions of the SJR. This approach would change the 17am ount and tim ing of Se loading to the Bay-Delta (CCVRW QCB, 1994b; 1996a; 1998a;
CSW RCB, 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 De fense Council et al., 1988; CALFED, 1999a; URS
Greiner W oodward Clyde, 2000).

• Changes in Se inputs will also be influenced by d ecisions about drainage of salts from the SJV. A recent state water right decision requiring the USBR to m eet salinity objectives at Vernalis on the SJR and at three locations in the interior of the southern Delta (CSW RCB, 1994; 1997; 1999a; EA Engineering, Science and Technology, 1999) and a state program aim e d at salt reduction (CCVRW QCB, 2000a) will affect m a nagem e nt alternatives. Currently, the salinity objectives adopted in 1991 are violated m o st m onths of the year (67 to 78 % from 1986 to 1998).

• Physical changes in water m a nagem e nt could result in greater inflows into the Bay-Delta from the Se-laden SJR. The 1994 Bay-Delta W a ter Accord (CSW RCB, 1994) m a ndated greater inflows to the Bay-Delta from the SJR. Inflows of Se from the SJR have traditionally been

sm all com p ared to other sources (Cutter, 1989; Cutter and San Diego-McGlone, 1990; Johns et al., 1988), because m o st 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

m a nagem e nt 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 m odifications of current dive rsion and export channel dim e nsions could also result in an exchange of Sacram ento River inflow for SJR inflow to the Bay-Delta (CALFED, 1998a; b). Any activity that results in m o re SJR inflow entering the Delta or Bay will result in

m o re 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 m a ss em issions reduction regulations (Table 2) (CSFBRW QCB, 1992a; b; 1993). In July 1998 refineries were required to m e et the goals set by the CSFBRW QCB (1996; 1997). This m eans that concentrations of at least som e form s of Se (i.e., selenite) in the Bay-Delta are decreasing (Cutter et al., in preparation), and that the predom inant cycling pathways could change. In Belews Lake, North Carolina, for exam ple

18(Lem ly, 1997a), exposures of fish to Se changed from water colum n -based pathways to
sedim e nt-detrital pathways after sources were elim inated.

• Refinery Se was dom inated by selenite; Se from the SJV is dom inated by selenate, with som eapparent conversions to organo-Se in receiving waters (Cutter, 1989; Cutter and San DiegoMcGlone, 1990, CSFBRW QCB, 1992a; b; 1996; 1997). Thus the predom inant biogeochem i cal
transf orm a tion pathways and bioavailability of Se could change as the predom inant sources to the Bay-Delta change.

• Changes in residence tim es of water in the south Delta and the North Bay could result from changes in water m a nagem e nt. For exam ple, greater diversion of water (another possible

outcom e of changes in water m a nagem e nt) could result in increased residence tim es in the BayDelta during som e tim es of year. Mean hydraulic freshwater residence tim es in Suisun Bay
were estim ated at 0.5 days during periods of hi gh flow and at 35 days for period of low flow (W alters et al., 1985). Longer hydraulic residence tim es seem to be associated with greater Se

contam ination in the food web (Lem ly, 1997a; Zhang and Moore, 1997a; Skorupa, 1998a). Biological changes also are occurring in the ecosystem , and som e of these appear to affect Se cycling. These changes include:

• The dom inant consum er 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
Luom a, 1995b). It is possible that this species is especially efficient at bioaccum ulating Se, although studies directly addressing the m echanism s of Se bioaccum u lation by P. amurensis are not yet com p lete (Brown and Luom a, 1995a; Luom a and Linville, 1997; Linville and
Luom a, in press). Invasion of this species was helped by a depauperate benthic com m unity in

m i d-1986 and the com p lexities of salinity gradients and hydraulic residence tim es present in the North Bay (Cloern and Nichols, 1985; Pete rson et al., 1989; Nichols et al., 1986).

• One im plicit goal of a successful restoration is to develop a m o re com p lex, native speciesdom inated food web (CALFED, 1998a; b and 1999a; b; c; d). Selenium m i ght bioaccum u late

m o re efficiently through m o re com p licated food webs (a question under study), which raises the question of the com p atibility of existing or greater levels of Se contam ination with restoration goals.

19• The cause of the declines of som e key species in the Bay-Delta (e.g. white sturgeon,
Sacram ento splittail, starry flounder, surf scoter) m a y include Se effects on reproduction and
ultim ately, survival of the population. Increased Se in the Bay-Delta could increase that threat.

• Marsh restoration in the Bay-Delta, if accom p anied by increased Se discharges, could result in trapping and recycling of increased quantities of Se in the system , with the possibility of greater Se contam ination in som e species. Under the worst scenarios, it is conceivable that

m a nagem e nt of concom itant issues—water and salt m a nagem e nt—rather than Se contam ination could create another ecological crisis in the Bay-Delta sim ilar to that created at Kesterson
National W ildlif e Ref uge. Ref i nem e nts of Se water quality criteria, especially f o r the Bay-Delta, also are likely. The current USEPA prom ulgated national Se chronic criterion for the protection of aquatic life (5 μ g Se/L) is based upon bioaccum u lation-related toxicity observed in Belews Lake and Hyco Reservoir (USEPA, 1987 and 1992). The USFW S recom m e nds a criterion of 2 μ g Se/L, based upon a series of case studies of
Se contam ination and effects on birds in we stern wetlands (Skorupa, 1998a; USFW S and NMFS, 1998
and am ended 2000). The Canadian criterion for wildlife protection is 1 μ g Se/L (Environm ent Canada/Health Canada, 1995; Outridge et al., 1999). The technical lim itations 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 previous ly, Se concentrations were below all recom m e nded 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 som e species and a concern to hum an health if those species were

consum ed (Table 2) (Linville and Luom a, in press; CDFG, 1988 and on-going; Fan et al., 1988;
CSFBRW QCB, 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 system atically describe the linked factors that determ ine effects of Se on aquatic food webs and higher trophic levels (see conceptual m odel, Figure 2). This holistic approach to the issue differs from earlier attem p ts to skip links in tying waterborne Se to the effects of
the elem ent. W e propose that the holistic approach offers opportunities to m o re accurately project

20ecological effects from loads and to identify resoluti ons 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 volum e provide the basis for determ ining the upper and lower
lim its 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,

m onthly, daily, and hourly variability of Se loading is necessary to address trends and patterns in discharges. The accuracy of Se load calculations on any tim e-scale is dependent on the

num ber and frequency of the m easurem ents taken to determ ine flow and Se concentration (Presser et. al., 1996). Large uncertainties are associated with data com p iled for annual average
loads of Se from agricultural and natural sources. Annualized, generalized averages of concentration, flow, and load hide infrequent sam p lings, sam p ling that does not reflect flowdependent concentration changes, or spatially dispersed sam p lings. Annual average data used here, although docum ented 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 determ ine transport of those Se loads to the Bay-Delta. A SLD extension or the SJR are the m o st likely m odes of conveyance (Figures 3 and 5). The SJR was m o stly recycl ed 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 m odels
exist that can be used as fram eworks for future m odeling (e.g. Cheng et al., 1993; Monsen, 2000). Throughput of SJR inflows could be influe nced by changes in water m a nagem e nt to aid fish passage including construction of elaborate De lta 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 Sacram ento River and SJR discharges are critical considerations in
determ ining 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 transform a tion of Se from dissolved to particulate form s. 21Understanding particulate Se and its speciation cycle is critical in determ ining biological
effects.

• Incorporating factors controlling the bioavailability and biotransfer of Se to macroinvertebrate primary consumers under the different concentration and speciation conditions

. Bioaccum u lation of Se is prim arily determ ined 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 clam s show elevated levels com p ared to uncontam inated reference areas (Johns et al., 1988; Brown and Luom a, 1995a; Luom a and Linville, 1997;
Linville and Luom a, in press). Exposure of predators is determ ined by the level of
bioaccum u lated Se in these prey organism s (CSFBRW QCB, 1992a; b; 1993; 1996; 1997).

• Estimating effects of Se on predators from tissue residues . Adverse effects have not been
dem onstrated in predators in the Bay-Delta prim arily because of the com p lexity of reproduction
in the m o st affected species (Conom os, 1979; C onom os et al., 1985; Nichols et al., 1986; Davis et al., 1991; Harvey et al., 1992; Monroe et al., 1992; and USFW S, 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 thr eats to the reproductive health of the predators (W hite et al., 1987; 1988; 1989; Cutter, 1989; Johns, et al., 1988; Cutter and San DiegoMcGlone, 1990; Urquhart and Regalado, 1991; Sa n Francisco Estuary Project, 1991; 1992;
CSFBRW QCB, 1992a; b; Luom a et al., 1992; Brown and Luom a, 1995a; Luom a and Linville, 1997; Linville and Luom a, in press). However, such estim ates of risk are derived from laboratory and field studies conducted el sewhere (USEPA, 1998; Lem l y, 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 m a jor sources of the Se in the Bay-Delta are (Figures 4 and 5):

22discharges 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 re fine crude oil from the western SJV along with
crude oil from other sources;
Sacram ento River inflows which is the dom inant freshwater inflows (high water volum e) to the Bay-Delta; and
Effluents from Bay-Delta wastewater treatm e nt plan ts and industries other than refineries are m i nor 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 com posed of m a rine sedim e ntary rocks that are enriched in Se (Figures 3 and 5) (P resser and Ohlendorf, 1987; Presser et al., 1990). An internal reservoir of salt (and by inference Se) has accum u lated through 1.0 to 1.2 m illion 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 m o st Se-rich regi on 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 clim ate (i.e., less than 10 in ches of precipitation and greater than 90 inches of evaporation) and poor drainage (i.e., clay layers im pede downward m ovem e nt of water causing waterlogging of the root zone). The SJV has a net negative annual water budget (evaporation exceeds precipitation). Prior to developm ent of the water m a nagem e nt system , a perm anent shallow groundwater table only occurred in groundwater discharge zones near the SJV trough. The present shallow ground water and attendant subsurface drainage flows are m a inly the result of water m a nagem e nt including m a ssive irrigation.
Micro-m a nagem e nt seem ingly has enabled agricultura l production to continue at a high rate without
excessive abandonm ent of lands. Massive irrigation leaches salt and Se and m oves them into aquifers and surface waters. Installation of subsurface drains increases the speed, volum e, a nd control of the drainage of shallow groundwater
that im pedes agricultural production. Collection of dr ainage from irrigated soils in drainage canals 23enables efficient discharge into surface waters. In 1960, both the federal governm e nt and the state of
Calif ornia com m itted to provide irrigation and subse quent drainage of irrigation wastewater f o r 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 a nd planning since the inception of a m a ster-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 W e stlands, Panoche, Broadview, Pacheco, and San Luis W a ter Districts of
the W e stlands and Grassland regions or subareas (U SBR, 1981) (Figures 3 and 5). It was hoped that the increased water supply (to satisfy m o isture dem a nd by clim ate and crops) would be balanced by salt leaching and drainage, even though am ounts of water required are on a m a ssive scale (USBR, 1955; 1962; 1978; CDW R , 1979). Sim p le water and m a ss 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 m a de between m a naging the

accum u lated hydrologic im balance (area of affected land) and m a naging the annual im balance (rate of water table rise) (CH2M HILL, 1988; SJV Drainage Program , 1989). Short-term objectives would work toward hydrologic balance by stem m i ng the rate of deterioration, while reclaim i ng existing “problem lands” would require releasing from storage a large accum u lation of water and salt. Achieving hydrologic balance would not achieve salt balance. Salts would continue to accum u late in the soils and aquifers of the SJV. Planned volum e of drainage discharge increased over the 100-year

m a nagem e nt period (USBR, 1978; 1983) (Appendix A, Ta ble A1). Salt loads were calculated for a period of 50 years into the future, with a m a xim u m re lease occurring after 40 years of discharge. Later
estim ates (USBR, 1983) also planned for 100 years of di scharge 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) ultim ately determ ines the degree of contam ination buildup in the SJV (Appendix A, Tables A2 and A3). Th e prim ary geologic inventory of Se in the Coast Ranges is the ultim ate source of influx. Drainage from the SJV is the source of efflux, whether natural or artificially accelerated by engineering m eans. The in ternal reservoir of labile Se in SJV is growing
because the rate of rem oval of Se-enriched salts from the valley is naturally slow. In general,
calculations of the am ounts of Se in the reservoir w ithin the Panoche Creek alluvial fan also confirm
the m a ssive nature of Se accum u lation in the SJV. Calculations based on two scenarios (Appendix A,
24Tables 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, ev en if influx of Se from the Coast Ranges could be curtailed. Drainage of wastewaters outside of the SJV m a y 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 sm all percentage of the total annual load except during infrequent large

m a gnitude storm s (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 sedim e nt sam p les, however, were relatively low historically and in 1998 (1-2 μ g/g), depending on the large m a ss of sedim e nt eroded during storm s to accounts for the large loading of Se during runoff (Presser, et al., 1990; Presser, unpublishe d data). Dissolved Se in runoff sam p les ranged
from 31 to 85 μ g/L in m onitored storm s in W Y 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 cal culated above can be seen in the quality of the ground water in the western SJV (Table 3). Extensive m easurem ent and study of the groundwater aquifers in
the SJV have been m a de 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 sum p s in the area of the Panoche Creek alluvial fan range from 140 to 4,200 μ g Se/L (Presser and Barnes, 1985). These concentrations are reflective of shallow groundwater conditions as opposed

to m a naged drainage, which m a y be blended. Studies in 1989 in the area of the Panoche Creek alluvial fan showed Se concentrations ranged from 96 to 7,300 μ g/L Se in individual sum p discharges or well

sam p les 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 num ber 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 μ g/L Se. A m o re recent com p ilation used in the evidentiary process (W anger, 1994; Stevens and Bensing, 1994; W W D , 1996) and in regulatory planning shows concentrations in shallow groundwater

25range from 75 to 277 μ g/L Se (range of m eans) (SJV Drainage Program , 1990a; CCVRW QCB, 1996c; d) (Table 3). Data presented in testim ony and by the state (Table 3) project an average concentration of Se in shallow ground water and hence, subsurface drainage, of at least 150 μ g/L Se in the farm ing 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 μ g/L Se) and above the
concentration estim ated that is possible with treatm e nt (50 μ g/L Se) (W W D , 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 m itigation and alternative habitat (CSW RCB, 1996c). The effect of the large reservoir of Se on r ecent subsurface drainage flow and quality is generalized
from data collected during frequent sam p ling of drainage source water (i.e. current agricultural discharges to the SJR in W Y 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 volum e of drainage increases, except in infrequent, extrem e precipitation events (Figure 6). Generally, m o re input of water to western SJV soils results in m o re 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. W h en considering Se source waters as opposed to receiving waters, Se concentration in source waters will increase as m o re irrigation water is applied and m o re discharge occurs. Therefore, Se loads increase over those seen without irrigation. Testim ony in the state water ri ght hearing sim ilarly confirm that the action of irrigation supply (m ainly from the Central Valley Pr oject) is the principal cause of the drainage discharge of salinity, and hence, the cause of violations of water quality objectives f o r salinity f o r the Bay-Delta (CSW RCB, 1999a).

26 Rem oval of salt (and Se) also is slowed by the recycling of the SJR (Figure 5). The SJR can be
alm o st com p letely diverted back into the SJV before it enters the Bay-Delta. In the past, recycling has occurred during m o st m onths of the year and duri ng all m onths of m a ny years (USBR Central Valley Operations Office, Daily Delta Outflow Com put ation; EA Engineering, Science, and Technology, 1999). The recycled SJR water is then used again in irrigation. As noted above, the degree of recycling is determ ined by water m a nagem e nt. W a ter m a nagem e nt began changing toward less recycling in 1994 and direct throughput of the SJR m a y increase in the years ahead to help restore SJRfish and fish habitat. A reduction in recycling and an increase in drainage discharge during seasons of elevated flows are strategies for slowing the salini zation of agricultural soils. However, m a nagem e nt

to m eet all goals including m eeting the salinity standard f o r the SJR at Vernalis is com p lex. Strategies

m a y include the need for storage or holding ponds to optim ize tim ed release of drainage and m e et the salinity standards for the SJR at Vernalis. Agricultural drainage outputs are not, in general, coordinated with periods of high rive r flows (Appendix A, Figure A11).

Drainage management Managem e nt plans have discussed “in-valley” and “out-of-valley” drainage m a nagem e nt alternatives. “In-valley” solutions im ply local stor age and treatm e nt of Se-rich drainage. Satisfactory

treatm e nt technologies have not yet been dem onstr ated and storage does not seem sustainable (SJV Drainage Program , 1990a). “Out-of-valley” solutions m ean export of the salt-laden drainage (and its Se load) to som e where else. The m o st frequently m e ntioned 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 accom p anying Se) from the SJV began in 1955 (Table 1). An 85-m ile section of the SLD was com p leted in 1975, to collect irrigation drainage water from one section of th e valley, the W W D (i.e., Figures 3 and 5, W e stlands subarea). The SLD began discharging concentrat ed drainage water in 1981 to Kesterson National
W ildlife Refuge (Figures 3 and 5), a heavily populat ed bird sanctuary on the Pacific Flyway (USBR, 1986; Presser and Ohlendorf, 1987). The Kesterson National W ildlife Refuge ponds were used as

term inal evaporation ponds until the rem a ining m iles of the canal could be built. In 1983 deform ed birds were discovered at Kesterson Reservoir, a re servoir consisting of twelve ponds, at the discharge point of the agricultural drainage. Subsequent m onitoring revealed elevated levels of Se in the organism s within the ponds (Saiki and Lowe, 1987). Avian deform ities were ultim ately linked to Se exposure from food chain contam ination (Ohlendor f et al., 1986; Presser and Ohlendorf, 1987). The SLD was ordered closed by the U.S. Departm e nt of Interior in 1985 and the low-lying parts of
Kesterson National W ildlife Refuge were buried under 18 inches (46 centim eters) of im ported topsoil in 1988 (USBR, 1986). Elevated Se concentrations persist in the rem e diated terrestrial ecosystem at Kesterson Reservoir (CH2M Hill, 1996; 1997; 1999a; 1999b; Presser and Piper, 1998). Managem e nt of Se differed am ong regions (suba reas) in the SJV in the 1990’s. The five subareas (i.e., Northern, Grassland, W e stlands, Tulare, and Ke rn) of the western SJV were designated based on
27hydrologic and geologic features and on options fo r m a nagem e nt of irrigation and agricultural wastewater discharge (SJV Drainage Program , 1990a) (Figures 3 and 5). Selenium -laden wastewater is stored as ground water in som e areas of the valley. In others, drainage is collected in privately owned evaporation ponds located on farm s, although reproductive im pacts, including teratogenesis (deform a tion of young) and death of avian offspring, were observed in som e of these ponds and associated wetlands (Skorupa, 1998a). Som e drainage is discharged into collector canals, sloughs, and wetlands that eventually discharge into the SJR. The Grassland Bypass Channel Project was
im plem ented in 1995 [i.e., water year 1996 (W Y 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 discharg ed into Mud Slough, a tributary of the SJR (Figures 3 and 5). The goal is to rem ove 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 sm aller area of ecosystem s while phased-in m a nagem e nt activities potentially reduce loads f r om historic levels and thus attem p t to com p ly with water quality standards (USBR, 1995; USBR et al., 1998; 1999).

Forecasting loads of selenium: general consideratons The problem of progressive soil salinizati on and the build-up of ground water contam ination could require collection of drainage f r om 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

m u st 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 estim at ed the extent of the acreage requiring drainage under varying conditions of water im port, water export, salinity, and groundwater levels. In general, all of these early studies predicted a worsening fa te if an out-of-valley drainage conveyance is not provided. For exam ple, 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 m o re 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 28actions 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 problem s) and volum es of problem water (the annual drainage water volum e that m u st be m a naged because of adverse im pacts to agriculture or aquatic resources) (Appendix B). The program developed an “in-valley” m a nagem e nt plan for agricultural subsurface drainage with specific m a nagem e nt alternatives (SJV Drainage Program , 1989; 1990a). The goal was to m a ke progre ss both in m a naging and treating drainage-water toxicants and developing long-term solutions to a ddress the elevated groundwater conditions and the annual salt build-up that eventually lim it the uses of valley lands and ground water. The SJV Drainage Program ’s regional studies and data provide m u ch of the inform ation used in our assessm ent of loads
from the subareas of the SJV (Appendix B). The benefits expected, during the 50-year m a nagem e nt period, included continued agricultural production at present levels without predicted abandonm ent of lands due to salinization; and restoration/protecti on of fish and wildlife resources from the adverse effects of Se in receiving waters. Recom m e nded m onitoring based on the developed regional
fram ework, if im plem ented, would add site-specific data and analysis necessary for long-term success of the SJV Drainage Program . Recom m e ndations fo r treatm e nt techniques were not included because success of technology on a large-scale was not prove n as of 1990 (SJV Drainage Program , 1990a).
Im plem entation of the m a nagem e nt plan was only partial and system atic m onitoring and data analysis has not occurred (SJV Drainage Im plem entation Program , 1998). The SJV Drainage Program m a nagem e nt plan (1990a) estim ated 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 estim ates of acreage, the SJV Drainage Program used a criterion of sufficiently elevated salinity and boron concentrations in ground water to lim it use of the water and affect crop selection (i.e., lands with an actual drainage problem ). The SJV Drainage Program also estim ated 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, estim ates 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 μ g/L) , 264,000 acres were projected as affected in 1990. It
was estim ated that 84,000 acres of land would have to be abandoned by 2000 and 460,000 acres by 292040 if the SJV Drainage Program m a nagem e nt plan was not im plem ented. Land retirem ent

recom m e nded by the SJV Drainage Program by 2000 was 21,000 acres and by 2040, 75,000 acres.
Further docum entation provided in 1992 for the San Lu is Unit Drainage Program sim p ly stated that
all the m a jor USBR and interagency studies (Table 1, 1955; 1962; 1964; 1972; 1979; 1984; and 1990)
found sim ilar m a gnitudes of the drainage problem (U SBR, 1992). As noted in recent testim ony given in state water right hearings, the total acreage of lands im pacted by rising water tables and increasing salinity is approxim a tely 1,000,000 acres in the SJV (CSW RCB, 1999a). A recently instituted land
retirem ent program has identified willing sellers of up to 15,000 acres in the W e stlands and Tulare subareas and has acquired several hundred acres as of 1998 (U.S. Departm e nt of the Interior, 1999; SJV Drainage Im plem entation Program , 1999b).

How to determine load One approach to forecasting Se loads is to exam ine 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. Fo recasts in this report were based on historical, annualized drainage volum es and assigned concentrations because these are the data and tools available (Appendix B). Recent m onitoring program s have failed to collect the data necessary to develop cause and effect relations, for exam ple, between Se distribution and concentration in ground
and surface water and im plem entation of m a nagem e nt actions. The lim itations of the available record are significant (Appendices C and D and see discussion of each subarea); nevertheless, broad estim ates are feasible. Managem e nt of Se loads involves three f actors (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 com ponents. In our analysis, the distinction m a de between problem water and subsurface drainage helps in forecasting future loads by enabling an assignm ent of water quality based on this distinction.

• The volume of drainage generated per acre . A factor is applied (acre-feet per acre) to the

am ount of affected acreage (acres) to estim ate the am ount of drainage generated (acre-feet). 30The average annual volum e of problem water generated from problem lands under conditions
in 1990 was estim ated as 0.7 acre-feet per acre per year (SJV Drainage Program , 1990a). The SJV Drainage Program predicted that changes in on-farm drainage m a nagem e nt practices could
reduce the volum e generated to approxim a tely 0.4 acre-feet per acre per year. Recent updates of conditions in the Grassland subarea show an average annual volum e 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 m e et Se load lim its in the Grassland subarea (Environm ental 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 c oncentration of Se in effluent drainage
reflects a m a naged balance of input, output, and storage. Treatm ent technologies (m ostly unspecified) or dilution with Se-poor water (blending) can be used to reduce concentrations below those found in shallow ground water. Mo st technical evaluations have not applied
concentrations to estim ates of drainage volum es to calculate potential loads of Se (e.g., SJV Drainage Program , 1990a). All three factors can vary greatly depending upon assum p tions about m a nagem e nt strategies. Two possible alternative m a nagem e nt futures we re defined by SJV Drainage Program : 1) no
im plem entation of the SJV Drainage Program m a nagem e nt plan, 0.60 to 0.75 acre-feet per acre per year generated drainage, nam e ly, “ without future ” and 2) with im plem entation of the SJV Drainage Program m a nagem e nt plan, 0.40 acre-feet per acr e per year generated drainage, nam e ly, “ with future ” (SJV Drainage Program 1989 and 1990a). A third cond ition 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, exem plifying the lowe st, although probably not realistic, irrigation water
return. The “ without future ” alternative, in which the m a nagem e nt plan is not im plem ented, result in
less volum e of drainage because of the predicted abandonm ent of approxim a tely 84,000 acres of land due to salinization by the year 2000 (Appendix B, Ta bles B11 through B17). If the SJV Drainage Program plan were im plem ented, the am ount of drainage would be reduced to 0.4 acre-feet per acre per year, but the total land in production would be preserved.
W e em ploy a m i xture of m e tric and English units in the forecasts and the following discussion. This is unconventional for a scientific report, but is done here to aid com m unicating our study to the 31widest audience in the m o st recognizable term s. The agricultural discharges of Se are expressed as loads of Se in pounds (lbs); area is described in acres and volum e of discharge is expressed in acre-feet (AF) or m illion acre-f eet (MAF); Se concentrations are expressed as μ g Se/L (equivalent to the regulatory term ppb), or μ g Se/g (equivalent to the regulatory term ppm ). Conversion between these units and scientific units, which are used in the anal ysis of Se ecological effects, can be found in Table
4. Selenium load (in pounds) is calculated using the equation:

[Se concentration ( μ g Se/L or ppb) X volum e of drainage (acr e-feet)] X 0.00272 = load of Se (lbs),

or [Se concentration ( μ g/L) X [(acres) X (acre-feet per acr e)] 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 ( μ g/L) Se in an
acre-foot of water.

Characteristics of agricultural subareas
The links between dem a nds for drainage and estim ates of potential loadings of Se require consideration of specific agricultural subareas in the SJV (i.e., Northern, Grassland, W e stland, 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 sum m a ry 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 W e stland 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 W ildlife Refuge from 1981 to 1986.
As a result of the ecological crisis associated with the Kesterson National W ildlif e Ref uge, W e stlands subarea now has a "no discharge" policy. Drainage is recycled onto farm lands 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 Appeal s decision (Hug et al., 2000), the USBR is ordered to initiate the process to provide drainage service to the San Luis Unit. The specif i cs of such drainage service have not been provided.

32The data record from the W e stland subarea is particularly lim ited with no specific m onitoring for Se since closure of the SLD in 1986. Only data on groundw ater elevations are available in the area m o st im pacted by geologic sources of Se (W W D , 1998). This area is potentially the greatest generator of Se load in the SJV because it, m o re than any other subarea, encom p asses the Panoche Creek alluvial fan area (Presser et al., 1990). This fan and interfan ar ea receive the m o st seleniferous runoff and erosion
from the Coast Ranges (Tidball et al., 1986; 1989; Presser, 1994b). Used here are the estim ates of areas of shallow groundwater that im pact farm ing presented in m a nagem e nt plans, testim ony, and a recent status report by W W D (1996; 1998). W e stla nds W a ter District contended (CSW RCB, 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 m a nagem e nt plans predicted 170,000 acr es of the W W D would be affected by salinization by the year 2000 and 227,000 acres would be affected by 2040. It is estim ated that im m e diate 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; W W D , 1996) (Appendix B, Table B2). No
form al long-term stipulations control the ultim ate fate of the drainage water in the W W D, but pressure to discharge W e stlands subarea drainage into a com p leted SLD extension to the Bay-Delta is increasing as lands becom e waterlogged, the quality of the soils declines, and ground water quality
declines. Because discharges from the W e stlands subarea were discontinued in 1986, no current direct

m easurem ents of ef f l uent quality are available. Historic discharges provide som e guidance. Average Se concentrations that were discharged to Kester son National W ildlife Refuge from the historic SLD ranged from 330-430 μ g/L Se in 1983 and 1984 (CSW RCB, 1985; Presser and Barnes, 1984; 1985) and as quoted from regulatory docum ents, from 230-350 μ g Se/L (Table 3) (W W D , 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). W e will term a cum u lative 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).
Testim ony in recent legal proceedings sum m a rized the data for Se in broader areas of shallow ground water in the W W D (Table 3). Mean concentrations ranged from 163 μ g/L to 300 μ g/L in different studies. The USBR suggested the m o st likel y estim ate of average Se concentration in shallow

33ground water is 150 μ g/L. W ith treatm e nt or blending, m a nagem e nt plans asserted that concentrations
could be reduced to as low as 50 μ g/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 agreem ent to provide drainage service (see San Luis Unit, Delta-M endota Service Area, Table 1). This area of the western SJV is to the north and downslope of th e W W D (Figure 3; SJV Drainage Program , 1990a). The Grassland subarea contains 70,000 to 100,000 acres of land that have historically contributed the

m a jority of subsurface drainage to the SJR (Appendi x B, Table B3). The adjacent Grassland federal, state, and private riparian wetlands contain the largest tract of habitat rem a ining in the SJV. Varying lengths of the com p lex 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 exam ples of tributaries that flow through the wetlands of the Gr assland Resource Conservation District and the San
Luis National W ildlife Refuge Com p lex. In 1995, the discharge from approxim a tely 100,000 acres of
farm land was consolidated into a 28-m ile segm ent of the original SLD (renam e d the Grassland Bypass Channel Project) in order to reduce contam inated wetland water supplies, but the inputs to the SJR

rem a in unchanged (USBR, 1995).
The available historical record from the Gra ssland subarea includes data from discharges to the SJR
that were collected m a inly to com p are 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 m easurem ents or estim ates of flow been conducted consistently, so lim ited data exists to determ ine Se loads (USBR et al., 1998; 1999). Historic data from the CCVRW QCB that docum ent Se and salt loading to the SJR were recently reviewed (CCVRW QCB, 1998f). Lim itations were described in m easuring flow and
concentration and in the m e thodology used to calculate loads and regulatory targets.
The ef f

ects of Se discharges on water quality are m onitored f o r 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 m onitoring 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 am ong 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). 34o Estim ated Se loads in the source waters (i.e., agricultural drains or canals) differ from load
estim ates for the SJR m onitoring sites. Som e downstream estim ates are higher and som e are lower than the drainage source estim ates. The difference am ong sites is usually sm all com p ared to the year-to-year variability in the initial load except for unusually wet years (e.g., 1995 and 1998). Reductions in downstream loads m a y occur because of uptake by sedim e nt and biota (Presser and Piper, 1998).

o Besides biochem i cal reactions, som e of the variability am ong sites undoubtedly occurs because
the m onitoring data have im portant deficiencies (Presser and Piper, 1998). As of 1999, the

m onitoring did not include determ inations of par ticulate Se, Se speciation, Se in sedim e nts, or sufficiently frequent analyses to accurately depi ct loading during variable flows. Discharge
schem e s that involve regulating concentrations or loads in the SJR will require m o re reliable

m onitoring. Despite som e deficiencies, Se concentrations in the drainage from the Grassland subarea are better
docum ented than in other subareas. Monthly average total Se concentrations in blended drainage ranged from 40 to 105 μ g Se/L in 1997 and 1998 (USBR et al., 1998; 1999) (Appendix B, Tables B9 and B10). The daily range was 15 to 128 μ g 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 μ g/L in W Y 1997 and 67 μ g/L in W Y 1998 (Table 5 and Appendix A, Tables B9 and B10) (USBR et al., 1998; 1999). These averages are co m p arable to the historical average of 64 μ g/L from 1986 to 1994 (Table 3) (CCVRW QCB, 1998 d; e; f; g; h). Modeled discharges from the Grassland
subarea have estim ated 80 to 150 μ g/L Se (Table 3) (SJV Drainage Program , 1990a; CCVRW QCB, 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 approxim a tely 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 tim e, no new ponds have been built and m a ny ponds have been closed,
CCVRW QCB, 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 dom inant geologic features.

35The lakebeds are little influenced by the Panoche Creek alluvial fan but are surrounded by geologic
sources of trace elem ents from both the Coast Ranges and Sierra Nevada. W a ter quality is characterized by elevated concentrations of Se, uranium , arsenic, m o lybdenum , and boron (Fujii and Swain, 1995). The geochem i stry is controlled in pa rt by oxidizing and reducing zones in the lakebeds and surrounding alluvial fan and basin zones. Ge om orphological features affect the placem ent and

num ber of subsurface drains installed in the subareas. Delineated water quality zones affect the
chem ical com position of the discharge to specific evaporation ponds. Currently, subsurface drains are

m a inly lim ited to lower elevations of the lakebeds (42,000 acres in Tulare subarea and 11,000 acres in Kern subarea) (SJV Drainage Program , 1989).
Current estim ates of acreage adversely affected by shallow ground water are “gross estim ates” due to sparse data and extrapolation over a 696,000-acre study-area selected for coverage by the CDW R (1997). The study area boundaries differ from those give n above as part of the SJV Drainage program designation. The CDW R has historically studied an area called the Tulare Lake region. Estim ates based on data collected by the CDW R after 1991 are considered of som e worth and could be used in
future com p arisons, but historic baseline values are suspect. The current disposition of ground water
within 0 to 15 f eet is unclear f r om the reported CDW R “gross estim ates”. Initial estim ates m a de 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. Estim ates for the Kern subarea show 64,000 acres are affected. For year 2000, the SJV Drainage Program estim ates of affected acres increase to 366,000 in Tulare and 100,000 acres in Kern subarea.
The Se m onitoring in Tulare and Kern subareas is lim ited to annual reporting by dischargers as required by the state as part of perm it requirem e nts for discharges to privately owned evaporation ponds (CCVRW QCB, 1993; 1997; 1998c; CSW RCB, 1996a; CCVRW QCB, Anthony Toto, personal

com m unication, 1998) (Appendix B, Tables B19 to B21) . Any discharges to evaporation ponds m u st be considered in estim ates of valley-wide Se loads, although it is not clear, in view of the im pacts to waterfowl populations (Skorupa, 1998a), whether these discharges will continue. Discharge from the Tulare subarea to private evaporation ponds is rem a rkable for being low in Se concentration when

com p ared to the Se concentration in discharge from W e stlands or Grassland subareas. The record is
lim ited, but values m easured in 1988, 1989 and 1993 through 1997 show m o st concentrations were
below 10 μ g/L Se, with the exception being the South Tulare Lake Drainage District discharge of up to
30 μ g/L Se. Som e higher Se concentrations, ranging up to 760 μ g/L Se, have been reported in som e 36discharges to sm aller ponds ( Table 3 and Appendix B, Tables B19 to B21). For the Kern subarea,
lim ited data on inflows to evaporation ponds in 1988, 1989 and 1993 to 1997 show Se concentrations range from 83 to 671 μ g/L, with the exception being the Lost Hills Ranch discharge of approxim a tely 2

μ g/L (CCVRW QCB, 1990 a and b). In general, Se c oncentrations in discharges from the Tulare
subarea are less than 50 μ g/L and for the Kern subarea are greater than 180 μ g/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. Estim ates of acres dem a ndi ng drainage have not been updated since 1990, nor are current records concerning Se available for com p ilation from this subarea. Most estim ates suggest that drainage needs are relatively sm all com p ared to other areas (CH2M HILL, 1988; SJV Drainage Program , 1990a) and will rem a in so if access to the SJR for drainage rem a ins available to the sam e degree (i.e., the subarea rem a ins in hydrologic balance).

Development of forecasts
W h ile m o st technical evaluations stop with estim ates of problem acreage and problem water
volum es, understanding the range of possible Se concen trations 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 em ploy three concentrations in conjunction with dif f

e rent estim ates of problem drainage volum e and acreage (Appendix B). In general, a concentration of 50 μ g/L Se in drainage is considered potentially available with treatment . Testim ony in court hearings have centered around the fact that a non-specified treatm e nt could lower the Se concentration to an overall 50 μ g/L; then this product water would be disposed of in an extension of the SLD. Therefore, one scenario is that such

treatm e nt options will be available, and/or m i xtures of drainage water will resem b le those presently being released from the Grassland subarea (i.e., 62 to 66 μ g/L Se). For this forecast we will use Se
concentrations of 50 μ g/L Se for treated or blended (i.e. diluted) drainage. Alternatively, another set of
forecasts will assum e a m a xim u m case (300 μ g/L Se), and one will assum e the interm ediate possibility [150 μ g/L Se, an average for present day subsurface drainage waters in the Grassland subarea (CCVRW QCB, 1996c), near the m ean (163 μ g/L Se) presented for the 42,000 acres in W W D (Stevens and Bensing, 1994), and a conservative estim ate (at least 150 μ g/L Se) in W W D by USBR (W anger,

371994)]. Given the quality of the ground water noted in our previous analysis of reservoir conditions (Table 3) and the lack of adequate m onitoring to trace groundwater m ovem e nt and Se concentrations
as a function of tim e, these estim ates m a y 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 com p ilation of data on Se concentration and load that has
becom e available from each subarea since the SJ V 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 lim itations. However, we stress the importance of collecting high quality hydro- and biogeo-chem ical 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
docum enting the im plem entation of m a nagem e nt actions and their effects is not available as part of public record. But, the scenarios m a y be m o re 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 m a nagem e nt option (im p lem e ntation, i.e., “ with future ”,
no im plem entation, i.e., “ without future ”, and “ with targeted future ”) and projected year (1990, year 2000, year 2040) and gives ranges of com b ined annual Se loads potentially discharged from all five subareas. A wide range of Se loadings in the futu re 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 som e extent, a ddressing the longer-term problem of an accum u lated
im balance of water, salt, and Se and the sustainability of agriculture in the SJV, rather than just

m a naging an annual im balance.
One alternative is that the volum e of drainage water will not increase beyond the volum e of subsurface drainage that existed in 1990. If 100,000 acre-feet volum e of subsurface drainage is discharged at an assigned concentration of 50 μ g/L Se, then 3,600 lbs Se per year are projected. Assigned Se concentrations of 150 μ g/L or 300 μ g/L would yield loads of 40,800 or 81,600 lbs Se per year, respectively.

38Total drainage can be projected using problem acreage across all subareas of the SJV (Table 6). Specifically, a forecast using an assigned concentration of 50 μ g/L Se to represent blended generic drainage in conjunction with the m o st quoted estim ate from the SJV Drainage Program of 314,000
acre-feet of problem water (i.e., year 2000 without im plem entation of the specified m a nagem e nt plan) yields a load of 42,704 lbs Se per year. For year 2040, the am ount 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 μ g/L
Se. A forecast using an assigned concentration of 150 μ g/L Se to represent generic subsurface drainage and the SJV Drainage Program estim ate 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
im plem entation of the SJV Drainage Program (303,600 acr e-feet per year), the discharged load would be 41,290 lbs Se per year. Using an assigned concentration of 300 μ g/L Se in year 2000 and the least am ount of estim ated 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 μ g/L Se would produce a load of 66,504 lbs Se per year. In year 2040, 223,000 acre-feet ( without future ) at 150 μ g/L Se would produce a load of 90,984 lbs Se per year.

Forecasting selenium loadings using data from individual subareas Using the sam e 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 μ g/L Se (Appendix B, Table B18). Appendix B (Figure B2a, b, c) illustrates use of a graphical tool to enable a predicti on or projection of an annual Se load for any of the three assigned concentrations given a specific draina ge volum e. Again, the ranges are due to varying
estim ates of predicted problem water and subsurface drainage under different m a nagem e nt alternatives.
In an effort to reduce the m a gnitude 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

com p ilation of currently available data on problem acreage , drainage volum e, and Se concentration (Appendix B, Tables B9, B10 and B19 to B21). The values based on current data show only that

39am ount 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 m a nage an annual im balance of water, salt, or Se (Table 7). Depending on the type of data available from each subarea, projections

were m a de concerning concentration or load. Because of the lim ited data and broad range of

m a nagem e nt alternatives across the subareas, m a xim u m and m i nim u m Se concentrations are given to bracket possible load scenarios at each specific volum e of drainage. The projected concentration range
is 5 to 10 μ g/L Se for the Northern subarea , 68 to 152 μ g/L Se for Grassland subarea, 49 to 150 μ g/L
Se for W e stlands subarea (note, no current data, only testim ony on acreage is available), 1.7 to 9.8

μ g/L Se for Tulare subarea, and 175 to 254 μ g/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

• W e stlands 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 + W e stlands + 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 com e from W e stlands subarea and Grassland subarea
because of their com b ination of high problem acreage , and thus problem water volum e, and high Se
concentration.

Loading scenarios
Table 8 illustrates the total Se load f r om various com b inations of subareas that m i ght be included in a drainage collection system . These projected loads of Se provide the basis for determ ining the upper
and lower lim its 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 determ ining the m a gnitude of Se load reduction that m a y becom e necessary to achieve a specif i c load of Se. Estim ates like those in Table 8 im plicitly assum e that Se loads will be prim arily

40driven by the dem a nd for drainage, with different de grees of m a nagem e nt superim posed. Of course,
different dem a nd scenarios than those shown are also possible.
The first four scenarios in Table 8 show that the load of Se increases from a m i nim u m of 6,960 lbs per year to 42,785 lbs per year as additional area is added to drainage collection and/or as drainage
volum e and quality is less m a naged. The scenarios are:

• Only the existing discharges to the SLD from the Grassland subarea would be carried to the Bay-Delta. It seem s unlikely that dem a nd would rem a in 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 f acility.

• Discharge from the Grassland subarea via the SLD or SJR would be discontinued and only the
W e stlands subarea would use an extension of the SLD.

• Grassland subarea discharges and W e stlands subarea discharges would both be carried to the Bay-Delta; this seem s a likely outcom e 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 m i ght call for draining all 444,000 acres of problem lands. The fifth and sixth scenarios in Tabl e 8 provide estim ates of Se loads for a valley-wide drain that includes all potential problem lands estim ated for the year 2000. The first of these calculations shows the range of Se loads expected if drainage m a nagem e nt f o llows the plan subm itted by the SJV Valley Drainage Program . If both quality (treating drainage to 50 μ g/L) and quantity (e.g. reducing acre-feet per acre per year of drainage fr om 0.7 to 0.4) are m a naged, loads would calculate at 19,584 lbs per year. If only quality is m a naged, total Se loadings for the problem lands would then be 42,704 lbs per year. It is also possible that no m a nagem e nt would be em ployed or m a nagem e nt becom e s less and less f easible. Drainage volum es in this scenario are not controlled and the quality of drainage deteriorates to 150 μ g/L. In this case, Se loads would rise from a m i nim u m in the range of 42,704 lbs per year to as m u ch as 128,112 lbs per year (all problem lands, 0.7 acre-feet per acre per year, and 150 μ g/L Se drainage).

41As a com p arison, the final forecast in Table 8 lists the load targets set in recent m a nagem e nt plans for discharge to the SJR from the Grassland subarea (USBR, 1995; CCVRW QCB, 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 determ ined by assigning a water quality goal to the drainage in a SLD extension and operating the drain at som e pre-defined capacity (Table 9). The drain is presently designed to flow at 300 c ubic feet per second (cfs) or carry approxim a tely 220,000 acre-feet per year. That capacity could be a factor lim iting loads, if a water quality standard is

em ployed. Forecasts are given for 1) 50 μ g/L representing an overall average given in testim ony that

treatm e nt technologies (so far unspecified) or ble nding could achieve and near present day discharge
from Grassland to the SJR (i.e., 62-67 μ g/L; 2); 150 μ g/L Se representing an average for current subsurface drainage without blending in the Gr assland subarea (CCVRW QCB, 1996c) and near the

m ean (163 μ g/L) presented for shallow groundwater from 42,000 acres in the W e stlands subarea (W anger, 1994); and 3) 300 μ g/L representing a concentration approaching that discharged from
W W D 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) th at the range of loadings derived from the 50
to 67 μ g/L quality forecast and that from a drain m a naged at full capacity is 30,000 - 40,000 lbs (Table 9), are within the probable forecast derived from drain dem a nd to m a nage the current annual im balance
from specific subareas in Table 8. If the drainage conveyance discharges 150 μ g/L Se, at full capacity, the loading forecast converges on that estim ated from all problem lands with little m a nagem e nt (Table 9). Despite the range of assum p tions and range of possible outcom e s considered in Tables 8 and 9,
there is som e convergence of the forecasts, irrespective of how they are derived. Load targets result in
the sm allest and m o st easily m a naged Se inputs to the Bay-Delta. Selenium loads based upon the
dem a nd for drainage converge on a m a ss discharge of 15,000 to 45,000 lbs of Se per year, if volum es and concentrations are carefully m a naged. Loads quickly grow beyond this level, if m o re land is
drained and/or volum es or drainage quality are poorly m a naged or controlled.

42The San Joaquin River as a conveyance facility, a de facto drain
The above estim ates present Se loads prim arily defined by dem a nd from agriculture, and collection
in an extension of the SLD. An alternative is to assum e that water quality in the SJR would determ ine Se discharges, and no drain would be constructed. Two approaches have been discussed historically. Both approaches consider only the am ount of dilution water available; no consideration is given to defining the assim ilative capacity of the receiving water (i.e., the SJR) based on the bioaccum u lative
nature of Se.
1. Total Maximum Daily Load or Total Maximum Monthly Load models . This alternative m odels
load allocations based on historical f l ows in the SJR. A water quality standard is applied to design flows to calculate a Se load lim it for dischargers (Environm ental Defense Fund, 1994). This is the technique m a ndated by USEPA for discharges to im paired water bodies such as the SJR (Clean W a ter Act, as am ended, 1987; USEPA, 2000). The SJR com p liance site for the
130-m iles of im pairm e nt is the SJR at Crows Landing. This site is below the confluence withthe 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 Tuolum ne and
Stanislaus Rivers flow into the SJR. Inherent in the TMDL m odel approach are an identification of sources and a program of lo ad reduction to achieve com p liance with water quality objectives.
2. Real-time model . This alternative goes one step further than TMDL m odeling in that discharges
are allocated based on real-tim e updates of flow (i.e., instantaneous m easurem ents). This

m eans m a intaining a constant Se concentration at or below the water quality criterion (5 μ g/L, the USEPA criterion is one suggestion) by varying load with flow (Karkoski, 1996). (Note: If
real-tim e discharge were instituted, salinity m easurem ents would need to act as a surrogate f o r Se m easurem ents, since technology is not available to assess Se on a real-tim e basis). Loads
based on real-tim e dilution m a xim i ze disposal of Se by adjusting the tim ing of discharges to coincide with dilution capacity of the river. Large loads m a y be released in m onths of high flow during the winter and spring. Holding ponds m a y be necessary for storage of drainage during low f l ow seasons in the SJR to avoid violations of water quality objectives. This

m e thodology provides no certainty for the am ount discharged per m onth or per year nor does it provide a m eans to assess long-term progress toward load reduction for im paired water-bodies.

43As 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 fo r derivation of loads for the SJR at Crows Landing and the load allocations for the dischargers using the TMDL, TMML, and real-tim e m odels. These

m odels encom p ass both quasi-static and dynam i c m odeling of flows. The quasi-static TMDL and TMDL derived loads range from 1,394 to 6,547 lbs Se per year. Initial estim ates for the dynam i c real
tim e m odel suggested loads would vary from 2,605 to 17,605 lbs per year (Karkoski, 1996) depending upon flow regim e s. Our estim ates 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 m a in consideration in our developm ent 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 environm ental protection a priority, rather than a load driven by agricultural dem a nd. The effects on the SJR itself, of m a naging the constant
concentrations in view of bioaccum u lation are not known and are not considered here.
To obtain these m odeled loads we used several assum p tions 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.

• alm o st com p lete SJR recycling is 220,000 AF com p arable 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 μ g 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 USFW S proposed criterion of 2 μ g 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 load ings to the Bay-Delta from the western San Joaquin Valley is large, current proposals, m a nagem e nt plans, and history narrow the possibilities into three groups, depending upon m a nagem e nt strategy:

44• Supply-driven management (3,000 to 8,000 lbs Se per year) : By this we m e an m a nagem e nt that puts priority on environm ental protection and targets a load that cannot be exceeded. For

exam ple, 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 μ g/L Se criterion depending upon flow regim e for the SJR. The present prohibition for discha rge 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 m ean Se loads are driven by the agricultural dem a nds for draining saline or waterlogged soils. W e assum e the quality and quantity of the drainage are controlled by m a naging volum e per acre and/or quality of the drainage. For exam ple, a range of loads projected from the am ount of problem water defined by the SJV Drainage Program for year
2000 with and without im plem entation of the m a nagem e nt plan (dem and driven volum e) in conjunction with a concentration of 50 μ g/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 m a nagem e nt (45,000 to 128,000 lbs Se per year): This will
occur if the dem a nd f o r restoring saline soils drives drainage and neither quantity nor quality objectives can be (or are chosen to be) m e t. For exam ple, a range of loads projected from the

am ount of problem water defined by the SJV Drainage Program for year 2000 without
im plem entation of the m a nagem e nt plan (dem and driven volum e) in conjunction with a
concentration of 150 μ g/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 m a naged

m a xim u m of 45,000 lbs per year and could approach as m u ch as 128,000 lbs Se per year or

even m o re.

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 μ g/L) (Cutter and San Diego-McGlone, 1990). So, refinery effluents have historically provided a quantitatively im portant load of Se to the Bay-Delta. Furtherm ore, the Se in these effluents is highly concentrated in a relativel y sm all volum e of wastewater, so inputs increase the

45am bient concentration of Se, especially around the Carquinez Strait (Cutter, 1989). In eight
determ inations of refinery effluents in 1987 and 1988, Cutter and San Diego-McGlone (1990)
estim ated that annual Se loadings could vary from 2,035 lbs per year to 4,641 lbs per year from all
refineries com b ined. Annual loads from 1986 to 1992 ranged from 3,103 to 7,457 lbs Se per year as reported by the (Table 10) CSFBRW QCB (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 im posed by the CSFBRW QCB, refinery inputs to the Bay-Delta declined after July 1998. The annual Se loads allowed for the five m a jor refineries by state perm it (CSFBRW QCB, personal com m unication, Johnston Lam and Khalil Abu-Saba, 2000) are listed in
Table 10 in com p arison to the annual range reported by the CSFBRW QCB from 1986 to 1992 (CSFBRW QCB, 1993). By this estim ate, refinery inputs declined by about half (to approxim a tely 2,200 lbs Se per year), from the am ount m easured from 1986 to 1992 (Cutter, 1989; Johns et al., 1988). On the other hand, refinery effluents also are regulated to concentrations of 50 μ g/L Se and to the
volum es discharged in the late 1980’s. If volum es of effluent rem a in what they were in the late 1980’s, the resulting Se load would be 1,400 lbs Se per year. Treatm e nt technologies in the refineries also

rem ove only selenite. So the Se discharged was, presum ably, m o stly selenate in 1999; historic discharges were >50% selenite. No m a ss balance m odel has yet been constructed to evaluate whether 1,400 lbs or 2,200 lbs Se per year best describe refi nery discharges, but the difference is relatively

sm all considering the variability within years and within ref i neries (Table 10). Prelim inary data suggest the selenite concentration peak near the refineries disappeared after the treatm e nt technologies
were im plem ented (Cutter et al., in preparation).

Inputs of Selenium from the Sacramento River Most of the river inflow to the Bay-Delta com e s from the Sacram ento River (Figure 5). The discharge ratio between the SJR (at Vernalis) and the Sacram ento River (at Freeport) is typically 10 to
15%. The dissolved Se concentrations in the Sacram ento River at Freeport are consistently low, averaging 0.06 ± 0.02 μ g/L (Cutter and San Diego-McGlone, 1990). Thus, the Sacram ento River represents a low concentration, high volum e source of Se. Using a concentration of 0.04 μ g/L Se (a

46conservative estim ate) and the inflows given below, the projected annual Se loads conveyed by the
Sacram ento River to the Bay-Delta are:

• 32 MAF, wet year 3,482 lbs Se per year

• 17 MAF, m e dian year 1,850 lbs Se per year

• 10 MAF, dry to critically dry year 1,088 lbs Se per year

• 5 MAF, m o st critically dry year 544 lbs Se per year
Selenium load increases with volum e of inflow from the Sacram ento River, because Se concentrations
in the river are low but constant. The Sacram ento River inflow therefore establishes the baseline flow and Se concentration entering the estuary.

Summary
In our m odel, four inputs in different propor tions determ ine the Se load to the Bay-Delta. The
Sacram ento River loadings vary purely as function of inflow volum es (1,859 lbs Se per year, m e dian precipitation year). The potential loadings from an extension of the SLD vary quite widely. Supplydriven loadings are lowest; dem a nd-driven loadings with m a nagem e nt and treatm ent capabilities f a ll within the range of 15,000 to 45,000 lbs Se per year. Loading rates escalate steeply if treatm e nt strategies are not applied. Loadings f r om 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. W e assum e oil ref i nery loadings will

rem a in at post-1998 values reflecting regulati on and treatm e nt technology (approxim a tely 1,400 to 2,200 per year). The sum s of com b inations of these scenarios represent the loadings under different

m a nagem e nt and hydraulic conditions. W e will consider a few specific, m o st likely, scenarios for the Bay-Delta in detail for forecasting Se concentrations in water, sedim e nt, 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

47proposed canal that would collect irrigation draina ge valley-wide or from the San Luis Unit (i.e.,
W e stlands 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 suba reas of the western SJV or, as configured, from
W e stlands subarea and Grasslands subarea only and release it directly into the Bay-Delta. The SJR is the only natural outlet from the SJ V. 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 alm o st com p letely diverted and recycled. That m eant little or none of the Se discharged into the SJR reached the Bay-Delta. After the 1994 Bay-Delta W a ter Accord (CSW RCB, 1994), water m a nagem e nt changed; m o re 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 m e rging of the Sacram ento River and SJR system s in the estuary and exports or water diversions
add com p lexity (Figures 9 and 10). The am ount of potentially Se-laden SJR inflow reaching specific locations in the Bay-Delta is influenced by (CSW RCB, 1999a; Monsen, 2000):

• tidal cycles;

• variable inflows of the Sacram ento River and SJR due to seasons and upstream withdrawals;

• quantity of water diverted f r om the Delta to the CVP, SW P and local water users;

• discharge of agricultural drainage from the SJ V and drainage inputs within the Delta itself;

• channel configurations and capacity; and

• artif icial barriers which periodically are constructed to route f l ows in the Delta Changes in both the channel configurations and ba rrier 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)

am ong:

• total river (Sacram ento River and SJR) inf l ow;

• SJR inf l ow;

• water diversions [i.e., pum ping 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.

48Total inflows and SJR discharges are very high in the first five m onths of a wet year, far exceeding diversions. In the fall, however, water diversion can exceed total inflows. In Septem ber through
Novem b er, SJR discharge at Vernalis can be a large proportion of total inflows. During this tim e of year, if SJR inflow is transported past the diversions, it can have a substantial influence on Bay-Delta waters. Manipulations of barriers, m odification 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 tim e of year. Better understanding of water m ovem e nt fromthe SJR thorough the BayDelta and processes within the estuary are critical to fu ture evaluations of Se issues. Evaluations of the
im plications of water m a nagem e nt decisions m u st consider effects on Se transport and residence tim e. A large range of residence tim es have been estim ated for freshwater in various parts of the Bay-Delta (W alters et al., 1985). The estim ated residence tim es (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 Dum b arton Bridge) 80/120

• Extrem e South Bay (south of Dum b arton Bridge) 40/70



### CONCENTRATIONS OF SELENIUM IN THE BAY-DELTA

Interpreting Effects of Source Water Se Load s on Receiving Water Se Concentrations Interpretation of m a ss loadings from individual sources requires understanding how load and
volum e in different source waters com b ine to produce concentrations in receiving waters. It is concentration in receiving waters that determ ines biological im pacts. So ultim ately the interaction between source water loading and receiving water concentration m u st be understood.
Load will increase with increased volum es of drainage, given the characteristics of Se concentrations in the drainage (Figure 6). Load also increases with volum es of inflow from the
Sacram ento River, because Se concentrations in the river are low but constant. On the other hand,
concentrations in the m i xture of waters where the sources com b ine will be dependent upon the sum of

49the volum es of the sources and the m a sses of Se in each of those sources. Dissolved Se com p rises 80 to 93% of the total Se (Cutter, 1989) in the Bay-Delta so loads based on total Se can be em ployed to
derive concentrations of dissolved Se.
The volum e of water (or the rivers) input to the Bay-Delta is determ ined by clim ate and water

m a nagem e nt. As a sim p lification, these inflows can be thought of collectively as the rivers, m eaning
the sum of the inflows of the Sacram ento River and the SJR. Monitoring of Se concentrations in the Bay-Delta receiving waters m u st take into account the m onthly, seasonal, and year-to-year variability of hydraulic discharge. A useful sim p lification is to consider the Bay-Delta watershed as characterized by a distinct seasonal cycle of high inflows from the rivers in January through approxim a tely June, followed by lower inflows through the last six m onths of the calendar year (Conom os, 1979; Conom os et al., 1985). In contrast to water volum es, the m a ss of Se in anthropogenic effluents such as oil refinery effluents is not highly variable because both volum es and concentrations are relatively constant (CSW RCB, 1992a; b). Monthly load target s 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.
Volum e s of agricultural drainage discharged from the Grassland subarea in 1997 varied from 1,274 to 4,867 acre-feet per m onth with concentrations varying from 25 to 106 μ g/L Se to enable a targeted
load. The W e stlands subarea during 1981 to 1985 discharged an average concentration of 330 to 430

μ g/L Se and the volum e ranged from 304 to 772 acre-feet per m onth. In all these cases, the degree of variability in volum e will be sm all com p ared to the variability in river inf l ows. As a result of the m i xing of variable inflows from the rivers (m ostly with low Se concentrations) and relatively constant anthropogenic inflows (with high Se concentrations) a strong seasonal fluctuation and year-to-year fluctuations of Se c oncentrations 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 ea ch 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 im pacts m u st consider the tim e 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 tim es that will drive im pacts) with regard to Se. Factors such as
residence tim es and exchanges within the Bay and Delta are also im portant, but the m odels necessary
to understand these sm aller scale effects (e.g. elevated concentrations near sources of input; detailed distribution within the Delta or Suisun Bay) are not adequately developed. Further developm ent of hydrodynam i c m odels (Cheng et al., 1993; Monsen, 2000; Burau and Monism ith in preparation),

m u ltiple m e dia m a ss balance m odels, and kinetic geochem i cal m odels are very im portant to def i ning detailed ecological effects of Se and resolutions to future Se problem s.

Existing Concentrations in the Bay-Delta

Regional baseline Dissolved Se concentrations are low (0.06 ± 0.02 μ g Se/L) in the Sacram ento River (at Freeport) (Cutter and San Diego-McGlone, 1990) and in the seawater (0.02 to 0.08 μ g Se/L) with which it m i xes (Cutter and Bruland, 1984) in all seasons. The regional Se baseline in the Bay-Delta is defined by

m i xing the Se concentrations in these two endm em bers, as determ ined by a salinity gradient through the estuary (Figure 11). A m o re com p lex case is one of a com posite freshwater endm em ber com p rised
of the Sacram ento River, the SJR, and the refineries effluents. The regional baseline can be com p ared
to a theoretical m i xing line for which the Se endm em ber concentration in the freshwater com posite represents anthropogenic sources. In Figure 11, the ex am ple m i xing profile gives a Se concentration of
0.23 μ g Se/L (Figure 11). The com posite freshwater endm em ber concentration is calculated from
annual Se loads and volum es in the Sacram ento 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 com posite endm em ber is diluted as a function of salinity. This type of m i xing m odel, which is driven by salinity, can forecast a range of expected Se concentrations in the Bay-Delta. This approach to m odeling Bay-Delta Se inputs illustrates that variation in Se loads delivered by an endm em ber consisting only of the Sacram ento 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 μ g/L Se). However, the sum of source input Se loads determ ines the Se concentration of the com posite freshwater endm em ber.

51Therefore, adding a low volum e/high concentration s ource of Se to obtain the com posite freshwater
endm em ber Se concentration will cause changes in the Se concentrations in the estuary system

. The spatial details of observed Se distributions can be com p ared to theoretical distributions to draw conclusions about internal sources or trapping of the property within the estuary. The projected Se
concentration in the theoretical com posite freshwater endm em ber used above (i.e., 0.23 μ g/L Se) is
sim ilar 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 em ployed reliable analyses of dissolved Se distributions in the Bay-Delta. Cutter (1989) sam p led the full salinity gradient of the North Bay in April and May 1986; Cutter and San Diego-McGlone (1990) rep eated that study in October 1987, Decem ber 1987, March 1988 and May 1988. Cutter et al. (in preparation; unpublished data quoted in Luom a and Fisher, 1997) sam p led 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 system atically 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 μ g Se/L level designated as the Canadian wildlife hazard level (Environm ent Canada/Health Canada, 1995; Outridge et al., 1999); the 2 μ g/L USFW S proposed chronic criterion for protection of aquatic life for all waters within the range of listed endangered species in the state of California (USFW S and NMFS, 1998 and

am ended, 2000); or the 5 μ g Se/L USEPA chronic criterion for protection of aquatic life (derived from freshwater studies) (USEPA, 1992). The m a xim u m concen trations of dissolved Se in m o st surveys are less than those observed in the adjacent watersheds (Cutter, 1989; Cutter and San Diego-McGlone, 1990; CCVRW QCB, 1992a; b; 1993) (Tables 2 and 5). Slightly higher concentrations are som e tim es 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 μ g Se/L in August 1993 (San Francisco Estuary Institute, 1994). The lowest concentrations were observed in the
Sacram ento River in Septem ber 1986 and June 1995 (0.048 to 0.052 μ g Se/L). No analyses have been

52conducted of Se concentrations in the Delta, although a recent CALFED supported study has begun

som e data collection in this area (Cutter et al., in preparation). The spatial f eatures 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 m i d-salinity ranges near Carquinez Strait; and 2) lowest in the river and oceanic
endm em bers. This suggests a source of Se exists in the m i ddle of the estuary. Cutter (1989)
determ ined 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. Estim ates of fluxes indicated that the export of Se from the Bay-Delta to the ocean was controlled by riverine sources during this m onth. During low flow seasons, dissolved Se concentrations increase and the peak in Suisun Bay becom e s m o re distinct. Cutter (1989) and Cutter and San Diego-McGlone (1990) showed that in Se ptem ber 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-tim es input s from the rivers in this m onth, and were the cause of the shape of the gradient. In March of 1987, duri ng a drought, refineries were 74% of the Se flux; in May 1987 they were 96%. Presum ably, this has changed since July 1998; but only prelim inary data
are available. Thus, while estuarine waters in the Bay-Delta are enriched in Se com p ared to the regional baseline,
the Se concentrations in the estuarine waters are low com p ared to m a ny contam inated freshwater
environm ents. The concentration of dissolved Se am ong rivers and estuaries in England (Measures and Burton, 1978) and several rivers in eastern North Am erica (Takayanagi and Cossa, 1985) range
from 0.049 μ g Se/L to 0.39 μ g Se/L. Presum ably som e of these sites were anthropogenically

contam inated like the Bay-Delta. This range is the sam e range as seen in the Bay-Delta. It is possible that physical or biogeochem i cal 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 contam ination described next. 53

### CHEMICAL FORMS OF SELENIUM (SPECIATION)
Concentrations of waterborne Se are not su fficient to predict the biological im plications of Se

contam ination. The geochem i cal speciation of Se is a critical consideration. Speciation of dissolved
Se ultim ately controls transform a tion reactions between dissolved and particulate form s (i.e. the
reactions with sedim e nts, detrital particles, and prim ary producers). Transform a tions and particulate
concentrations are im portant factors determ ining the biological effects of Se; but they cannot be forecast without consideration of speciation.
Selenium is a natural trace elem ent, num ber 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 f o r S -2 in proteins seleno-m e thionine and seleno-cysteine •

•

•

•

• Selenite (+4 or IV) the oxyanion selenite (SeO 3 -2 ), an analog to the sulfur com pound sulfite Selenate (+6 or VI), the oxyanion selenate (SeO 4 -2 ), an analog to the sulfur com pound sulfate Although dissolved Se in aerobic waters can som e tim es occur predom inantly as an organic form (Takayanagi and W ong, 1984; Cutter and Bruland, 1984), selenate and selenite are the m o st com m on form s in m o st waters. Selenate is the therm odynam i cally-predicted stable form of Se in oxic waters, but due to its slow oxidation rate in natural waters, selenite can be an im portant species (Cutter, 1982).
Selenite is the m o st bioavailable of the dissolved phase inorganic species (Maier et al., 1993; Skorupa, 1998b). Com p arative toxicity laboratory studies dem onstrate that som e form s of organo-Se are also very bioavailable and hence toxic to tested algae, invertebrates, and fish (Maier et al., 1993).
Exam ples exist in nature where each of the three m a jor species of Se is predom inant: 1) selenate predom inates in m o st irrigation drainage inputs to wetlands (Presser and Ohlendorf, 1987; Zhang and Moore, 1996; 1997a; b); 2) selenite can predom inate in system s affected by industrial wastes, especially those associated with wastes from fossil fuel products or consum ption (Cutter and San Diego-McGlone, 1990); and 3) organo-Se can predom in ate where Se is strongly recycled (Takayanagi
and W ong 1984). In the Bay-Delta, speciation differed am ong the source waters in 1980’s (Cutter and Diego-McGlone, 1990):
Sacram ento River inflow was 30 to 70% selenate, depending upon season; organo-Se was the
other m a in com ponent. SJR inflow was 70% selenate and 22% organo-Se.

54r e f i n e r y w a s t e w a t e r s a v e r a g e d 6 2 % s e l e n i t e

. •

•

• during low flow in Carquinez Strait, as m u ch as 50% of the Se was selenite in the late 1980’s, reflecting the predom i n a n c e o f r e f i n e r y i n p u t s

. prelim inary studies in Suisun Bay in the late 1990’s showed less selenite, but selenite plus organo-Se could com p rise 60% of the m a ss of Se.



### PARTICULATE AND SEDIMENT-ASSOCIATED SELENIUM

Processes Affecting Particulate Selenium

Partitioning
One of the m o st im portant biogeochem i cal steps or links controlling the bioavailability and ef f

ects of Se is the partitioning reactions that determ ine the distribution between dissolved and particulate phases, where particulate phases include prim ar y producers (e.g. phytoplankton), bacteria, detritus, suspended inorganic m a terial and sedim e nts. There are several reasons these reactions are im portant:

• The pathway for nearly all Se transfer to the second trophic level in the system is via particulate
form s (i.e., anim als bioaccum u late Se from their food to a m u ch greater extent than they take up
Se from water, at the distributions typical of nature, Luom a et al., 1992).

• The transform a tion efficiency from dissolved to particulate Se ultim ately determ ines food web
concentrations of the elem ent (i.e., higher Se concentrations on particulate m a terial m eans greater contam ination in the food web, although the form of the Se in the particulate can also be
im portant);

• Concentrations of Se on particulates can differ by as m u ch as 100-fold, at the sam e dissolved concentration, depending upon the biogeochem i cal transform a tion reactions governing the dissolved particulate interaction. Thus, fo recasts of effects depend upon understanding what
transf orm a tions will occur. The largest inventory of Se in a contam inated ecosystem usually occurs in sedim e nts. For exam ple, 90% of the inventory of Se in Kesterson Nati onal W ildlife Refuge was deposited in sedim e nts (Tokunaga et al., 1996). However, the proportion of Se on suspended particles, at any one tim e, m a y be only a sm all fraction of the total quantity of Se in the water colum n. For exam ple, in April 1986,

55Cutter (1989) found that only 7% of total Se in the water colum n of the North Bay was particulate; in Septem ber 1986, only 13 ± 7% was particulate. The larg e inventory of Se in sedim e nts results either because suspended particulate Se is progressively deposited in sedim e nts over tim e and/or because
reactions within the sedim e nts progressively strip Se from solution. The concentration per unit m a ss on the particulate m a terial is m o re critical than the m a ss in suspension (per unit volum e of water). In fact, the m o st im portant m e asure of Se in any environm ent

m a y be the concentration of Se per unit m a ss of suspended particulate m a terial. This concentration
determ ines the exposure of the m a ny species that feed on such m a terial. Each species' exposure to Se is partly determ ined by how that species "sam ples" the com p lex water/sedim e nt/particulate/organism

m ilieu that com poses its environm ent. Many species are able to ef f i ciently gather large quantities of particulate m a terial from the water colum n, even when particulate concentrations them selves are relatively low. Bioaccum u lation is then determ ined from the μ g Se/g food or particulate m a terial, along with the efficiency with which that concentration is assim ilated (Luom a et al., 1992).
Assim ilation efficiency (AE) is the proportion of i ngested Se that is taken up into tissues; and AE varies with the type of food or the form of particulate Se.
Direct determ inations are rare of Se concentrations per unit m a ss on suspended sedim e nts. This is at least partly a result of the dif f i cult challenge of collecting a sufficient m a ss of suspended m a terial for direct analysis.

Transformation Several different prim ary reactions can transform (o r affect transform a tion of) dissolved species of Se to particulate Se. Transform a tion reactions in clude biological, redox, and physical processes. The

m o re im portant reactions are:

• Assimilatory biological uptake and transformation . In an oxygenated water colum n, a prim ary transform a tion is the biochem i cal transform a tion of Se(IV), Se(VI) and/or dissolved organo-Se [Se(-II)] to particulate Se(-II) via uptake by plants or, perhaps m i croorganism s. Microbes, plants, and m i croflora (phytoplankton) reduce the Se they concentrate to Se(-II). Most
biochem i cally transform e d Se is found within the cell solution, at least in phytoplankton (Reinfelder and Fisher, 1991), and is highly bioavailable to anim als that consum e the

m i croorganism s for food. W h en cells die and breakdown the plants release both Se(IV) and

56Se(-II) back to the water colum n in dissolved form . Biotransform ed Se (-II) can also be sequestered in sedim e nts or suspended particulate m a terial, as detrital Se(-II).

• Dissimilatory ( extra-cellular) biogeochemical reduction . W h en Se in water contacts reduced particles (little oxygen) or reduced sedim e nts, sequestration onto or into sedim e nts by bacteria
can occur. The m o st im portant m i crobial transform a tion reaction under these conditions is
dissim ilatory reduction (Orem l and et al., 1989). Dissim ilatory reduction of either Se(IV) or Se(VI) generates predom inantly elem ental Se [Se(0)] in sedim e nts; but it m a y also generate

som e operationally defined organo-Se [Schlekat et al., in press (b)]. Elem ental Se can be
f u rther transf orm e d within the sedim e nts by reactions such as precipitation as f e rroselite (FeSe 2 ), incorporation into solid phases such as pyrite (Velinsky and Cutter, 1991), or uptake by plants to ultim ately form detrital organo-Se (Zhang and Moore, 1997a; c).

• Oxidation state . The particulate Se generated by the transform a tion reactions can occur in different oxidation states depending upon the tran sform a tion reaction and subsequent exposure to geochem i cal conditions. Understanding the f o rm of particulate Se is critical to evaluating
im pacts of Se contam ination, because each form has a different biological availability (Luom a et al., 1992). Reduction/oxidation status, determ ined by the balance of redox couples, is especially im portant in determ ining particulate form . Possible particulate form s include: adsorbed/coprecipitated selenite (SeIV) and selenate (SeVI), organic selenides, either in the
form of intracellular Se(-II) or detrital Se(-II), or elem ental Se (Se(0)).

• Adsorption . Geochem i cal adsorption can occur in the water colum n, if reduced sedim e nts are

m i xed back into an oxygenated water colum n and oxidized (Dowdle and Orem land, 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. Biogeochem i cal volatilization of Se is well docum ented in wetland soils (Cooke and Bruland, 1987; Thom pson-Eagle and Frankenburger, 1992) and in evaporation ponds (Fan and Higashi, 1998). Volatilization rates depend upon physical/chem i cal conditions, vegetation, water m a nagem e nt or other rate lim iting factors (Flury et al., 1997; Zhang and Moore, 1997a; c; Hansen et al., 1998). The influence of volatilization on Se
concentrations in sedim e nts (the relevance to this discussion) is determ ined by the m a ss of Se volatilized, com p ared to that in sedim e nts. A caref ul m a ss balance including determ ination of Se inputs, outputs and internal inventories is th e only way to verify effects of volatilization on 57Se inventories. Studies that present a full com p lem e nt of such analyses are rare; so significant
uncertainties rem a in about the role of volatilization. Cooke and Bruland (1987) originally
observed f r om lim ited data that approxim a tely 30% of the incom i ng Se was volatilized at Kesterson Reservoir. Zhang and Moore (1997d) and Hansen et al. (1998) reported results consistent with that figure for other wetland system s. If this value of 30% is typical, it is possible to calculate the ef f

ect of volatilization on Se concentrations in a wetland that receives a continuous input of Se. If 90% of incom i ng dissolved Se is trapped in the sedim e nts, and if
30% of that is volatilized, then the net ef f

ect of volatilization is to reduce the progressive

accum u lation of Se in particulate m a terial to: 0.90 trapped X 0.30 volatilized = 0.63 trapped X
100 = 63% of incom i ng Se retained. Thus volatilization could slow Se accum u lation to a rate less than would otherwise be achieved. However, in no known case has volatilization
elim inated Se contam ination or alleviated water quality problem s. W e tland trapping can

rem ove Se from contam inated waters, but m o st of the Se rem a ins in the sedim e nts; ef f

o rts to

com p letely volatilize Se to the atm o sphere have not proven successful. If Se inputs to the
wetland were elim inated, eventual rem oval by volatilization is a theoretical possibility. However, this also has never been observed in natural sedim e nt with a high Se load (e.g., Flury et al., 1997).

Range of distribution coefficients (Kd’s)
The distribution coef f i cient (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 m a ss particulate m a terial versus Se per unit volum e water, in equivalent units. An exam ple of a calculated Kd for the Bay-Delta
from typical 1986 data (Cutter, 1989) is: (700 μ g particulate Se/kg particulate)/(0.315 μ g dissolved Se/L) = 2.2 X 10 3 L/kg. Speciation of dissolved Se and transform a tion reacti ons have a com b ined influence on the distribution
coefficient of Se. The Kd oversim plifies both with the result that Kd’s based upon total concentrations in natural waters vary by as m u ch as two orders of m a gnitude. Nevertheless, the Kd is a first order

m easure of partitioning and em ploys the data m o st widely available f r om a variety of system s. Table 11 lists Kd’s typical of the variety of ecosystem from which reliable geochem i cal data are available. The Kd’s in various field studies have ranged from 0.3 X 10 3 to 2 X 10 4 , reflecting the com p licated
transform a tion reactions and processes described above. Skorupa (1998a) also sum m a rized the range 58of dissolved and sedim e nt data found in various fiel d studies. Median Kd’s from that list, although not calculated by Skorupa (1998a), show a sim ilar 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 biogeochem i cal m odels.

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 transform e d to particulate form s in the m a rshes of the SJR and the wetland/lakes of the Delta by either dissim ilatory reduction to Se(0) or biotransform ation to Se(-II). Very little is yet known about Se trapping or transform a tion within the Delta itself.

• Allochthonous (external) sources : It is possible that Se contam inated particles produced in the SJR could be transported to and trapped in the Delta. Particulate Se transform e d within the
Delta m a y 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 tim es occur in Suisun Bay, as inflows recede or during low inflows. Longer residence tim es progressively increase the
likelihood for biotransform ation by local m i croflora and m i crobes in the water colum n, on surface sedim e nts or within sedim e nts (Lem ly, 1997a). Long residence tim es and contact between the water colum n and the redox interface in sedim e nts are critical factors in progressively accum u lating Se in the sedim e nts of wetlands or shallow waters (Zhang and Moore, 1997a; b). Thus the tim e of greatest vulnerability in the Bay or Delta are low inflow seasons and low inflow years when residence tim es are longest. The places m o st likely to generate particulate Se are wetlands and shallows with long residence tim es. Restoration activities could affect
Se contam ination in the SJR-Bay-Delta system if they change hydraulic residence tim es or generate a larger area of the kinds of system s that trap Se, without rem e diating Se inflows.

Particulate selenium in the San Joaquin River Direct inputs of irrigation drainage to the SJ R have long occurred, via canals and wetlands. Since 1996, the SLD has also directly discharged drainage from the Grassland subarea to the river. 59Difficulties arise in drawing generalizations about tem por al trends or spatial distributions of particulate Se in the SJR, however, because there are few consistent, extensive or system atic surveys. W h ere such surveys exist, sam p ling m e thodologies do not allow elim ination of biases caused by changes in river discharge, concentrations of suspended m a terial, Se concentrations on suspended m a terial in different
seasons or bed sedim e nt characteristics like particle size and differences in organic carbon concentrations. A detailed, system atic and carefu lly designed study of particulate Se occurrence and trends would be relatively easy to im plem ent 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 μ g Se/g dw in sedim e nts 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 μ g Se/g dw; the higher values probably reflect contam ina tion from historic Se inputs to the slough.

• Downstream of SLD, before 1996 discharges : The range of concentrations, am ong several ad
hoc studies, in sedim e nts of the SJR downstream of the inactive discharge site (pre-1996) was
0.3 to 1.9 μ g Se/g dw. One value of 5.2 μ g Se/g dw was reported from the SJR near Vernalis.

• Downstream after current operations began : In Septem ber 1996, after operation of the SLD began, Se concentrations of 0.1 to 0.76 μ g Se/g dw were determ ined in sedim e nts im m e diately below the discharge, in Mud Slough. Concentrations 6.6 m iles downstream from the discharge
were 0.7 to 1.9 μ g Se/g dw. Recent data show Se increasing to 4.8 μ g/g dw in sedim e nts in a seasonal backwater tributary of Mud Slough where residence tim e increases (USBR et al., 1999).

• Suspended sediments . Several surveys also have analyzed suspended sedim e nts in the SJR or adjacent m a rshes or sloughs. In all cases, concentrations in suspended sedim e nts exceeded
concentrations in bed sedim e nts. In a backwa ter where stagnant conditions would be expected (high hydraulic residence tim e), a concentration of 4.4 μ g Se/g dw was determ ined. The range of concentrations in suspended sedim e nts was 0.91 to 6.7 μ g Se/g dw. System atic studies of seasonality, relationships to hydrology or form s of Se could be instructive with regard to
sources and causes of the large range of variability.

60Particulate selenium in the Delta Little is known about Se concentrations in the Delta. In 1986-88, Johns et al. (1988) sam p led
Corbicula and sedim e nts near-m onthly at a station in the Old River channel near Clifton Court Forebay. At that tim e and location, Se concentrations in both indicators ( Corbicula sp., m ean 3.1 μ g Se/g dw and particulates grand m ean, 0.19 ± 0.03 μ g Se/g, dw) were significantly lower than found within Suisun Bay ( Corbicula sp., range of m eans, 3.9 to 5.2 μ g Se/g dw and particulates range of grand m eans 0.23 to 0.53 μ g Se/g dw); and sim ilar to concentrations found in the un-enriched
Tuolum ne River, which drains the Se-poor geology of the eastern San Joaquin Valley. No system atic
Se studies were conducted in the Delta after SJR inflows to the Delta increased in the m i d-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 som e locations.

Particulate selenium in existing portion of the San Luis Drain Transport, re-suspension and re-oxidation of the particulate m a terial in the existing SLD, if extended, m i ght also be a source of bioavailable par ticulate Se to the Bay-Delta. Transform a tion of dissolved Se(VI) into particulate Se has been dem onstrated within the existing SLD. Early surveys conducted when the SLD was carrying W e stlands subarea drainage to the Kesterson National W ildlife Refuge observed a m a xim u m sedim e nt concentration of 210 μ g Se/g dw and an average of 84 μ g Se/g dw in the SLD (Presser et al., 1996; Appendix E, Table E1). A com p ilation of 1994 surveys, after the Grassland Bypass Channel Project had begun, showed a m a xim u m of 146 μ g Se/g dw and an average
of 44 μ g Se/g dw in SLD sedim e nt sam p les (Appendix E, Table E1). In whole core sam p les collected
in 1997 from the SLD, the range of concentrations was 3.8 to 100 μ g Se/g and the m ean was 30 μ g Se/g dw (USBR et al., 1998). The elevated Se con centrations and the wide range of concentrations
docum ented in bed sedim e nt of the SLD are consis tent with observations from wetlands (including Kesterson Reservoir) where m i crobial dissim ilato ry reduction and biotransform ation by prim ary 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 sedim e nt was probably approxim a tely 90%
elem ental Se, also suggestive that m i crobial dissim ilatory reduction was especially im portant in that
environm ent. Contact m a y occur within the drain between oxidized water and a sharp redox gradient

61in sedim e nts, which is apparently suf f i cient to transf orm a signif i cant quantity of incom i ng Se to particulate form (Presser et al., 1996; Presser a nd Piper, 1998). Re-suspension and transport of
sedim e nts from the SLD, therefore, m u st be considered as a source of Se for the SJR, deserving of further study. Sim ilarly, re-suspension of sedim e nts in a SLD extension to the Bay-Delta could provide a sim ilar direct source of highly contam inat ed particulate Se to the Bay-Delta. The hydraulic
residence tim e of the North Bay at low flows is about 60 days (W alters 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. Elem ental Se m i ght also be expected in sedim e nts in the Bay-Delta where conditions favor biogeochem i cal deposition (anoxic sedim e nts). Such conditions m i ght be present in m a rshes near any discharge from a SLD extension or within sedim e nts deposited within the SLD itself.
None of the sam p ling protocols referenced a bove included sam p ling of algal m a ts as part of the suspended or bed sedim e nt fraction. Seasonal al gal bloom s occur in drainage canals and sloughs receiving agricultural drainage. Data collected during the discharge of the SLD into Kesterson
National W ildlife Refuge showed that Se was concentr ated in algal m a ts associated with evaporation ponds (Presser and Ohlendorf, 1987). Thus, algal m a ts and bloom s m a y represent a significant fraction of total Se in an aquatic ecosystem from a m a ss balance basis that has not been system atically
docum ented during surveys of suspended or bed sedim e nt. The surficial layer of bed sedim e nt m a y be
the m o st affected by accum u lations of decaying organic m a terial (Presser et al., 1996)

Sedimentary selenium in Suisun Bay and San Pablo Bay
W e tland transform a tion of Se in the Bay-Delta has not been well studied, nor have surveys of m a rsh
sedim e nts been conducted system atically. Zawislan ski and McGrath (1997) reported concentrations of
1.0 to 1.25 μ g Se/g in the sedim e nts of a m a rsh on Carquinez Strait. Concentrations were sim ilar in

core sam p les collected down to 15 cm depth in the sedim e nt. Com p ared to dissolved concentrations in Carquinez Strait (0.1 to 0.3 μ g Se/L), the Kd for the m a rsh sedim e nts varied from 3.33 X 10 3 to 1.25 X
10 4 . Zawislanski and McGrath (1997) also reported pore water concentrations of 2 to 10 μ g Se/L, but further verification of such high values is necessary.
Bed sedim e nts that have been studied to date in shallow water habitats of the Bay-Delta are not heavily contam inated with Se. For exam ple, Se concentrations were determ ined in fine-grained
sedim e nts from a core collected in Richardson Bay, near the m outh of the estuary (Hornberger et al.,

621999). Concentrations of Se (0.2 to 0.4 μ g 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 μ g Se/g in mudflat sediments adjacent to a marsh in Carquinez Strait. Johns et al. (1988) found mean concentrations of 0.31 μ g 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 μ g Se/g dw) and varied, the most widely of any station, from 0.2 to 1.0 μ g 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 μ g Se/g dw and median concentrations of dissolved Se are 0.2 μ g Se/L.
These data show that the sediment water distri bution coefficient is approximately 1.5 to 2.5 X 10 3

, 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 extre m ely high river inflows, the m axi m um concentration of Se on particulate m aterial near Carquinez Strait was 0.64 μ g Se/g dw particulate and an average concentration throughout the North Bay was 0.33 μ g Se/g dw particulate.

• In September 1986, during low inflows, the concentration of particulate Se averaged 0.75 μ g/g dw, with a m axi m um of approxi m ately 1.25 μ g/g dw. The particulate Se concentrations were approximately 5 X 10 3 to 1 X10 4 greater than the concentration per unit mass dissolved in the
water column.

• In June 1995, during a prolonged period of very hi gh inflows, particulate Se concentrations ranged from 0.53 to 0.99 μ g Se/g dw with an average concentration among six samples of 0.68

μ g Se/g dw. The Kd for median concentrations in this sampling was: [0.075 μ g Se/L] / [0.75 μ g Se/g dw] = 1 X 10 4

. 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 μ g Se/g dw were observed in suspended material in the Sacramento River channel at Rio Vista and 3.57

μ g 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 m aterial were approxi m ately 1.54 to 2.51 μ g Se/g dw, with an average concentration in eight bay samples of 1.98 μ g Se/g dw [i.e., more than two times higher than the mean (0.75

μ g Se/g dw) in September 1986]. The Kd’s for the median Suisun Bay concentrations for the October 1996 survey were therefore: [0.18 μ g Se/L] / [2.1 μ g Se/g dw] = 1.17 X 10 4

• For the landward site at the head of the estuary with highly elevated concentrations, the Kd was: [0.18 μ g Se/L] / [5.6 μ g Se/g dw] = 3.1 X 10 4

. Summary
Concentrations > 1 μ g Se/g dw in suspended materials are common and concentrations as high as 8

μ g Se/g dw are observed in a few instances. The s ources and frequency of the highest concentrations are not clear. Kd’s in these surveys are consistently > 1 X 10 4 . 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 anim als 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; • 64prim ary producers taking up Se and they them selves being consum ed by anim als: and/or •

• direct uptake of detrital or sedim e ntary Se-enriched particles via f ilter-f eeding or deposit feeding. In laboratory studies of the m u scle Mytilus edulis , dissolved selenite [ S e(IV)] is the m o st bioavailable form of inorganic Se taken up from solu tion, but the uptake rate is slow com p ared to m a ny trace elem ents (W ang et al., 1996). Luom a et al. (1992) showed that the uptake rate of dissolved selenite explained less than 5% of the tissue burden of Se accum u lated by the clam Macoma balthica at concentrations typical of the Bay-Delta. The role of dissolved organic selenides in Se bioaccum u lation 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 im portant as uptake from diet (Luom a et al., 1992; Lem l y, 1993 a). Dissolved Se speciation strongly influences uptake by prim ary producers (e.g. phytoplankton) and m i crobes. Uptake of selenite by phytoplankton is substantially m o re efficient than uptake of selenate. But if
selenate concentrations are 10-tim es those of selenite, and uptake rates differ by 10-tim es, then the two
form s could be equally im portant. Concentration factors by phytoplankton, for selenite, can be as high as approxim a tely 10 4 or 10 5 (e.g., Butler and Peterson, 1967; Fowler and Benayoun, 1976; W r ench and Measures, 1982). Once taken up, selenite is incorporated into seleno-am ino acids within phytoplankton (W rench, 1978), which are then transferred to the next trophic level with great efficiency. Assim ilation efficiencies for phytopl ankton-associated Se vary from 55 to 90% am ong different invertebrates (e.g., Reinfelder et al., 1997). Selenium uptake from non-living particulate

m a terial or detritus has not been well studied. In ge neral, it is probably less efficient than uptake from living plant m a terial; although som e fraction of m o st natural form s appears to be bioavailable (W ang et al., 1996; Luom a et al., 1992). For exam ple, Luom a et al. (1992) studied uptake of particulate
elem ental Se produced from the m i crobial reduction of 75 Se-selenate. The particulate Se(0) was
form ed by sim u lating the biogeochem i cal transform a tion process thought to be predom inant in
wetlands. The assim ilation efficiency of elem ental Se was 22%.

Selenium in Invertebrates from the Bay-Delta Fish and birds are the wildlife of greatest concern w ith regard to Se contam ination. However, fish
and birds are m obile, im practical to sam p le in large num bers, and difficult to m onitor routinely. On 65the other hand, consum ption of prey, com p rised of prim ary and secondary consum er species, is the route by which these predators are exposed to Se. Consum er species like bivalves, polychaetes,

am phipods or zooplankton can be practical to em ploy as resident bioindicators of Se exposure (Phillips and Rainbow, 1993; Brown and Luom a, 1995b). As disc ussed below, the predators with the highest tissue concentrations of Se in the Bay-Delta are be nthivores that consum e bivalves in their diet.
Theref ore, the m o st relevant bioindicators to these sensitive predator species are bivalves. Interpretations are least am biguous when Se concentrations in bioindicator species are com p ared to clearly defined reference concentrations. For our m odel, we assum e 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 μ g Se/g to 2.66 μ g 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 environm ent to the Sacram ento River (San Francisco Estuary Institute, 1994; 1995; 1996). Johns et al. (1988) found a m ean reference concentration and 95% confidence lim its of
3.08 ± 0.28 μ g Se/g dw in C. fluminea from apparently uncontam inated sites near Clifton Court Forebay and in the Tuolom ne River (Figure 14a).
Bivalves from the Bay-Delta have elevated Se concentrations com p ared 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 μ g Se/g dw in a single deploym ent of transplanted

m u ssels ( Mytilus sp. ) in Carquinez Strait, and concentrations of 5.0 to 7.4 μ g Se/g dw near Mare Island in Suisun Bay. Anderlini et al. (1975) reported concentrations of 4.5 to 6.7 μ g Se/g dw in the clam M.
balthica near Mare Island in 1974. Although conducted m o re than 20 years ago, both these studies analyzed their sam p les 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. Fi gure 14a com p ares the frequency distribution
in 129 com posite sam p les 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 m ean concentration
and 95% confidence lim its am ong the Suisun Bay data was 5.08 ± 0.17 μ g/g dw, significantly different than the reference values (p<0.001). These historic data show that the habitat in Carquinez Strait was

66contam inated two-fold or m o re with Se com p ared to reasonable reference locations, and that

contam ination 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 dom inant food of benthivore predators in the ecosystem (N ichols et al., 1990). Figure 14b adds to the C. fluminea distribution, the frequency distribution of Se am ong 62 com posite sam p les of P. amurensis , collected between May 1995 and June 1997, from Carquinez Strait (Linville and Luom a, in press). The m e an concentration and 95% confidence lim its am ong all data for P. amurensis was 12.94 ± 0.75 μ g/g dw.
A wide distribution of concentrations was also obs erved, ref l ecting substantial tem poral variability. Thus, the m ean concentration of Se in the dom inant resident bivalve in Suisun Bay ( C. fluminea in
1985-86 com p ared to P. amurensis in 1996) has m o re than doubled since 1985-86. It is therefore likely that the total am ount of Se experienced by birds and fish that feed on bivalves has sim ilarly
doubled. The 1995-1997 m ean concentration in P. amurensis exceeds the dietary threshold (10 μ g Se/g dw) for predators that has a high certainty of producing adverse effects in predators. During 1995 - 1997, 32% of P. amurensis sam p les from Carquinez Strait contained greater than 15 μ g Se/g dw.
Lem l y (1997a; b; c) cites case studies that indicate that concentrations of Se in prey species of 5 to 20

μ g Se/g dw initiate teratogenic deform ities in fish and load the eggs of som e bird species beyond teratogenic thresholds (see discussion below).
Se concentrations in P. amurensis from Carquinez Strait vary seasonally. Concentrations varied approxim a tely three-fold with tim e during 1995 to 1997. The highest concentrations were observed in October 1996 (20 ± 1 μ g/g dw) and the lowest concentrations were observed in May 1995 (7.13 ± 0.34

μ g Se/g) and May 1997 (6.2 ± 0.2 μ g/g) (Figure 15). The changes in concentrations coincided with seasonal changes in m ean m onthly 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 in flow-driven differences in residence tim es of local
waters could also be im portant, 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 determ ine how concentrations of Se
in P. amurensis com p are am ong different locations in the North Bay. Se concentrations were

67determ ined in replicate com posite sam p les of P. amurensis at 22 locations (Figure 16) (Brown and
Luom a, 1995a; Linville and Luom a, in press). The October 1996 sam p ling included an extensive investigation of the shallow habitats adjacent to m a rshes and m udflats of San Pablo Bay and Suisun Bay, as well as deeper channel stations. Selenium en richm e nt, com p ared to historic concentrations in previously dom inant 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). Am ong 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 m outh of the SJR. Selenium concentrations in P.
amurensis from the shallows, adjacent to m a rshes in Honker Bay were higher than concentrations in Grizzly Bay and San Pablo Bay. The two sites with the lowest m e an concentrations were found in Grizzly Bay, in particular in association with in flows of Sacram ento River water through a location
called Suisun Cutof f

.

Summary of Selenium in Invertebrates from the Bay-Delta
In sum m a ry, Se bioaccum u lation data from invertebrates show the following:

• Selenium enrichm e nt in prim ary consum er species (bivalves) has been evident in Suisun Bay
since the 1970' s.

• The spatial pattern of historic contam ination was consistent with an origin from refinery effluents (as shown by water colum n analyses), which have been discharged to the Bay-Delta since approxim a tely 1900.

• The highest Se concentrations reported in the Bay-Delta in consum er organism s in a species of
bivalve that is now the dom inant benthic species in Suisun Bay were found in the 1995 to 1997
studies of Linville and Luom a (in press). No system atic studies of Se concentrations in clam s are available since that tim e.

• Selenium enrichm e nt was apparently spread through all of Suisun Bay and all of San Pablo Bay
in 1996.

• Tem poral variability was not signif i cant in m onthly sam p les of C. fluminea in 1985-86; but
three-f o ld seasonal variability in Se concentrations is now observed in P. amurensis near Carquinez Strait. Concentrations in P. amurensis increased during low river inflow regim e s, decreased during higher river inflow regim e s

68• In the m o st recent survey, Se concentrations in P. amurensis near Carquinez Strait exceed 10

μ g/g dw in m o st m onths of the year (all m onths of som e years), and 32% of values m easured between October 1995 and June 1997, exceed 15 μ g/g dw. Thus, thresholds for chronic Se toxicity in the food of birds and fish (> 10 μ g/g, Skorupa, 1998a) are exceeded regularly.

• It is not yet clear whether the high Se contam ination 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 af f

ected by a variety of f

actors. Models are the m o st ef f

ective f o recasting
tool to encom p ass a range of factors involving a range of assum p tions. Realistic exposure m odels need to be geochem i cally robust (i.e., include considerati on of geochem i cal form ), biologically specific, and flexible for a variety of environm ental circum stances . Predictions from the m odel should be verifiable in nature. The USEPA approach (Peterson and Nebeker, 1992) uses the following sim p le ratio:
Bioaccum u lation = [concentration in organism ]/[concentration in environm ent],
where environm ental concentrations are either those in water (the BAF, bioaccum u lation factor) or
sedim e nt (the BSAF, biota to sedim e nt accum u lation factor). The flaw of this approach is that it does not allow consideration of effects of speciation in water or of particulate m a terial on bioaccum u lation. Thus BAF’s can vary by as m u ch as 50-fold for a given species in different environm ents, and m u ch m o re than that am ong species. An alternative m odeling approach, the Dynamic Multi-pathway Bioaccumulation Model or DynBaM uses different experim e ntally established uptake rates for different form s of dissolved and particulate Se, along with
environm ental concentrations of these form s, to determ ine bioaccum u lation in tissues (Luom a e t a l

. , 1992). The advantages of this approach have been discussed extensively by Luom a and Fisher (1997) and Schlekat et al. [in press (a)]. One advantage for the Bay-Delta evaluation is that bioaccum u lation can be derived for different speciation regim e s. Th e speciation consideration is very im portant because speciation will change as sources change, and relations with total Se or individual species of Se will also change (e.g., CSFBRW QCB, 1992a). Another substantial advantage of the approach is that m odel predictions can be verif i ed by com p arison to analyses of Se in tissues of resident species. W e will

em ploy DynBaM in all predictions of Se effects on predators from forecasts of Se loadings.

69The m a them atics of the sim p lest kinetic m odel with food and water pathways illustrates the necessary data:
d C m /dt = (I f + I w ) - C(k e + g) (1)

C m, t = [I f + I w /(k e + g)] [1 - e -(k t + g ) t ] (2)
C m, s s = I f /k e ( 3 ) where, C m is concentration in anim al, t is tim e, I f is gross influx rate from food, I w is gross influx rate
from water, k e is rate constant of loss (slowest com p artm ent), and g is growth. For C m, s s or concentration at steady state
C m, s s = I f + I w /k e (4)
if

we assum e that growth is not im portant. Mechanistically, the m a them atics state that
bioaccum u lation results from a com b ination 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 com e from water or from food and is a species-specific function of
the concentration of bioavailable elem ent.
For influx rate from food alone, in μ g Se/g tissue per day:
I f

= FR X C f X AE (5) where FR is feeding rate in g food/g tissue per day, C f is concentration in food (particulate m a terial) in g Se/g dw, and AE is assim ilation efficiency. Infl ux rate from water can be broken into its com ponents sim ilarly (W ang et al, 1996), but because the influx rate from water was determ ined experim e ntally for specific species of Se by Fowler and Benayoun (1976) , W a ng et al. (1996) and Luom a et al. (1992), the
rate will be em ployed directly here as μ g Se/g tissue per day.
From Reinfelder et al. (1997), the ultim ate c oncentration of Se that a bivalve would bioaccum ulate
under each environm ental condition can be calculated from :

C ss = [Iw + (FR X C f X AE)]/k e (6)

70

### BIOACCUMULATION OF SELENIUM BY PREDATORS

Num e rous studies have dem onstrated that a sm all increase in waterborne Se will result in a disproportionately large elevation of Se concentra tions in fish and wildlife (Skorupa, 1998a). Several attributes affect Se uptake by these organism s: Processes that affect Se retention and inter-organ distribution are im portant considerations for fish and birds that range and feed widely over areas with varying Se exposure pathways. •

•

• Dietary exposure and, in m o st cases, progressive biom agnification through the food web is the pathway that leads to the disproportionately large bioaccum u lation of Se in upper trophic
levels.
Som e im plications of dietary uptake are:

o waterborne Se concentrations are poorly linked to predator bioaccum u lation because
environm ental factors affect transform a ti on of Se and uptake by invertebrates;

o where data on predators is difficult to obtain directly, invertebrates m a y be the best
indicator for m onitoring predator exposures;

o a predator’s choice of food, which varies widely am ong species, could result in som e trophic pathways being m o re efficient accum u lators of Se than others. For exam ple, longterm studies of the terrestrial environm ent created by burial of the contam inated evaporation ponds at Kesterson Reservoir show that invert ebrate carnivorous and scavenger species tend to be higher than herbivorous species as a route to vertebrate exposure (CH2M HILL, 1996; 1999a).

Dietary Exposure
Lem l y (1982; 1985) was one of the first to show that dietary uptake was responsible for the largest proportion of bioaccum u lated Se in fish. This study was at a reservoir (Belews Lake, North Carolina)

contam inated by the wastes of a coal-fired power plant (Cum bie and Van Horn, 1978). He com p ared
concentrations of Se in bluegill and largem outh bass collected f r om the lake, with concentrations of Se in those species when exposed to sublethal concentr ations of Se in water alone in a laboratory study.
He found a lower concentration factor from water alone than from bioaccum u lation via dietary plus waterborne sources. This finding was corroborated by the observation that piscivorous fish, at the highest trophic level, accum u lated the m o st Se in the lake. All piscivores and om nivores eventually

71succum b ed to the poisoning, while a few lower trophic level fish survived. Other studies have since verified directly and indirectly the overwhelm i ng im portance of Se bioaccum u lation from food, as

com p ared to direct uptake from water. If the prim ary source of Se to wildlife is diet ary, then it should not be surprising that waterborne or
dissolved Se is an im precise predictor of the Se exposure of birds and fish (Skorupa and Ohlendorf, 1991). Differences in speciation, transform a tion to pa rticulate form (s), speciation on particulates and
invertebrate bioaccum u lation all influence how waterborne Se is transferred to a predator. These processes are affected by the nature of the source and the environm ental 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 transform e d differently than Se discharged to an estuarine water colum n ). Physical processes like hydraulic residence tim e are also im portant. Particulate transform a tion of Se in a river (e.g. the SJR) m a y occur far downstream from the source of input; while transform a tions in a wetland or an estuary with a long residence tim e m a y occur near the input. Biological processes that affect exposure of the predator include differences am ong predator species in feeding, behavior, and physiology.
An exam ple 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 sam e exposure to Se (20
to 30 μ g Se/g dw found in eggs) at Chevron Marsh in the Bay-Delta as at Kesterson Reservoir (25 to
37 μ g Se/g dw in eggs), but the source water in Chevron Marsh contained about 10% the concentration of Se found at Kesterson (m axim um s: 20 vs. 300 μ g 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, com p ared to Kesterson, because the original form of the elem ent was selenite.
Because of the above com p lexities, the str ongest correlative predictor of Se concentrations in predator tissue that reflects Se exposures is proba bly Se concentrations in invertebrates (prey).
Invertebrates m a y be the optim al indicator to use in m onitoring Se in an ecosystem because they are practical to sam p le and are m o st closely linked to pr edator exposure (prey are the prim ary source of Se for the predators). Few authors have fully explor ed feeding relationships and resultant correlations
with Se bioaccum u lation in food webs. One repeated observation in contam inated ecosystem s is that predator species differ in their
bioaccum u lation of Se. In general, this variable accum u lation seem s to be related to the diet of the predators. In Belews Lake, concentrations fo llowed the ranking: piscivores (bass and perch) > 72om nivores > planktivores. These feeding guild s were probably too broad, however. In Lake Oltertjarn, Sweden, af ter treating the lake with sele nite for two years, Se tissue concentrations in northern pike ( Esox lucius ) averaged 4.6 μ g Se/g, whereas in perch ( Perca fluviatilis ) the average was
23 μ g 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-colum n-feeding fish with low Se concentrations. Differences in Se exposure am ong predators also seem to be the case in the Bay-Delta. Fish (e.g. white sturgeon, starry flounder, and probably Sacram ento splittail) that ingest benthos, and especially bivalves, have higher Se concentrations (e.g., Urquha rt and Regalado, 1991) than predators that feed
from the water colum n, like striped bass ( Morone saxatilis ) (Saiki and Palawski, 1990). Further system atic study of such hypotheses is im portant because it could focus attention on the species m o st likely to disappear first from excessive Se contam ina tion. It is likely that the species experiencing the highest exposure of Se are at the greatest risk of extinction or to suffer population dam a ge. It also
should be rem e m b ered that biom agnification is suffici ent to elim inate species at the top of the trophic structure, even when waterborne Se concentrations are in the 2 to 5 μ g/L range (Lem ly, 1985; 1997b; d). So som e Se contam inated system s m a y alrea dy have lost vulnerable food web linkages. Study of system s with less extrem e contam ination m a y be one way to understand where those vulnerable linkages occur.

Existing Selenium Concentrations in Tissu es of Birds and Fish in the Bay-Delta
The CDFG conducted extensive sam p ling of a variety of bird and fish species in the Bay-Delta
between 1986 and 1990 in a Selenium Verification Study for the CSW RCB (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). The Selenium Verification Study was one of the m o st extensive surveys of Se contam ination in a food web ever conducted. Fish sam p les from the Bay-Delta were

com p ared to fish from Hum boldt Bay (Table 12), an area with no known source of Se. The greatest differences between the two ecosystem s occurred in bottom

- feeding fish [e.g. English sole ( Parophrys
vetulus ) with 3.05 ± 0.2 vs 1.78 ± 0.2 μ g Se /g in flesh, respectively; and starry flounder with 9.2 ± 2 vs
3.6 μ g Se/g in liver, respectively]. Although the sam p ling was lim ited in num ber, Dungeness crab
from Suisun Bay contained a m ean concentration of 14 μ g Se/g dw tissue, com p ared to a m e an concentration of 5 μ g Se/g dw tissue in Hum boldt Bay. Selenium concentrations in Pacific herring

73( Clupea pallasi ), speckled sandabs ( citharichthys stigmaeus ) and longfin sm elt ( Spirinchus thaleichthys ) were not different between the two ecosystem s. Uptake of Se by striped bass in the North Bay also did not appear problem atic in sam p lings in 1986 (average, 1.3 to 1.9 μ g Se/g dw) (Saiki and Palawski, 1990). Thus, som e bottom

- feeding fish bioaccum u lated Se in excess of the reference area, but fish (e.g., herring, striped bass) that were prim arily herbivorous, or fed from the water colum n, showed little dif f

e rence in Se tissue concentrations between the two ecosystem s. The highest concentrations of Se were f ound in white sturgeon in the Bay-Delta (Figure 17). However, white sturgeon were not found for com p ar ison in Hum boldt Bay. W h ite sturgeon is a longlived benthic predator, that spends its life in the Bay-Delta, the Sacram ento River, and to a sm all extent, the SJR (Kohlhorst et al., 1991). W h ite sturgeon are voracious consum ers 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 sam p led in 1986 were 9.2 ± 2.9 μ g Se/g (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). In 1989-90, 42 white sturgeon livers were sam p led; the average concentration of
Se was 30 ± 21 μ g/g in liver. Although variability was high (as expected for anim als that m ove over large areas), the average Se concentration after the P. amurensis invasion was m o re than double that
before the invasion.
W h ite sturgeon were analyzed m o re recently in two surveys conducted to determ ine exposure of sport fisherm a n to contam inants (Davis et al ., 1997; Fairey et al., 1997; San Francisco Estuary Institute, 1999). The num ber of white sturgeon analyzed were m a ny fewer than determ ined for the Selenium Verification Study , and theref ore the ability to detect dif f

e rences or trends (the statistical power) was weak. Locations of sam p ling and fish size were also highly variable. From this data it is not possible to draw conclusions about Se contam ination 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

m a jor resource species in the system . Striped bass are also anadrom ous fish, like white sturgeon, but they feed prim arily on crustaceans from the water colum n . Contam inants in juvenile striped bass were studied in detail in 1986 by Saiki and Palawski (1990). They analyzed whole body fish sam p les from
22 stations from the upper SJR downstream through Sa n Pablo Bay. Som e of their observations about Se concentrations in whole-body sam p les of striped bass included:

74• The highest Se concentrations were found in the m a in channel of Mud Slough and in the SJR,
im m e diately downstream from Mud Slough.

• The m ean Se concentration am ong the six m o st contam inated sites was 5.3 μ g Se/g dw.

• Se concentrations were low above Mud Slough a nd also downstream in the SJR, as tributary dilution increased (range of 1.03 to 2.9 μ g Se/g in the lower SJR, below the Merced River). So
bioaccum u lation was responsive to expected inputs of contam ination.

• Mean Se concentrations in the North Bay were 1.3 to 1.9 μ g Se/g dw. These values are at least five-fold lower than the average concentration in white sturgeon from the Bay-Delta, at that
tim e (Table 12, when Se in flesh is converted to Se in whole-body sam p les).
In sum m a ry, striped bass do bioaccum u late m o re Se in environm ents where m o re Se is present. However, these anim als are not exposed to as m u ch Se in their food web as are sturgeon, resulting in
less bioaccum u lation 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 bioaccum u lation and adverse effects need to be studied, perhaps com p aratively, in these species. Eleven species of waterfowl were also analyzed in the Selenium Verification Study (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991) (Figure 18) . In addition to fish tissue data, bird tissue data also suggest that the m o st contam inated aspect of the food web is in those species that

consum e bivalves. Data from California referen ce areas (Hum boldt Bay, Grays Lodge W ildlife Area,
and the Sacram ento National W ildlif e Ref uge) showed the following average Se concentrations in liver tissue: dabbling ducks, 3 to 8 μ g Se/g; shorebirds, 4 to 12 μ g Se/g dw, and corm orants 18 μ g Se/g dw (W hite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991). Average concentrations in greater and lesser scaup liver were 9 μ g Se/g dw and in surf scoter liver were 17 μ g Se/g dw. These values are typical of uncontam inated areas elsewhere in the wo rld, as well (Goede, 1994). Concentrations of Se
in m a llard ( Anas platyrhynchos ), Am erican bittern ( Botaurus lentiginosus ), northern shoveler ( Anas clypeata ) , and double-crested corm orant ( Phalacrocorax auritus ) were not different between the BayDelta and the ref e rence areas. Mean concentrations in two species of shorebird—willet ( Catoptrophorus semipalmatus ) and Am erican avocet ( Recurvirostra americana )—were about 20% higher in Bay-Delta than in reference areas. Mean Se concentrations in livers of Am erican coot and scaup from Suisun Bay and San Pablo Bay were 2-4 tim es those in sam p les from reference areas. The highest concentrations of Se in aquatic birds in the Bay-Delta were found in surf scoter (range 13 to

75368; average 134 μ g Se/g range in liver) from Suisun Bay and San Pablo Bay. Annual averages from Suisun Bay ranges from 80 to 240 μ g Se/g for the period 1986 to 1990. These annual averages in surf
scoter liver are from 7 to 11 tim es those averages in sam p les from Hum boldt Bay for the period 1986 to 1989 (annual averages, 11 to 16 μ g Se/g). These concentrations also exceeded concentrations found
in surf scoter from Morro Bay, the Central Ba y and the South Bay (W hite 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 rem a rkably am ong bird species with different food preferences in San Pablo and Suisun Bay. The m o st contam inated birds (s urf scoters) had Se concentrations in their livers that were up to two orders of m a gnitude higher than the Se concentrations in m a llards and Am erican bittern. Because of feeding habits, it seem s that vegetarians exhibited som e of the lowest Se
concentrations am ong bird species, whereas benthic predators had the highest concentrations. More specifically, anim als whose prey included bivalves were m o st contam inated. Surf scoter, for exam ple, are benthic feeders whose prey include bivalves, gastropods and crustaceans, with som e plants,

m acroalgae, insects, polychaetes and fish (Henny et al., 1995; Hoffm an et al., 1998). In general, scaup obtain approxim a tely 40% of their diet from anim al food sources versus scoter who obtain approxim a tely 95% of their diet from anim al food sources.
In 74 sam p les from an array of st udies, Skorupa and Ohlendorf (1991) reported m ean concentrations in bird eggs from reference sites as 1 to 3 μ g Se/g. More than 90% of values were
below 3 μ g Se/g. The authors concluded that concentrations above 3 μ g Se/g in eggs represent

contam ination (Skorupa and Ohlendorf, 1991). Thus, data exist to com p are Se concentrations in bird eggs in the Bay-Delta. However, only lim ited 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 elem ent necessary for the form ation and proper functioning of glutathione peroxidase, an im portant antioxidant enzym e . Th e window between required concentrations and toxic
concentrations of this elem ent is narrow com p ared to other toxins (e.g., National Research Council, 1976; W ilbur, 1983; Hodson and Hilton, 1983; Presse r and Ohlendorf, 1987; SJV Drainage Program , 1990b). In excessive am ounts, Se is erroneously substituted for sulfur in enzym e s and the structure of

76the proteins is disrupted. The result is dysfunctional enzym e s and proteins. Reproductive failure and/or teratogenesis (deform ities in developing young) are the earliest m a nifestations in the organism

. W h en eggs hatch, the developing soft tissues and hard tissues of the young are deform ed, because of disrupted protein structure. In fish, teratogenesi s is induced when larval fish are relying on their attached yolk sac for nourishm ent and developm ent. Once external feeding begins Se will not cause
f u rther def o rm ities in the juvenile f i sh. Thus the vulnerable pathway is m o ther to egg to developing larvae and fry.
Def o rm ities m a y not always be lethal them selves, but they lower the probability that the def o rm ed
individual will survive. In f i sh, def o rm ed larvae either die or quickly f a ll prey to predators and thus are rare in the juvenile or adult populations (Lem ly, 1993c). This circum stance was evidenced in Belews Lake, North Carolina by a decreased incidence of def o rm ities in juveniles, but not f r y, when

m o re predators were present. Thus, in assessing pr evalence of teratogenic effects it is im portant to focus on newly em erging larvae and fry.
Com m unity sim p lif ication (including local extinction of som e species) is ultim ately the result of
excessive Se contam ination. Sixteen of the twenty fi sh species that originally inhabited Belews Lake disappeared when Se contam ination increased. Kesterson Reservoir was thought to contain a m u ltispecies assem b lage of warm water fish before disc harges of irrigation drainage waters began (Skorupa, 1998a). Only m o squitofish ( Gambusia affinis ) persisted after Se contam ination was introduced (Saiki, 1986; Saiki and Lowe, 1987; Saiki et al., 1991; Skor upa, 1998a). Ham ilton (1999) recently presented the hypothesis that Se contam ination 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 pikem i nnow ( Ptychocheilus lucius )] and continues to inhibit their recovery. Ham ilton (1999) cites four lines of evidence linking Se as a causative factor in sim p lifying this fish com m unity:

• 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 dem onstrated at the level
of contam ination that occurs presently;

• disappearance of large Colorado pikem i nnow and razorback sucker was docum ented 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
recruitm ent) was the cause of the population collapse.
Ham ilton (1999) concludes that reservoir constr uction and introduction of exotic species have undoubtedly contributed to the decline of endangered fish species in the Colorado River, but that Se

m u st also be included as an im portant contributing factor. Restoring native species in the Bay-Delta
and its watershed is an im portant goal of the CALFED Ecosystem Restoration Plan (CALFED, 1998a; b; 1999a; b; c; d). The lessons from the Colorado Ri ver suggest that Se cannot be ignored as an issue
that can inhibit accom p lishm ent of that goal.
Selenium concentrations in food and concentrations in tissues have both been em ployed to evaluate how the exposure of Se experienced by an anim al 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
determ ined from field data (unlike toxicity test s which require extrapolation from independent lab waters to field exposures). To determ ine effects in ecosystem s like the Bay-Delta, Se concentrations in
invertebrates can be m onitored to estim ate concentrations in food and critical exposure in the predator
itself can be determ ined from concentrations in liver, flesh, or eggs.

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

Fish Concentrations of Se greater than 3 μ g/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 μ g/g load eggs beyond the teratogenic threshold (Table 13 and Lem l y, 1998a). Extinctions of fish species occurred in Belews Lake, when Se concentrations in invertebrates were in the concentration range of
20 to 80 μ g/g dw. Concentrations in invertebrates in Kesterson National W ildlife Refuge were greater
than 100 μ g Se/g dw in the presence of Se-induced bird def o rm ities and disappearance of m o st species
of fish.

Birds Laboratory studies have evaluated dietary con centrations of different form s of Se that affect reproduction in birds. Concentrations of 20 μ g Se/g causes food avoidance, weight loss and m o rtality

78in adult m a les (Heinz and Fitzgerald, 1993). Effect s were enhanced during cold winter weather.
Selenom ethionine in food at concentrations of 16 μ g Se/g causes com p lete reproductive failure in

m a llards (Heinz et al., 1989). A diet of 8 μ g Se/g selenom ethionine com p ared to 1 μ g Se/g fed to

m a llards caused a 33% reduction in hatching success and a 17% reduction in survival of ducklings; approxim a tely 7% of the unhatched eggs had defo rm ities (Heinz et al, 1989; Stanley et al., 1996). According to Heinz et al. (1989) the 8 ppm diet resulted in a m ean decrease of 43% in the num ber of 6- day-old ducklings com p ared to controls. Most recently, Heinz (1996) concluded that the dietary threshold that results in teratogenic effects was between 4 and 8 μ g Se/g dw; above 8 μ g Se/g the percentage of def o rm ities rose rapidly. Ohlendorf (1989) reported that bird eggs genera lly contain 1 to 3 tim es the dietary Se of breeding
fem a les. Heinz et al. (1989) showed that Se in eggs of m a llards (experim e ntal exposure) was closely related to hen’s dietary exposure to Se (fed sele nom ethionine). Average egg concentrations were 2.5
to 4.0 tim es dietary concentrations. However, diets supplem ented with inorganic Se result in Se concentrations in eggs that are only 0.1 to 0.18 tim es dietary concentrations. Skorupa and Ohlendorf (1991) concluded that, if assim ilation of Se in the wild is sim ilar to Se-m ethionine in the laboratory, then dietary Se of 5 μ g Se/g dw would yield 15 μ g Se/g dw in eggs. This level in eggs was the lowest

m ean concentration associated with em bryo terat ogenesis at Kesterson Reservoir. Ohlendorf (1989) concludes that hatchability of eggs is reduced when dietary concentrationa are 6 to 9 μ g Se/g. So,
sim ilar to fish, 5 to 9 μ g Se/g dw in food encom p asses 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 μ g Se/g, Table 13 and Figures 14 to 16) are beyond the threshold of Se concentrations in food that are likely to cause reproductive dam a ge and teratogenesis in bivalve predators.

Relating Selenium Concentrations in Tissue to Effects in Predators

Fish
A num ber of studies have related tissue concentr ations of Se in fish to teratogenic or reproductive effects (Table 14). Reproduction has the advantage of being a very sensitive endpoint to study. But,
environm ental factors as well as Se can affect reductions in reproductive success in nature. Short-term

79studies always suffer from the difficulties of separating causes of changes in reproductive success. Long-term studies can be m o re effective, in that environm entally-caused effects on reproductive success tend to fluctuate, whereas pollutant caused changes are m o re 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 m easure of Se ef f

ects, but has the very attractive advantage of being a m o re Se-specific outcom e (i.e., m a ny fewer f actors cause teratogenesis than affect reproductive success). From a review of the literature, Le m l y (1998b) recom m e nded the following toxic effects
thresholds from Table 14: whole body, 5 to 7 μ g Se/g dw; •

•

•

•

• skeletal m u scle, 6 to 8 μ g Se/g dw; liver, 15 to 20 μ g Se/g dw; ovary and egg, 5 to 10 μ g Se/g dw, larvae/fry, 8 to 12 μ g Se/g dw.
Deform ities increase rapidly in prevalence once Se in fish eggs exceeds 10 μ g/g dw. High proportions of som e fish populations showed deform ities above 20 μ g Se/g dw whole-body tissue. Reviews of field and lab studies (Table 14) show that the lower whole-body tissue threshold for effects

m a y be between 4 and 6 μ g Se/g; and it seem s quite certain that teratogenesis and reproductive failure consistently begin to appear at tissue concentrations in excess of 15 μ g/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 dif f i cult to evaluate, the values are in agreem ent with case
studies from Belews Lake, North Carolina; Sweit zer Lake, Colorado; and lakes in Sweden (Skorupa, 1998a; b). In the Bay-Delta in 1989-90, the m ean Se concentration found in 62 sam p les of white sturgeon m u scle was 15 μ g/g dw and in 42 sam p les of liver was 32 μ g/g dw (Table 12 and Figure 17).
Both m eans are above the levels at which deform ities are likely to occur (Table 14) and som e levels in individual fish (range 6 to 80 μ g Se/g, liver; 2 to 50 μ g Se/g, m u scle) far exceed tissue thresholds for reproductive effects. However, the relation of reproduction and Se-induced teratogenesis has never been studied in white sturgeon. A lim ited study of white sturgeon caught in San Pablo Bay and the
Sacram ento River showed Se concentrations in ovaries and egg yolk com ponents above thresholds for effects (Table 14) (Kroll and Doroshov, 1991).

80Birds
Tissue thresholds in birds are not too different from those in fish. Heinz (1996) stated that the

em bryo is the avian life stage m o st sensitive to Se poisoning. Skorupa (1998 a; b; c) has concluded that Se concentrations in eggs are a good choice for a risk m e tric to determ ine avian em bryonic exposure and response. Skorupa and Ohlendorf ( 1991) originally suggested that teratogenesis
thresholds were between 13 and 24 μ g Se/g dw m ean egg Se. This range rem a ins consistent with later studies (Table 15), if dry weight is assum e d to be 4 to 5 tim es wet weight. Hatchability is m o re sensitive than teratogenesis; but it is m o re am biguous to interpret in the field, because it is also
sensitive to non-contam inant perturbation. Com p aring Kesterson National W ildlife Refuge and a reference site, Ohlendorf et al. (1986) showed a strong correlation between em bryonic Se exposure and

em bryonic viability (hatchability). Hatching failure started increasing rapidly above 10 μ g Se/g dw egg. Skorupa (1998a) suggests the critical exposure concentration causing reduced hatchability, for sensitive birds, is 6 to 7 μ g 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 em bryo def o rm ity threshold f o r ducks is 15 to 20 μ g Se/g (Skorupa, 1998 a; b; c). In black-necked stilts the critical concentration in eggs for em bryo deform ity
is 18 to 25 μ g Se/g dw, and in avocets it is 38 to 60 μ g Se/g dw. In Martin Reservoir, Texas (Skorupa, 1998a), Se at 11 μ g Se/g in red-winged blackbird ( Agelaius phoeniceus ) eggs was associated with 50% depression in egg hatchability, although patterns of cont am inations were not as clear as in other field

cases. Hepatic (liver) concentrations m a y be a less precise indicator of pathological conditions than are egg concentrations (Table 15). Heinz (1996) concluded that concentrations in liver greater
than 10 μ g Se/g wet wt (40 μ g Se/g dw based on 75% m o isture content) should be considered possibly
harm ful to the health of young and adult birds. A very high risk of em bryo deform ity exists when the

m ean Se concentration (wet weight) in the liver of a population of birds exceeds about 9 μ g Se/g (36

μ g Se/g dw). Reproductive im pairm e nt occurred at 3.5 μ g Se/g on a wet wt basis (14 μ g Se/g dw) and
at 4.7 μ g Se/g on a wet wt basis (18.8 μ g Se/g dw) (Heinz et al., 1989; Heinz, 1996). O’Toole and Raisbeck (1998) argue that tissue re sidues should be interpreted flexibly, and used

m a inly as an index of exposure. They suggest that it is necessary to exam ine all possible causes of lesions before attributing cause and effect. They al so suggest that field-observed effects levels should be consistent with those experim e ntally induced (the basis for the thresholds).

81Loss rates of Se are another im portant considerati on for m i gratory waterfowl or fish. Surf scoter, greater and lesser scaup, and white sturgeon m a y e xperience high Se exposures during their residence
tim e in the Bay-Delta, but Se concentrations m a y decline as the anim als m ove to less contam inated breeding grounds. Many aspects of the reproductive effects specific to the Bay-Delta rem a in unstudied, especially in the species that are m o st 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 m ean 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 ra nge of Se concentrations in livers of ducks, coots, grebes, and stilts sam p led at Kesterson Reservoir in 1983-1984 (Table 15). Hoffm an et al. (1998) in a study of adult m a le surf scoter (n = 11) and greater scaup (n = 11) in Suisun Bay in 1989 found a m ean of 67 μ g Se/g dw in greater scaup and 119 μ g Se/g dw in surf scoter. Surf scoter populations are also rapidly declining in North Am erica, and they rem a in one of the least understood of the m i gratory waterfowl species (Henny et al., 1995). Selenium concentrations seem to rise extraordinarily in scoter in response to Se exposures. Henny et al. (1995) ha ve suggested that caution should be exercised in linking tissue concentrations to effects in anim als with strong bioaccum u lative capabililties. For

exam ple, in other ecosystem s bottle-nosed dolphins ( Tursiops truncates ), Risso’s dolphins ( Grampus griseus ), and corm orants seem to bioaccum u late high concentrations of Se com p ared to other species. Mineral granules rich in Se are com m on in these species (Nigro and Leonzio, 1996). It could be speculated that som e species concentrate Se in non-toxic form s, and, in such species, thresholds for
adverse effects m a y be higher than in other species. This hypothesis rem a ins 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

m i gratory fauna. Data from both food exposures and tissue residues strongly indicate that these
anim als are at or near signif i cant risk. Despite the com p lexities, planning an ef f

ective restoration of the Bay-Delta ecosystem depends on studies of the effects of Se on reproduction, population biology,
and life histories of m i gratory waterfowl and anadro m ous fish that are such im portant com ponents of the Bay-Delta ecosystem

. 82Comparison to Selenium Haz a rd Index
Lem l y (1995; 1996a; b) defined hazard as a toxic thr eat to birds and fish that can be characterized by
Se concentrations in the environm ent (water, sedim e nt) and exposure of fish and birds to that hazard (tissues). His system atic approach can be applied to data com p iled for the Bay-Delta from 1986 to
1996.
Lem l y defined five categories of hazard:

• High Hazard : Im m i nent, persistent threat sufficient to cause com p lete reproductive failure in

m o st species of birds and fish.

• Moderate Hazard : Persistent toxic threat suf f i cient to substantially im pair, but not elim inate reproductive success. Som e species will be severely affected; others will not be affected.

• Low Hazard : Periodic or ephem e ral toxic threat that could m a rginally affect reproductive
success of som e sensitive species, but m o st species will be unaf f

ected.

• Minimal hazard : No toxic threat identified but concentrations of Se are slightly elevated as

com p ared to uncontam inated reference sites.

• No hazard : Se concentrations are not elevated in any ecosystem com ponent com p ared to reference sites (Lem ly, 1995; 1996a).
Lem l y developed a scoring m e thod which assigned point s to define Se hazard in specific system s: no hazard = 5; m i nim a l hazard = 6 to 8; low hazard = 9 to 11; m oderate hazard = 12 to15; high hazard = 16 to 25 (Lem ly, 1995; 1996a). The scores represented sum m a tion for the lines of evidence (i.e.,

sam p lings of water, sedim e nt, invertebrates, fish e ggs and bird eggs). The aggregate rather than the average was chosen as the best representation of h azard because any route, alone, can cause toxicity.
W e can further define three levels of certainty of the statem ent of hazard:

• The greatest certainty occurs if waterborne, particulate, bioaccum u lation, and predator lines of
evidence are accom p anied by direct observations of teratogenesis or reproductive im pairm e nt. A strong level of certainty is possible if data are available from all links in the chain of processes, but no observations of reproductive im pairm e nt are available.

• Moderate certainty results if m o re 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.

83Table 16 shows the results of the hazard analysis from several ecosystem s (Lem ly, 1985; 1995; 1996a; 1997c; Kroll and Doroshov, 1991) com p ared to conditions in the Bay-Delta using data gathered
in from 1986 to 1996. This table com p aring hazard ratings from different ecosystem s illustrates the diversity of conditions that can occur in ecosystem s receiving Se discharges. Most notably, high
dissolved Se concentrations in som e rivers (e.g., LaPlata, Mancos, Anim as Rivers in Colorado, New Mexico, and Utah, respectively) can be accom p anied by low concentrations in sedim e nts. Invertebrates are m oderately contam inated in som e of those system s and not in others. Nevertheless,

m oderate to high contam ination was noted in fish eggs. Obviously, Se cycling, Se speciation, as well
as form and concentration in suspension are not sufficiently known from m a ny of the surveys to identify the factors critical to determ ining Se hazard. In all the reservoirs and pond environm ents surveyed by Lem l y (1995; 1996a;b; 1997a; b; c), elevated dissolved Se concentrations are

accom p anied by Se contam ination in sedim e nts, substantial contam ination of invertebrates and a high hazard to fish and bird eggs. Lem l y (1997c) suggested that long retention tim es in reservoirs
contributed to the contam ination of all m e dia and the high hazard. He suggested that as residence
tim es increased, the potential increased for Se to be bioaccum u lated, to be deposited in and recycled
from sedim e nt, and to adversely affect fish and birds. For hazard evaluations Lem l y (1995; 1996a) suggested that sam p led 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 m i nnows, sunfish (centrarchids), suckers, catfish, and trout. Our studies of Bay-Delta suggest these species are
not the m o st 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 ba sed on feeding habits of species at risk. Suisun Bay seem s to be typical of a system with high residence tim e subjected to Se contam ination. Using data from the above analysis, a ranking of Suisun Bay under the conditions of 1990-96 is possible using Lem l y’s schem e . The results of the aquatic hazard assessm ent 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 m o st sensitive predators is not possible in the Bay-Delta because the m o st contam inated species are m i gratory. This lack of data adds som e uncertainty to the hazard rating. Nevertheless, the certainty, as defined previously, is high. Selenium
data were available from water, particulate m a terial, bioaccum u lation in invertebrates, and predator
bioaccum u lation (in the latter case, m o re than one species). Further, toxicity threshold/extinction
84inform ation, in general, can be related to the Se data for both birds and fish. So the high hazard rating
can be m a de with relatively high certainty. It is possible that the hazard level declined after 1998, when refinery discharges declined. Studies underway m a y help determ ine further site-specific ratings. If an out-of-valley solution to the Se problem resu lts in carefully m a naged discharges of Se to the Bay-Delta via the SJR (for exam ple at 7,000 lbs per year), the forecast suggest the resulting hazard could be high. Selenium from the SJV replaces, in term s of food web exposure and effects, the Se

rem oved in refinery cleanup. If an SLD is constr ucted and it discharges during low flow seasons, a high hazard seem s 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 schem e above at its appropriate tim e scale in relevant detail.



### FORECASTS

A m a jor goal of this report is to illustrate a system atic approach or m echanism for conducting forecasts of Se effects on prey (food) and predators. Several feasible future conditions are used to develop exam ples of forecasts. The choices of conditions are not nearly as im portant as the process of evaluating those choices. However, the results of the chosen forecasts them selves provide guidance to help narrow the range of possible m a nagem e nt alternatives. The approach can be used with any set of explicitly stated conditions. From each set of assum e d
conditions we:

• calculate or forecast loads, volum es, and concentrations;

• define speciation and transform a tion;

• m odel bioaccum u lation 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 linki ng Se load and Se concentration under assigned hydraulic
conditions and tim e duration is: composite freshwater endmember concentration = composite input load/composite input volume
Four m a jor inputs m a ke up a com posite input load: agricultural drainage via direct discharge to the Bay-Delta, effluents from the North Bay refineries, SJR inflows, and Sacram ento River inflows. The

85com posite input volum e in the Bay-Delta is m o st affected by inflows from the Sacram ento River and SJR (Figures 9 and 10). W e will constrain each of the inputs and volum es to a given set of conditions as we construct feasible forecasts for Se loads to the Bay-Delta. The projections or outputs of the m odel are presented by season, where a season is defined as six

m onths of predom inantly high river inflows (Decem ber through May) or six m onths of predom inantly low river inflows (June through Novem b er). Seasona l presentation (high flow season versus low flow season) is the least com p licated approach to account for riverine influences which are very different in
different seasons. Flows are also variable on tim e scales shorter than season. To illustrate the effects
of these shorter tim e scale changes, (and to further illustrate the m e thodology), several forecasts for Se
concentrations were determ ined from m onthly load ings. Riverine influences also depend upon water year type. In com b ination 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 m a nagem e nt 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;

• dem a nd for drainage from agriculture or the Se load targeted by environm ental 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) assum i ng Se discharge was continuous and are presented here as discharged load per six m onths (i.e. one-half the annual load under a constant rate of loading). W e 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 m onths). The
value we will use f o r the targeted loads will be toward the m a xim u m projected by the TMDL/TMML process: 6,547 lbs per year or 3,274 lbs in six m onths. W e will assum e 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 assum e d during the low flow season of both wet and dry years. During the high flow season of a wet year, we assum e 1.1 MAF is allowed to enter the BayDelta.

862. SJR as a de facto drain (range of 381 to 15,300 lbs in six m onths). If the TMDL/TMML process resulted in m a nagem e nt of a constant concentration of Se in the SJR year-around, a
different load would result than if m a nagem e nt is based upon load. The Se load delivered to the Bay would also depend upon how m u ch of the load is passed through the Delta. Little is presently known about water m ovem e nt 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. Exam ples of Se loads that could be transported via the SJR are given below (also see exam ples in Table 9). Load is managed at the USEPA criterion of 5 μ g Se/L in a wet year . If an annual discharge of 3 MAF for the SJR at Vernalis is assum e d and it is assum e d 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 m onths). •

• Load is managed at the USFWS proposed criterion of 2 μ g 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 m onths).

• Dry years . If annual discharge fromthe SJR is 1.1 MAF and 25% reaches the BayDelta, as m i ght be expected in below norm a l precipitation, then the annual Se loading would be 9,262 lbs from the SJR at the 5 μ g Se/L criterion and 3,705 lbs at the 2 μ g Se/L criterion (1,852 or 4,631 lbs Se in six m onths).

• Restored ecosystem . Load is m a naged at a constant 0.5 μ g 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 μ g/L is lower than both the USEPA criterion (5 μ g Se/L) and the USFW S proposed criterion (2 μ g Se/L). In this case an annual load of 4,080 lbs is conveyed by the SJR assum i ng 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 m onths).
3. Demand-driven loads with management of drai nage quantity and quality in an extension of the
SLD . For our specif i c calculations of SLD ef f

ects, we will assum e that a) dem a nd f o r drainage

87is m e t 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 m onths (half design flow capacity of existing SLD, 150 cfs) or 0.11 MAF each six m onths (full design flow capacity of SLD, 300 cfs); and c) Se concentrations in the SLD will vary with the success of treatm e nt. 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 m onths). W e 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 μ g/L. Under this condition, 6,800 lbs Se would be discharged in six

m onths. W e assum e , in a second forecast, that 62.5 μ g Se/L drainage is discharged at full capacity (0.11 MAF); the loading would be 18,700 lbs Se discharged in six m onths. These two loads bracket the lowest end of the range of cum u lative potential loadings
from the different subareas (or com b inations 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 m onths). W e will calculate two forecasts for this
condition. Minim a l treatm e nt could result in direct (unblended) discharge of existing shallow ground water and no control on the quantity of discharge. Thus, this forecast

em ploys 150 μ g/L Se concentrations in the SLD with the drain running at full capacity (0.11 MAF in six m onths) (44,880 lbs Se discharged in six m onths). The second case
will assum e 300 μ g Se/L and 0.11 MAF of discharge in six m onths (89,760 lbs Se discharged in six m onths), assum i ng little regional m a nagem e nt (as described earlier). These two loads bracket potential loadings from a valley-wide system draining m o st potential problem lands, with m i nim a l m a nagem e nt (Tables 6 through 8). In order to calculate the total Se load to the Bay-Delta, and the resulting Se concentrations,
clim ate, oil refinery loads, SJR recycling, and Sacram ento River condition are included in the forecasts
as f o llows:
1. As noted previously, the m a gnitude and fate of the Se loads are highly dependent upon clim atic regim e . Clim ate 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 im portant condition to consider. The data for this
calculation were taken from 1994.

• Wet year . W e used data from 1997, a wet year by the California DW R definition.
2. W e will assum e in all forecasts that oil refineries m eet the 1998 perm it requirem e nts of approxim a tely 1,360 lbs Se per year or 680 lbs per six m onths (Table 10).
3. In dem a nd-driven load forecasts during dry years, we assum e that Se loadings from the SJR are very low. The forecasts im plicitly assum e that use of the SLD could relieve the pressure for discharge of drainage in the SJR. The forecasts also assum e continued substantial recycling of the SJR, so only 500 to 1,000 AF of SJR water with a concentration of 1 to 2 μ g Se/L reaches the Bay-Delta in dry years during high or low flow seasons (3-5 lbs Se in six m onths).
4. During wet years in periods of high flow, less recycling of the SJR occurs, with substantially

m o re SJR throughput to the Bay-Delta. To accurately reflect this condition in dem a nd-driven load forecasts, we assum e 2 MAF of SJR inflow reaches the Bay-Delta. W e assign a
concentration of 1 μ g Se/L for this inflow (5,440 lbs Se in six m onths)

. 5. Loadings from the Sacram ento River will be determ ined at 0.04 μ g/L Se tim es the hydraulic discharge. Table 17 shows the inputs to the Bay-Delta, the clim atic 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

em ployed in the m odeling of bioaccum u lation and pred iction of effects on predators. Specific cases will be highlighted in sum m a ry tables that f o llow. The exam ples 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 Ultim ately, Se concentrations in the Bay-Delta will be determ ined by the sum of all Se loads f r om different sources, the choice of conveyance to the Ba y-Delta, and the sum of all freshwater inflows as influenced by clim ate and m a nagem e nt. To forecast concentration ranges for Se in the estuary under different scenarios, the m odel assum e s all Se inputs are confined to a single location at the head of theestuary. Then it is assum e d that the com posite Se input is diluted through the estuary, as freshwaters

m ove toward the sea (Figure 11). W e will represent Se concentrations by values f o r com posite freshwater concentrations expected at the head of the estuary (i.e., landward value) and by the concentration expected at half the value of seawat er [approxim a tely 17.5 psu (practical-salinity units)] (i.e., seaward value) based on the salinity gradient. The chosen seaward location is sim ilar 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 rem e m b ered that hydrodynam i c m odels (e.g., Cheng et al., 1993; Monsen, 2000; Burau and Monism ith, in preparation) are necessary to forecast the spatial
detail under sim u lated physical SLD discharge conditions. Developm ent of such m odels for Se is feasible and should be a high priority in future ev aluations of effects of a SLD extension directly discharging to the Bay-Delta. In lieu of regionally specific m odels, a sim p le m i xing m odel approach provides a useful first order estim ate of m ean regional Se concentrations.

Comparing forecasted selenium concentrations to observed conditions prior to refinery cleanup To initially test the validity of the approach, an average com posite f r eshwater endm em ber Se
concentration was calculated for conditions resem b ling those that were docum ented 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, sim ilar to conditions selected for projections of
future conditions. The Sacram ento River flow for six m onths of high flow was taken from 1997 data (17 MAF). The Sacram ento River inflow dur ing six m onths of low flow in 1997 and 1994, respectively, provide two other cases (i.e., 2.3 MA F 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 m onths) m easured before refinery cleanup (average 1986-1992, 2,505 lbs per
six m onths) (CSFBRW QCB, 1992a; b; 1993; Cutte r and San Diego-McGlone, 1990) and no SLD discharge is included. The calculated average com posite freshwater concentration of Se during six m onths of high flow in a wet year is shown in Table 18. The forecast concentration is 0.22 μ g Se/L, using a m ean concentration of Se in the Sacram ento River of 0.04 μ g/L Se and in the SJR of 1 μ g Se/L. This is

com p arable to the Se concentration of 0.16 μ g Se/L determ ined after high flows in April 1986 (Cutter, 1989). The contrasting influences of the SJR and the Sacram ento River are interesting to note in this

exam ple. Concentrations of Se in the SJR are m u ch higher than concentrations in the Sacram ento 90River (1 μ g Se/L vs. 0.04 μ g Se/L, respectively). The load of Se from the SJR is also substantial

com p ared to the load from the Sacram ento River (2,992 lbs vs. 925 lbs Se per six m onths, respectively). Concentrations of Se are as low as 0.22 μ g Se/L at the head of the estuary because of dilution by the high volum e of low-Se water from the Sacram ento River. A Se concentration of 0.11

μ g/L is projected at our selected seaward location of Carquinez Strait. The concentration of Se at 17.5 psu (i.e., a pproxim a te location of Carquinez Strait) during the six

m onths of low flow in a wet year is projected as 0.20 μ g Se/L; in a critically dry year it is 0.27 μ g Se/L (Table 18). Selenium concentration is highest duri ng periods of low flows, because dilution from the
Sacram ento River is reduced in years of low rainfall. The concentration forecasts are rem a rkably close to the range of values found within the estuary by Cutter (1989) (0.15 to 0.44 μ g/L Se). The correspondence of these calculations with observed data confirm s 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 im pacts 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 clim atic conditions and feasible loadings described earlier.
1. 6,800 lbs Se discharged in six months if m a nagem e nt of drainage quality and quantity were a high priority (half-capacity or 150 cfs of drain water with a Se concentration of 50 μ g/L). In
the three different clim ate regim e s (Tables 19 through 21), the six-m onth average Se concentration at the head of the estuary during the low flow season would range from 1.21 μ g Se/L in a wet year (Table 20) to 2.07 μ g Se/L during a critically dry year (Table 21). In the high flow season of a wet year, six m onths at this load would result in an average composite
freshwater concentration of 0.28 μ g 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 sim ilar to that in the Grassland Bypass Channel Project (i.e., 62.5

μ g/L). This forecast is one of the m o re likely dem a nd-driven loadings in the long-term if
successful treatm e nt technology is applied to drainage and the am ount of problem land is that considered by the SJV Drainage Program (Table 6). In the three different clim ate regim e s, concentrations at the head of the estuary during the low flow season of a wet year would

91average 2.99 μ g Se/L and would average 5.07 μ g Se/L over six m onths of low flow in a critically dry. Concentrations would average 0.51 μ g Se/L at the head of the estuary during the
six m onths of high flow in a wet year.
3. 44,880 lbs Se discharged in six months if drainage contained 150 μ g/L Se, and the drain operated at full capacity. This loading would provide for drainage from problem lands without
investm e nt in m a nagem e nt of the drainage (e .g., direct discharge of shallow ground water). Even during high flow, Se concentrations would exceed 1 μ g Se/L (i.e., 1.02 μ g Se/L) at the head of the estuary under these conditions. During low flow six-m onth average concentrations would always exceed the USEPA criterion no m a tter what the rainfall (6.97 to 11.87 μ g Se/L).
4. 89,760 lbs Se discharged in six months if the m o st severely salinated soils supplied a drain at full capacity and no treatm e nt technology was available. This scenario is not highly likely given expected em phasis on source control and treatm e nt. However, if it should occur,

extrem ely high Se concentrations would be found in the estuary under low flow conditions (13.8 to 23.5 μ g Se/L) (Tables 19 through 21). Average concentration at the estuary (1.9 μ g Se/g) would approxim a tely equal the USFW S recom m e nded criterion (2 μ g 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 assum e s Se load is targeted for regulatory or environm ental purposes at 7,000 lb Se per year load lim it and 3,500 lbs Se discharged in six m onths. Conveyance is fully via the SJR

. The projected range of Se concentrations in the freshwater
endm em ber for the Bay-Delta during the low flow season scenarios is 0.57 to 0.86 μ g/L Se;
concentrations would be 0.28 to 0.43 μ g/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 μ g/L Se at the head of the estuary and 0.20 to 0.27 μ g/L at Carquinez Strait) (Table 18). So, in term s of total Se concentrations, this load of Se from the SJV would replace the Se

rem oved by investm e nt in refinery waste tr eatm e nt. During a six-m onth high flow season during a wet year if 3,500 lbs of Se were discharged (Table 19), concentrations would be twofold lower (0.12 μ g Se/L at the head of the estuary and 0.06 μ g Se/L at Carquinez Strait) than

92conditions prior to refinery cleanup (0.22 μ g Se/L at the head of the estuary and 0.11 μ g Se/L at Carquinez Strait, Table 18).
2. Regulating concentrations in the SJR: a restoration forecast . Environm ental restoration is often vaguely defined. A specific “restoration” scenario for the SJR m i ght place explicit lim its
on Se concentrations in the river and em phasize increasing SJR inflows (less recycling of the SJR) to the Bay-Delta to aid fish m ovem e nt in certain seasons of the water year (CALFED, 1998a; b; 1999a; b; c; d; EA Engineeri ng, Science, and Technology, 1999). Managing concentration in the SJR contrasts to previous scenarios in which Se load was m a naged. In calculating the effect of such “restoration” on Se concentrations in the Bay-Delta, the concentration assigned in the “restoration” scenario is 0.5 μ g/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 m a nagem e nt 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 μ g 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;

• assum e the SJR inflow for a wet year is 3 MAF annual flow and a dry year is 1.1 MAF;

• control industrial inputs to m eet the July 1998 m a ndate of approxim a tely 1,400 lbs Se per

year;

• vary Sacram ento River inputs with flows as they do now (i.e., 0.04 μ g Se/L at 19.3 MAF annual inflow in a wet year and 0.04 μ g 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 com posite
freshwater Se concentration is 0.11 to 0.15 μ g Se/L for a wet year and a dry year, respectively. In the low flow season of a wet year, the com posite freshwater Se concentration is 0.23 μ g Se/L. In the low flow season of a dry year, the com posite freshwater Se concentration is a
sim ilar 0.24 μ g Se/L. These Se concentrations would be less than those that occurred prior to refinery cleanup (com pare Tables 18 and 22). An im provem e nt also is achieved over the targeted load scenario (com pare Tables 19, 20, 21, and 22). Conditions would be m o st

93im proved, com p ared 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 Sacram ento 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 m a nagem e nt scenario does have som e lim its in the low flow season and if Se concentrations in the SJR increase. The concentration objective at which the SJR is held constant by im plem entation of a m a nagem e nt plan is increased in a series of scenarios illustrated in Figure 19. If the Se concentration in the SJR inflow is a constant 1

μ g/L using the sam e conditions as defined above, the concentration at the head of the estuary is
0.36 μ g/L during a wet year in the low flow season. During a dry year in the low flow season,
the concentration is com p arable at 0.32 μ g Se/L. However, if the concentration is a constant 2

μ g/L, the concentration at the head of the estuary is 0.60 μ g/L during a wet year in the low flow

season, as com p ared to 0.46 μ g/L Se during a dry year in the low flow season. In this case, the low flow season of a wet year is m o re 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

m u ch by increased flows as occurs seasonally.

Monthly waterborne selenium concentrations
The six-m onth scenarios described above represent average seasonal Se concentrations (i.e., low flow season versus high flow season). Six-m onth averaged forecasts could be m i sleading, however,
because flows are variable over shorter tim e scales. To illustrate the effects of these shorter tim e scale changes, and to further illustrate the m e thodology, Se concentrations were forecast that would result
from m onthly loadings. The forecasts are based on wet year flows (1997). The results of the m onthly forecasts are presented graphically in Figures 20 and 21 and supplem ental data are given in Appendix F, Tables F1 and F2. The forecast conditions are:

941. 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 μ g Se/L) . The annual load of Se
from the SLD would be 36,720 lbs (or approxim a tely 18,700 X 2 = 37,400 lbs, Table 17). Although SLD m onthly inputs are constant (3,060 lbs per m onth) in this scenario, Se concentrations at the head of the estuary increase progressively from 0.24 μ g Se/L in January to
4.5 μ g Se/L in October (Figure 20). The range of concentration change is dram atic, because dilution declines through the year as river inflows decline. The peak concentration in October would be a perm anent feature of m onthly 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
Novem b er), but a detailed m onthly analysis shows that vulnerability is at a m a xim u m in the f a ll

m onths when water exports m o st exceed river in flows (Figures 9 and 10). Figure 20 expresses this scenario as a function of both input load and com posite freshwater endm em ber Se concentration. Figure 21 shows the com posite freshwater endm em ber concentration at both the head of the estuary and at Carquinez Strait for com p arison.

95 2. Management of the SJR at 2 μ g 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 m onthly concentrations that m i ght develop at the head of the estuary as a result of m a naging a constant SJR input concentration. The annual load of Se discharged to the Bay-Delta from the SJR in this forecast is very sim ilar 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 (approxim a tely 10,400 lbs each m onth) are discharged in January and February. The highest Se concentration at the landward reach is 1.2

μ g/L (Appendix F, Table F1). Two periods of m a xim u m concentration occur, in March through June and in Septem ber through Novem b er (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 m u ch lower from April through Decem ber if the SJR is the conveyance vehicle than if the SLD is the conveyance. This disparity in loading is because

m onthly loads from the SJR decline as hydraulic discharges decline and m o st of the load is released with the highest flows. W e ighting with flow prevents the extrem e 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 im portant problem with releasing Se via an artif icialconveyance facility. Additional lim itations also exist when high loads are released during high flows (see Figure 19 and later discussion).
3. Management of the SJR at 1 μ g 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

m onthly trends are the sam e as those under the 2 μ g/L Se scenario, but the am plitude of the fall peak is reduced (Figure 20). The highest concentrations in the landward reach of the estuary
are 0.60 and 0.68 μ g Se/L in Septem ber and October (Appendix F, Table F2), respectively (about 1.5 tim es the m a xim u m 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 μ g Se/L) observed prior to refinery cleanup based on as seasonal analysis (Table 18), although speciation would probably be di fferent (see later discussion).

Summary of forecasts In general, a sum m a ry of the forecasts for the SLD conveyance and SJR targeted load scenarios (Table 23; Figures 22 and 23) shows that the m o st 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 m a nagem e nt plan and SJR inflows are increased, wet years

are m o re 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-m onth hydraulic di scharges (em phasizing lower flow regim e s), and a wide range of Se loads. Each line illustrates a Se concentration that would result f r om the dif f

e rent

com b inations of these variables. From this figure, the com posite freshwater endm em ber concentration of Se (i.e. that concentration at the head of the estuary) can be estim ated from any com b ination of
clim ate (as indicated by differing total river inflow s) and Se load. The strong dependence of Se

contam ination on weather and water dem a nd (which, together, determ ine discharge to the estuary) is evident. Figure 23 illustrates the extrem e vulnerability of the estuary to Se inputs during low flow seasons (cum ulative discharges of 1 to 2 MAF over six m onths). For exam ple, for total input loads of approxim a tely 7,700, 20,000 and 46,000 lbs Se at defined cum u lative volum es of 1.3 and 2.3 MAF during low flow seasons, the range of estuary Se concentrations would be from 1.2 to 12 μ g Se/L.

96 Using the range of loading forecasts em ployed previously, seleniumconcentrations in the BayDelta will increase under all scenarios that include a SLD extension, and especially as the flowcapacity of the SLD is achieved and/or if concentra tions of Se increase in the discharge (Table 23 and Figure 22). A m i nim u m estim ate of loads from a SLD extension is 6,800 lbs in six m onths (or 13,600 lbs annually). This scenario can only be achieved if the drain is m a naged at a flow of 150 cfs and the

m o st optim istic treatm e nt technologies are invoked. Even under this scenario, com posite freshwater
endm em ber Se concentrations would increase two to four-fold over concentrations typical prior to refinery cleanup (see also Table 18). Freshwater endm em ber Se concentrations in the driest of years
could exceed the 2 μ g Se/L toward the head of the estuary. If a SLD extension is built to the Bay-Delta, pressure m a y be strong to m a xim i ze its potential to carry salt-laden waters. Under this condition, loads from the SLD m a y approach the level of 18,700
lbs in six m onths (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-m ont h low flow season of a wet or dry year are forecast
to exceed the USFW S recom m e nded criterion of 2 μ g Se/L through all of Suisun Bay (Table 23 and Figure 22). This exceedance would also occur at Ca rquinez Stait during the low flow period of dry

years. If treatm e nt technologies are not developed or if dem a nd becom e s m o re im portant than load

m a nagem e nt, then the quality of discharged draina ge could drop. If, on average, drainage quality
becom e s sim i l a r t o t h a t o f s u b s u r f a c e d r a i n a g e ( > 150 μ g Se/L) rather than blended drainage in the western SJV, and that is com b ined with full flow in the SLD, then extrem e concentrations would occur in the Bay-Delta. Under a forecast load of 44,880 lbs Se in six m onths , Se concentrations of >6.97 μ g Se/L at Carquinez Strait are projected during the low flow season of both wet and dry years.
A concentration of 1 μ g Se/L is three tim es higher than presently found in the Bay-Delta in a

norm a l rainfall year (Cutter 1989; Cutter and San Diego-McGlone, 1990; and CSW RCB, 1992a; b; also see Table 18) and represents the Canadian quality guideline (Environm ent 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 m onths (Figure 22). In the high flow season of a wet year, concentrations forecasts at the Carquinez Strait are 0.14 to 0.94 μ g Se/L.
An im portant com ponent of the m onthly analysis (not evident in the six m onth analyses) is the very high Se concentrations that result each year in the fall. The strong dependence of Se contam ination on
weather and water dem a nd, which, together, determ ine discharge to the estuary, is also evident.

97Concentrations in excess of 2 μ g Se/L would extend through m u ch of Suisun Bay and San Pablo Bay in the SLD forecast. It is possible that the dilution assum p tions em ployed here m i ght understate the geographic extent of Se distributions in projections for October. Sophisticated physical m odels are being developed for Suisun Bay and could be very helpful in describing such im portant details (Monsen, 2000; Burau and Monism ith, in preparation).

Forecasts of Speciation and Transformation Speciation of Se in the Bay-Delta is controlled by physicochem i cal processes and speciation in the sources of input (Cutter, 1989). Speciation will change as sources change in im portance. Prior to 1998, refinery inputs of selenite were a principal in fluence 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 lik ely that the proportion of selenate in inputs would increase if a SLD extension were used to convey i rrigation drainage to the Bay-Delta or if/when SJR inflows to the Bay-Delta increase. As we for ecast, biotransform ation to Se(-II) and/or sedim e nt

accum u lation and recycling of Se(-II) in the Bay-Delta are highly likely under increased SJR loading if
the transform a tion conditions prevalent at present in the Bay-Delta are operable on the SJR discharge. This influx of Se(-II) could be accentuated if m a rshes are restored in areas subjected to inflows from
the SJR or a SLD extension. As discussed previously, speciation is a critical c onsideration in estim ating ecological effects of Se. Speciation drives the transform a tion reactions that de term ine particulate Se concentrations and form s. Bioaccum u lation from particulates is the prim ary route by which Se enters the food web, so the
reactions that determ ine particulate concentrations are critical to eventual trophic transfer. Trophic
transfer determ ines food web exposures and effects on predators.
Ultim ately, forecasts of Se speciation should be derived from biogeochem i cal, kinetic speciation

m odels (Bowie et al., 1996). This type of m odel is not yet ready for application to the Bay-Delta, although the com p letion of its developm ent should be a high priority. In the absence of a m odel, speciation is included in our analysis by forecasting based upon m i xes of species that have been
observed in nature under circum stances possible for the Bay-Delta. W e will then forecast how each

m i x of species would affect transform a tions of dissolv ed Se to particulate Se (i.e. speciation is im plicit
in our choice of transform a tion reactions).

98Transf orm a tion will be quantitatively expressed by the distribution of Se between particulate and
dissolved f o rm s, the Kd (see previous discussion). The ef f

ect of speciation and transf orm a tion 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 regim e . For each com b ination of Kd and speciation, we will also incorporate the
form of particulate Se observed under those circum stances at other locations (Table 11) to enable a projection of overall bioavailability.

Defining speciation, transformation, and bioavailability Three sets of speciation regim e s and Kd’s in wh ich we assum e a specific distribution of Se am ong particulate f o rm s are presented below. These speciation and biochem i cal behavior patterns will be used throughout the forecasting of concentrations of Se in particulates, bivalves, and predators.

• High Bioavailability Speciation : h i g h p r o p o r t i o n o f s e l e n i t e p l u s o r g a n o

- S e ( > 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 assum e that Se(IV) and at least part of the Se(-II)
contribute to biotransform ation to organo-Se. Prelim inary studies in the late 1990’s showed
that as m u ch 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 becom e a larger proportion of the dissolved Se (Cutter et al., in preparation). In Suisun Bay, this speciation regim e is

accom p a n i e d b y a p a r t i c l e / d i s s o l v e d d i s t r i b u t i o n ( K d ) o f > 10 4 . For exam ple, distribution coefficients for estuarine suspended m a terial in m o st of the Bay-Delta were 8.2 X 10 3 to 2.1 X
10 4 , between Septem ber 1986 and October 1996. Biotransform ation m a y explain these high
Kd’s. Som e species of diatom s, the m o st com m on phytoplankton in the North Bay, have Kd’s higher than 10 4 in laboratory experim e nts. For bioavailability calculations, we will assum e d
the form of the particulate Se under these conditions is 60% biotransform ed Se and 40%
oxidized m a terial of m oderate bioavailability. Biologically, this Kd is m o st relevant to water
colum n -f eeding species of consum er organism s, like f ilter-f eeders.

• Moderate Bioavailability Speciation : low proportion of biotransformable (Se(IV) or bioavailable Se(-II) ) (< 30%) 99Kd : 3 X 10 3 (C2)
Precedent : typical of shallow water estuarine sediments or marine waters Particulate bioavailability : 60% moderate and 40% highIf 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) rem a ins high, it is possible that the bioavailability of Se(-II) is le ss than Se(IV). To account for either of these possibilities we will assum e 30% of total Se contributes to biotransf o rm ation at the rate of Se(IV). A speciation regim e of 30% biotransform able Se and 70% less reactive Se is sim ilar to
that often observed in undisturbed m a rine waters, and so it is a scenario with som e precedent.
Shallow water estuarine sedim e nts also show a distribution coefficient of 3 X 10 3 to 1 X 10 4 (Table 9 , Velinsky and Cutter, 1991; Cutter et al., in preparation). Again, this Kd coincides
with a m i xed speciation regim e [ 60% Se(VI) and 40% Se(IV) plus Se(-II)] . W e will also

assum e that this speciation and Kd com b ination results in particulate Se that is 60% in a form
of

m oderate bioavailability [ d etrital Se(-II) or particulate Se(IV) + (VI)] ; and 40% in a f o rm of high bioavailability (biotransf orm e d organo-Se). Biologically, this scenario applies to biota that predom inantly ingest sedim e nts with concentrations diluted by non-transform e d load.

• Low Bioavailability Speciation: p redominantly Se(VI)
Kd : 1 X 10 3 (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 assum e s that m o st of the Se entering the Bay-Delta rem a ins as Se(VI). Selenate
is transform e d, but the Kd’s of selenate-dom inated waters are typically lower than where a higher proportion of the species are organo-Se. Circum stances exist, such as near the irrigation inflows of Benton Lake, Montana, where Kd’s are approxim a tely 10 3 (Zhang and Moore, 1996). This value is also at the lowest end of the partitioning constant range characterizing Bay-Delta sedim e nts and is probably the m o st optim istic scenario that can be hoped for, in

term s of generating particulate Se and ultim ately biological effects. For forecasting bioavailability, we will assum e this m a terial is 50% slurry-generated Se(0) of relatively low bioavailability, 40% oxidized m a terial of m odera te bioavailability, and 10% organo-Se of high
100bioavailability. This scenario would apply m o st readily to deposit f eeding benthos, especially those feeding within sedim e nts. In general, we recognize that the Kd-concept used above has lim itations and that there areuncertainties about future speciation should a SLD extension begin discharging Se loads to the BayDelta. Nevertheless, the three speciation/transform a tion regim e s 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 form s.

Comparison to Bay-Delta conditions prior to refinery cleanup It is instructive to visually com p are projections from the Kd’s to existing data for the Bay-Delta. In Figure 24, suspended particulate Se concentrations (C utter et al., in preparation) are plotted against dissolved concentrations. Lines describing predicte d particulate concentrations using Kd’s of 1 X 10 3
and 1 X 10 4 are superim posed on the plots. A Kd of 1 X 10 3 (C3) is too low to describe any of the existing suspended sedim e nt data m a king it a low probability forecast. The October 1996 data (the highest concentrations observed in any survey) exceed 1 X 10 4 (C1) and the Septem ber 1996 data fall between the two values. In Figure 25, sim ilar 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 descri bed above forecast three different trend lines for particulate concentrations through the estuary. The October 1996 particulate data is superim posed upon these projections. The superim posed data illustrate that a Kd of 1 X 10 4 (C1) is the best choice
for this data set. A Kd between 3 X 10 3 (C2) and 1 X 10 4 (C1) would best fit the Septem ber 1996 data if it were plotted sim ilarly. The three Kd’s used for the forecasts were, of course, developed based

upon em pirical observations. So it is not surprising th at direct com p arison 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 sedim e nt to fish and birds is via the aquatic food
chain. Sedim e nt guidelines are based on sedim e nt c oncentrations as predictors of adverse effects

101through the food chain. Proposed sedim e nt quality guidelines for Se ( μ g Se/g in particulate m a terial or
sedim e nt) provide a context to evaluate forecast particulate Se concentrations:

• no effect concentration: <1 to 2.0 μ g Se/g. Concentrations lower than this value produce no
discernible adverse effects on fish and wildlife and are typical of background concentrations in

uncontam inated environm ents (Skorupa, 1998b).

• threshold for effects and the level of concern for Se in sediment: 2 to 4 μ g Se/g. Concentrations in this range are elevated 10 to 20 tim es above typical background concentrations (Engberg et al., 1998; Skorupa, 1998b).

• site-specific for Suisun Bay, potential for increase in adverse effects: >1.5 μ g Se/g

. Concentrations in this range m a y produce discernible adverse effects in som e circum stances (Luom a et al., 1992), whereas Engberg et al. ( 1998) and Skorupa (1998b) suggest such levels rarely produce discernable adverse effects in freshwater environm ents.

• observed effect concentration: 4.0 μ g Se/g (Canton and Van Derveer (1997).

• toxicity threshold of > 4 μ g Se/g. Concentrations in excess of this value have a high certainty of producing toxicologic and reproductiv e effects (Engberg et al., 1998). Skorupa (1998b) provided a com p ilation of background and biotic effects levels as part of the U.S. Departm e nt of the Interior’s National Irrigation W a ter Quality Program . Canton and Van Derveer’s (1997) conclusions about sedim e nt-based criteria are based upon less data and a relatively insensitive

com m unity analysis (Ham ilton and Lem l y, 1999).

Particulate selenium concentrations (all concentrations are in μ g Se/g dry weight, dw) Tables F3 to F5 in Appendix F show detailed data for four load scenarios under three different
clim ate regim e s should Se be released directly to Suisun Bay via a SLD extension (also see Tables 19 through 21 for com posite freshwater endm em ber concentrations). Transform a tion constants typical of suspended sedim e nts (C1), shallow water bed-sedim e nts (C2), and low reactivity conditions (C3) are

em ployed in each set of calculations. Table 24 sum m a rizes 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 com p ared to data reflective of conditions prior to refinery cleanup. Sedim e nt quality guidelines for Se are also shown.

102The 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 assum e d Kds (C1, C2, and C3) result in particulate concentrations >2.0 μ g Se/g at the head of the estuary.

• only under the lowest SLD extension discharge assum p tion (6,800 lbs in six m onths) com b ined with the lowest Kd (least likely, C3), would a particulate Se value be observed (2.07 μ g Se/g)
below the observed effects concentration of 4.0 μ g Se/g. In all other cases the certainty of
effects would be elevated.

• if the Kd of suspended m a terial were that obser ved in all existing studies of the Bay-Delta (C2), projected loads of Se from a SLD extension woul d result in particulate Se concentrations in upper Suisun Bay of 6.2 to 35.6 μ g Se/g. The certainty of effects would be high to very high.
Under all but the m o st optim istic transform a tion scen arios, forecast loads with m a nagem e nt of quantity and quality of 6,800 to 18,700 lbs per six m onths would yield particulate Se concentrations in the upper estuary that would exceed 4.0 μ g Se/g. Selenium concentrations of 5 to 119 μ g Se/g are possible
if m a nagem e nt is not a priority. A low flow season in a wet year would yield pa rticulate Se concentrations that are approxim a tely 60% of those forecast for a dry year (Table 24):

• if a load of 6,800 lbs were discharged in six m onths via a SLD extension, the forecast range of

m o st likely concentrations (C1 – C2) is 4 to12 μ g Se/g (rounded off).

• if the SLD was m a naged at full flow capacity and with Se concentrations like those in the Grassland Bypass Channel Project (18,700 lbs in six m onths), particulate concentrations of 9 to
30 μ g Se/g are forecast under C1 and C2 conditions. The latter concentration is >7X higher than the level at which toxicologic and repr oductive effects are highly likely (Engberg et al, 1998).

• Under a C3 transform a tion, only SLD loads in the range of the lowest loading scenario for the SLD (6,800 lbs in six m onths) would result in particulate Se concentrations of <1.5 μ g/g.
If m onthly forecasts are considered, values in the late fall m onths would be considerably higher than
these six-m onth averages [com pare waterborne Se da ta trends presented on a m onthly basis (Figures 20 and 21; Appendix F, Tables F1 and F2)].

103Releases 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 assum e d SLD discharges only if Kd’s of 1 X 10 4 (C1 , typical of suspended sedim e nt) characterize tran sform a tions (Table 24). However, it should be recognized that the forecast concentrations are av erages over the six-m onth high flow period. Flows are very variable during this period, so the actual period of lower concentrations will probably be
shorter than six m onths. This is also the tim e period when particulates from the SLD extension are

m o st likely to add to the Se load in the estuary. The forecast for the targeted load (3,500 lbs per six m onths) 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 μ g Se/g if transform a tions are typical of suspended sedim e nt (C1), but not if
shallow sedim e nt-type transform a tions prevailed (C2).

• During the high flow season of a wet year, particulate Se concentrations rem a in below 1.5 μ g Se/g for all three transform a tions 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 sim ilar to those that would occur during the targeted load scenario (i.e., below 1.5

μ g 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 rem a in below 2.5 μ g/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 m odeled prior to refinery cleanup are predicted to occur:

• in the “restoration” scenario for the SJR in all m odeled water year types and seasons; and

• in the SJR targeted load scenario during the high flow season of a wet year.

Cumulative summary
A cum u lative sum m a ry of Se loads and concentrations is given in Table 25. Com posite freshwater
endm em ber and particulate Se concentrations at the head of the estuary are shown for an agricultural load input of 18,700 lbs released during six m onths via a SLD extension or of approxim a tely 3,500 lbs

104released during six m onths via the SJR (see Tables 19 through 21 for com posite loads). The forecasts for prior to refinery cleanup are given for com p arison. The forecasts highlight the im portance of reactivity in determ ining particulate concentrations . Clearly, benefit would com e from knowing these dissolved/particulate transform a tions with m o re certainty for the Bay-Delta. For each com posite
freshwater endm em ber Se input, we illustrate three assum e d alternative particulate transform a tions [low reactivity (C3), shallow sedim e nt (C2), and suspended sedim e nt (C1)]. For the SLD scenario of 18,700 lbs per six m onths (Table 25), it is notable that exceedance of the
USEPA waterborne criterion of 5 μ g Se/L (low flow season of a dry year) is always accom p anied by exceedance of the proposed observed effect particulate criterion (4.0 μ g Se/g), no m a tter what the reactivity of the Se. Also under this load scenario, the USFW S proposed waterborne criterion of 2.0

μ g Se/L is exceeded in the com posite freshwater endm em ber concentration for the low flow season of a wet year. At a com posite freshwater endm em ber Se concentration of 2.0 μ g Se/L, particulate Se
concentrations m i ght exceed the lowest proposed no effect concentration (1.5 μ g Se/g), but not the observed effect level. However, a typical estu arine Kd (C2) would result in particulate Se
concentrations of >4 μ g 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 m onths (Table 25), com posite freshwater
endm em ber Se concentrations rem a in below 1 μ g Se/L. However, particulate Se concentrations only

rem a in below 1.5 μ g/g at low reactivities (C3) or during the high f l ow season of a wet year. During low flow seasons of both wet and dry years, particulate Se concentrations exceed 1.5 μ g/g, and in cases of high reactivity (C1) could exceed 4 μ g Se/g.
In sum m a ry, loadings, inf l ows, and biogeochem i cal transf orm a tion rates are critical to determ ining particulate Se concentrations and thus im portant de term inants 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 estim ates of no effect and observed effect particulate Se guidelines. This is especially true if
the transform a tion 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 “resto ration” scenario f o r the SJR results in f o recast

105particulate 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 predom inant dissolved f o rm in that discharge will be Se(VI). On a purely geochem i cal basis, it

m i ght be asserted that dissolved Se(VI) will not be reactive in the Bay-Delta ecosystem

. This

m i nim a l reactivity would require that dissim ilatory reduction to sedim e ntary Se(0) not occur in
sedim e nts or wetlands, no adsorption because of com p etition with sulfate, and no selenate uptake by prim ary producers. Biotransform ation of Se is, indeed, m i nim i zed in at least som e flowing water (lentic or river/stream ) system s, com p ared to wetlands. However, there is no precedent in nature for a com p lete absence of Se biotransform ation to particulate
concentrations. At least a Kd of 0.5 X 10 3 is usually seen, especially if residence tim es are sufficient. Thus, the argum ent of m i nim a l reactivity is extrem ely unlikely as inflows recede seasonally, during low inflow years, and in wetlands and shallow water environm ents of the system

.

• Direct SLD discharge of suspended particulate Se from an extension of the SLD . Input of suspended particulate m a terial 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 treatm e nt f acility by rem oving Se f r om agricultural drainage and sequestering it in
sedim e nt and biotic m a terial that had settled in the bottom of the drain (Presser and Piper, 1998). Sedim e nts that are highly contam inated with Se have accum ulated in the SLD to date and are likely to continue to accum u late during its renewed use by the Grassland subarea to convey drainage to the SJR (Appendix E, Tables E1 and E2). Selenium concentrations in SLD
sedim e nt have exceeded the hazardous Se waste criterion for solids (100 μ g Se/g, wet weight)
at tim es in the past and alm o st all concentrations are above that designated as a toxic threshold
in sedim e nt for biotic effects (> 4 μ g/g) (Engberg et al., 1998). Re-suspension and at least

som e transport of those sedim e nts during elevated flows seem s a reasonable forecast should the SLD be extended to the Bay-Delta. For exam ple, 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 106be estim ated with any reasonable certainty. The discharged particulate Se would probably originate as prim arily Se(0), but oxidation would also occur with longer residence tim es in suspension or in the water colum n. Source m a terial also m a y include algal m a t that m a y contain organic-Se [i.e., bioavailable Se(-II)]. The following forecast of direct discharge of suspended particulate Se f r om a SLD extension is instructive, but speculative. It illustrates how

even sm all inputs of the existing contam inated SLD sedim e nts could affect the Bay-Delta.

o If the SLD inflow is 5% of the flow of rive r inputs to the Bay-Delta and suspended m a terial
concentrations are sim ilar in both the Sacram ento 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 μ g Se/g and particulate
Se in the Sacram ento inflows is 0.2 μ g Se/g.

o Then 5% of the particles in the Bay-Delta at the conf luence of the two will be SLD particles and the Se concentrations in the particle m i xture will be: [(0.05 X 100 μ g Se/g) + (0.95 X 0.2 μ g Se/g)] = 5.19 μ g Se/g from direct particulate input.

o During a critically dry year particulate Se concentrations would be twice this value.

o Particulate Se transform e d from the dissolv ed inputs from the SLD would add to these concentrations, therefore our estim ate is conservative in this respect.

• Local hotspots . The Se concentration estim ates discussed above represents broad scale average
concentrations that would result from m i xing. This approach does not allow determ ining the spatial details of distributions. More sophisticated hydrodynam i c m odels would be necessary to provide such detail (Burau and Monism ith, in preparation). However, hotspots of particulate
Se contam ination could develop in an ecosystem subjected to direct SLD discharges. Most notably, wetlands close to a SLD-extension discharge would be likely to accum u late 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 em ployed in the DynBaM m odel for bivalves in the Bay-Delta. The m odel is for a generic bivalve (i.e., physiological constants are averages over a sm all range from several bivalve species, Reinfelder et al ., 1997; Lee et al., in preparation). Calculationsspecific to P. amurensis and C. fluminea also could be conducted. Som e data for these species are recently available. The com m on param e ters for a generic bivalve used in the m odel are as follows:
1. Ingestion rate (or feeding rate) of 0.25 gram food/gram tissue dw per day (estim ate for m a ny bivalves based on review of literature in Luom a 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. Assim ilation ef f i ciencies (AE) approxim a tely 20% (low bioavailability) to 80% (high bioavailability) as a f unction of particle type (see below).
Com b ining the above factors and the range of particle transform a tions that affect bioavailability (Table 26), bivalve bioaccum u altion will be cast in term s of assim ilation efficiencies (AE in percent):

• Inefficient transformation: Kd = 1 X 10 3

. The particulate form s are 50% Se(0) of relatively low bioavailability, 40% oxidized m a terial of m odera te bioavailability, and 10% organo-Se of high bioavailability. The AE derived f r om this m i xture is 35%: AE1 (0.23 X 50%) + (0.4 X 40%) + (0.79 X 10%) = 35%

• Shallow water estuarine sediments: Kd = 3 X 10 3

. The particulate form are 60% of m oderate bioavailability [ d etrital Se(-II) or particulate Se(IV) + (VI)] ; and 40% in a f o rm of high bioavailability (biotransf orm e d organo-Se). The AE derived f r om this m i xture is 56%:
AE2 (0.40 X 60%) + (0.79 X 40%) = 56%

• Estuarine suspended material : Kd = 1 X 10 4

. The particulate form s include 60%
biotransf o rm ed Se of high bioavailability and 40% oxidized m a terial of m oderate bioavailability. The AE f r om this m a terial (presum a bly by an estuarine f ilter-f eeder, 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 transform a tion to Se(-II). AE4 (0.79 X 100%) = 79%.

• To com p lete the range of considered AEs, a fifth AE is derived for all particulate m a terial being
of

a f o rm of low bioavailability, Se(0). The AE derived is 23%: For range (0.23 X 100%) = 23%

108Comparing model predictions to Bay-Delta conditions prior to refinery cleanup Generic bivalve data (Table 26) were em ployed to forecast bioaccum u lation of Se for a range of concentrations using two extrem es of AE, 80% (all biotransform ed) and 20% (all elem ental Se) (Table 27). The purpose of this calculation was to verify that the m odel bracketed reasonable predictions of
Se bioaccum u lation. The range of particulate Se concentrations used in the calculation spanned the
concentrations of Se determ ined in surveys of the brackish Bay-Delta (0.5 to 3.0 μ g Se/g dw) and at the head of the Bay-Delta (0.5 to 8.0 μ g Se/g dw). Three observations from the forecasts of Bay-Delta conditions prior to refinery cleanup are of interest:

• The forecast concentrations of bioaccum u lated 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 environm ental values collected through field studies, bound bioaccum u lation with reasonable accuracy (results sim ilar to those reported by Luom a et al., 1992 and W a ng et al., 1996).

• A four-fold difference in bioaccum u lation would be expected if the particulate form of Se changed. At the sam e concentration of particul ate Se, bivalves would bioaccum u late four-tim es

m o re Se from the biotransform ed particulate Se than from elem ental Se. Although this
bioaccum u lation is significant, the effect is rela tively sm all com p ared to the effects of changing
the m a ss of Se in the load.

• The f i eld validation results verif y that the m odel will be usef ul in f o recasting the range of

consum er organism bioaccum u lation under different input scenarios for Se.

Bivalves as food for predators
The m o st sensitive response of ecosystem s to Se occurs in higher trophic level predators (e.g., birds and fish) (Ohlendorf, 1989; Ham ilton et al., 1990; Lem l y, 1996b; c; Skorupa, 1998a; Ham ilton et al., 2000a; b). Effects on predators (see reviews in Lem l y, 1998b; Skorupa, 1998a; Ham ilton et al., 2000b)
have been defined based on:

• Se concentrations in their food

• effects on predators them selves expressed as Se residues in tissue. Bivalves (clam s ) are an im portant food source for the predators of interest in the present evaluation (Luom a et al., 1992). So one type of guideline for bivalve tissues should be based upon their use as a

109food source for fish and birds. Guidelines for pr edators based on food are (see also Tables 13 through 15):

• 10 μ g Se/g in food = Threshold of effects on predators . Concentrations in predator food (invertebrate tissues) above 10 μ g Se/g dw have been conclusively im plicated in adverse effects on reproduction in predators (Saiki, 1986; Hods on and Hilton, 1983; Johns et al., 1988; Coyle, et al., 1993; Lem l y, 1985, 1993a; c; 1997b; Ham ilt on et al., 1990; 2000b; Adam s et al., 1998;
Linville and Luom a, in press). Many studies s uggest effects begin at lower concentrations, but
10 μ g Se/g can be considered the value of least uncertainty. W h en invertebrate tissues exceed
10 μ g 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 μ g Se/g in food = Observed conditions that coincide with extinction of some fish species.
This is the annual m a xim u m concentration of Se in P. amuren sis observed between 1995 and 1996 near Carquinez Strait in Suisun Bay (Table 13; Figures 14 through 17)

• 40 μ g Se/g in food = Extinction of numerous fish species . In field studies, all but the m o st tolerant populations of fish species have been elim inated when Se concentrations in
invertebrates reach 40 to 100 μ g Se/g (Lem ly, 1985; 1993a; 1997c; Saiki, 1986; Saiki and Lowe, 1987). So we m i ght define values > 40 μ g Se/g dw as invertebrate tissue Se
concentrations where risks of extinction of m u ltiple 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 μ g Se/g in food = Widespread invertebrate toxicity . Although large-scale invertebrate toxicity is probably not the m o st sensitive response to Se, it could be an additional outcom e of

extrem e Se contam ination. Very rarely are invertebrates found in ecosystem s when Se concentrations in invertebrates are greater than 150 μ g Se/g (Lem ly, 1993a; 1997c; Saiki and Lowe, 1987). For the sake of discussion, we will assum e 100 μ g 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 endm em ber Se concentrations, particulate Se concentrations, and generic bivalve Se concentrations are shown at three different Kd’s (transform ation constants) and four

110different AE’s (generic bivalve assim ilation efficien cies) in Appendix F, Tables F6 to F9. Table 28

sum m a rizes these projected concentrations of Se in particulate m a terial and in generic bivalve tissue as
a function of four com b inations 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 m onths) for a SLD extension release and for a SJR discharge of a targeted load of 3,500 lbs Se per six m onths under three different clim ate regim e s. Also included for com p arison is a forecast of Bay-Delta conditions prior to refinery cleanup. The forecasts show that, contam ination of pr ey would be sufficient to cause widespread extinction of fish species (> 40 μ g Se/g in food) during the low flow season of any year, but especially in dry years (Table 28), if Se transform a tion occurs at a Kd of 3 X 10 3 or higher and:

• the proposed SLD extension discharges at 300 cfs, even if m a nagem e nt succeeds in holding
concentrations to 62.5 μ g Se/L (44,880 to 18,700 lbs per six m onths). Som e of these scenarios could also cause widespread elim ination of invertebrates in addition to predicted effects on predators (> 100 μ g Se/g in food).

• the proposed SLD extension discharges at 150 cfs (half capacity) and with a drainage
concentration of 50 μ g Se/L (6,800 lbs per six m onths) and the highest reactivity of suspended
sedim e nt (C1/AE3 or C1/AE4 ) occurs.

• sub-extinction threats to reproduction of birds and fish (concentrations between 10 and 40 μ g Se/g dw in food) would result In low flow seasons from discharges of 6,800 lbs per six m onths
via a SLD extension. For loading of 3,500 lbs per six m onths via the SJR, sub-extinct threats exist during the low flow season of a dry year at typical shallow-water bed sedim e nts (C2) reactivity and during the low flow season of a wet year at the highest reactivity assum e d (C1).
Concentrations less than 10 μ g 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 μ g Se/L (6,800 lbs per
six m onths) and if Se transform a tion 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 m onths
and if Se transform a tion 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

m onths are released during high f l ows and reactivities are that of bed sedim e nt or lower (C2 and C3). At the lower load, a higher reactivity (C1/AE3 or C1/AE4) also result in prey of < 10

μ g Se/g, but not at 6,800 lbs Se. In general, SLD discharges that would m eet de m a nds for drainage pose risks to fish and bird reproduction and the risk of fish extinction via contam in ation of their invertebrate food (Table 28). If biogeochem i cal conditions like those today in the Ba y-Delta predom inate during projected discharges, low flow periods would be a tim e of extrem e risk for fish and bird species, especially those that include filter-feeding bivalves am ong their prey. Som e low flow conditions include forecasts where extrem e risks m i ght be som e what reduced. Most of those conditions are of low likelihood (reactivities that
result in a Kd of < 10 3 ) in that such low Kd’s are not typical of the Bay-Delta. Sim ilarly, the targeted load scenario for the SJR results in prey containing < 10 μ g Se/g only if reactivities are low (C3/AE1) during low f l ow seasons. At other reactivities (C2/ AE2, C1/AE3 or C1/AE4) during low f l ow seasons, concentrations in prey approach (i.e., 8.7 μ g Se/g) or exceed 10 μ g Se/g (12 to 38 μ g Se/g). Loadings of Se from 6,800 to 18,700 lbs per six m ont hs, if released during the highest flows only, would result in exceedances of the effects levels only if the highest Kd’s, of 1 X 10 4 (C1) were observed (i.e., if the particulate Se turns out to be as reactive as observed during longer residence tim es than usually occurs at high inflows). Thus, re leases during high flows carry less risk for fish extinctions. However, it is im portant that releases during high flows be studied carefully before it is concluded that they lower risks. The fate of Se th at enters the Bay-Delta estuary during high inflows is not fully known. For exam ple, it is not known how m u ch is retained and reacts during subsequent low flow periods or how m u ch is transported to the S outh Bay during high flows and subsequently retained (Conom os et al., 1979; 1985; Nichols et al., 1986; Pe terson et al., 1989). Also during high inflows, highly contam inated particulate m a terial from either the SJR or the SLD is m o st likely to add to the Se load in the estuary (although, at present, suspended particulates are not typically highly contam inated during high inflows).
For com p arison, forecasts of conditions in the Bay-Delta prior to refinery cleanup show exceedances of
the 40 μ g Se/g threshold during the low flow season of a dry year at high reactivity (C3/AE4) and of
the 10 μ g Se/g threshold at bed sedim e nt reactivity (C2/AE2). During the low flow season of a wet

112year, 10 μ g 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 μ g Se/g.

Effects on predators based on selenium concentrations in food
W e take two forecasts, one for a SLD extension load of 18,700 lbs Se per six m onths and one for a SJR targeted load of approxim a tely 3,500 lbs per six m onths, forward to link uptake by bivalves and effects on predators (Table 29). Forecasts are shown for three clim ate seasons and for three
transform a tions previously selected (C1/AE3, C2/A E2, and C3/AE1). This cum u lative sum m a ry also
shows the com posite freshwater endm em ber Se concentrations and particulate Se concentrations at the head of the estuary for these scenarios. The forecast invertebrate Se bioaccum u lation is com p ared to the guidelines for effects on fish and birds from contam inated food. In this case we assum e clam s constitute that food. The projection for the SLD scenario (18,700 lbs Se per six m onths ) shows that (Table 29):

• Com posite freshwater endm em ber Se concentrations in the Bay-Delta would reach the USEPA
criterion of 5 μ g 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 contam inated food (9-266 μ g Se/g dw) would be expected, no m a tter what the reactivity of the Se (i.e., concentrations posing a serious risk would be reached under all feasible biogeochem i cal conditions).

• Com posite freshwater endm em ber Se concentrations would fall between the USEPA guideline
and the USFW S proposed criterion of 2 μ g Se/L in the dry season of a wet year. If Se is of the lowest possible reactivity, bioaccum u lation would not reach the 10 μ g Se/g dw food guideline under these conditions. A typical estuarine Kd would result in exceedance of the 40 μ g Se/g dw guideline and threaten an array of fish and birds with extinction from the estuary. So, in the

m o st likely circum stances (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 elim inated during this period.
In sum m a ry, under a loading scenario of 18,700 lbs Se per six m onths , 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 μ g Se/g)

113during the six m onths or m o re of each year when river inflows are reduced. This condition is the m o st likely if the transf orm a tion prevalent at present in the Bay-Delta is operable in the f u ture. Biogeochem i cal transform a tion rates and AE’s are criti cal determ inants of the degree of contam ination of the food of predators in the Bay-Delta and need to be better understood. The projection for the SJR scenario (approxim a tely 3,500 lbs Se per six m onths ) shows that:

• Under the m o st likely biogeochem i cal conditions (Kd = 3 X 10 3 , C2) risks to predators are greatly reduced com p ared to SLD discharge scenarios. Invertebrate concentrations of Se would
f

a ll just within the 10 to 40 μ g Se/g dw range of elevated risk to reproduction in critically dry years under the m o st likely reactivity scenarios. Risk at this or lower reactivity would be reduced in intensity com p ared to prior to refinery cleanup, based upon contam ination of bivalve

prey.

• Contam ination of food would be sufficient to suggest risk of fish extinctions (> 40 μ g 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 m a terial 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 elim inated, even under this m o st carefully m a naged condition.

Forecast of Selenium Concentrations in Tissues of Predators

Choice of predators
W h ite 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 m o st data is available for the Bay-Delta (i.e., the Selenium Verification Study : W h ite et al., 1987; 1988; 1989; Urquhart and Regalado, 1991), and these
data rem a in the best available data on predators.

• These are the upper trophic level species that bioaccum u late the m o st 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 bioaccum u lation in the Bay-Delta are also likely to be
the m o st at risk for adverse effects. Observations from other system s show that fish with thehighest bioaccum u lated concentrations of Se are the first to disappear from contam inated reservoirs (Lem ly, 1995; 1996a).

Relation of selenium concentrations in bivalves to selenium concentrations in predators As discussed previously, pharm acokinetic m odels are the optim al approach for forecasting how changes in Se concentration or form m i ght affect bioaccum u lation by predators. Unfortunately, such

m odels are not available for predators relevant to the Bay-Delta. An alternative approach is to statistically link predator bioaccum u lation to bi oaccum u lation by prey (food). Urquhart and Regalado (1991) determ ined Se in white sturgeon, surf scoter, greater scaup, and lesser scaup at a num ber of
tim es and locations when they or others also determ ined 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
Hum boldt Bay and from San Pablo Ba y in 1988 (Urquhart and Regalado, 1991). Potamocorbula
amurensis invaded North Bay initially in 1986, and by the late 1980' s was established as the dom inant 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 m i ght be used to estim ate concentrations
in 1990.
W e have assum e d that the bivalves listed above were a m a jor 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 (W hite 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 Hum boldt 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 com m on year and

com m on location (Table 30). Mean Se concentrations in the liver and flesh of white sturgeon, surf scoter, greater scaup, and lesser scaup are signi ficantly and strongly correlated with m ean Se
concentrations in bivalves If data for P. amurensis is em ployed to m a tch the predator data in 1990,
the correlation rem a ins strong. The 1990 concentrations in C. fluminea are not as strongly correlated as other years with the predators, but P. amurensis was the predom inant benthos in 1990 in both San Pablo Bay and Suisun Bay.

115The regressions in Tables 30 and 31 were em pl oyed to forecast Se concentrations in predators under the different conditions of loading and clim ate season em ployed previously. In Table 30, the m ean bivalve Se concentration was m a tched to the m ean 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 m ean for each year of data for the North Bay or Hum boldt 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 sm all set of data available. Nevertheless, the
calculation adds an im portant and highly relevant perspective to the forecasts presented earlier. Once these concentrations are forecast they can be com p ared to toxicity thresholds known for the tissue Se
concentrations in birds and fish. This line of evidence is a second dem onstration, in addition to concentrations in food, of how Se m i ght affect predators in the system

.

Selenium concentrations in predators Table 32 shows forecasts of hepatic (liver) concen trations of Se in white sturgeon, surf scoter, greater scaup, and lesser scaup that result from regression with forecast bioaccum u lation by bivalves, in two possible Se discharge scenarios (18,700 lbs per six m onths for a SLD extension discharge and an approxim a tely 3,500 lbs Se per six m onths for a targeted SJR discharge). The forecasts are for the low flow season of a dry year, which is the m o st re levant tim e period for the m i gratory predators (see discussion below). The forecasts include consideration of all three possible reactivity scenarios (C1/AE3, C2/AE2, and C3/AE1). Shown for com p arison, is a range of threshold Se concentrations for
adverse ef f

ects on predators based on Se concentrations in liver tissue. The guidelines illustrated show a range from 20 to 50 μ g Se/g dw based on data com p iled in Tables 13 through 15.
W h ite 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. W h ite sturgeon generally m i grate to freshwater in March to breed; the m i gratory waterfowl m ove north for the sam e purpose shortly thereafter. A lag occurs in the decline of Se concentrations in bivalves in response to increased river inflows, so in m o st 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 m i gratory predators would carry as they leave the Bay-Delta would probably be reasonably cl ose to that forecast in Table 32. The low flow

116condition forecasts m a y depict the high-end of the risk to these anim als, 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

m onths 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 approxim a tely 3,500 lbs per six m onths also threatens these species if partitioning
of

Se f o llows the suspended sedim e nt partitioning obser ved in the past. If partitioning to particulate Se follows the Kd typical of shallow sedim e nt, bi valve bioaccum u lation would be sim ilar to what probably existed prior to refinery cleanup, with a resultant forecast of risk sim ilar 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 m onths, if conveyed to the Bay-Delta by the SJR, would have the effect of replacing the Se
scheduled for rem oval through treatm e nt by the oil refiners in 1998 (Table 10).



### CONCLUSIONS

Cumulative Impacts on the Bay-Delta
Som e uncertainty characterizes transform a ti ons and other aspect of the analysis given above. However, enough is known about the biogeochem i stry and biotransfer of Se that, using m u ltiple lines of evidence, the relevant conditions and outcom e s can be bracketed for the Bay-Delta. The m odel and
forecasts dem onstrate that m a ny of the m o st likely com b inations of load, hydrology, clim ate, Se reactivity, and Se bioavailability pose a signif i cant ecological risk to the Bay-Delta. In general, SLD discharges that would m eet dem a nds for drainage pos e risks to fish and bird reproduction and the risk
of fish extinction via contam ination of their invert ebrate food. If biogeochem i cal conditions like those today in the Bay-Delta predom inate during projected Se discharges, low flow periods would be the
tim e of greatest risk f o r f i sh and bird species, especially those that include f ilter-f eeding bivalves

am ong their prey. W h ere Se undergoes reactions typi cal of low flow or longer residence tim e, highly problem atic bioaccum u lation is forecast to result. There are som e conceivable scenarios of increased Se discharge to the Bay-Delta where the potential of risk is reduced. For exam ple, 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. 117Most of those conditions are of low likelihood in that such low particulate and suspended m a tter reactivity is not typical of the Bay-Delta. Discha rge of Se from the SJV would be predom inantly selenate, rather than the selenite released by refineries prior to 1998. Transform a tion of selenate to particulate Se is observed throughout nature where residence tim es are extended. The efficiency of this
transform a tion and the resulting particulate Se concentrations are key to forecasting Se
bioaccum u lation and effects.

! Dry year and wet year, low flow season The dry years and low f l ow seasons will be the ecological bottleneck (the tim es that will drive
im pacts) with regard to Se. Surf scoter, greater and lesser scaup, and white sturgeon arrive in the estuary during the low flow season and leave befo re high flows subside. Anim als preparing for reproduction, or for which early life stages develop in Septem ber through March, will be highly vulnerable. So, low flow forecasts are probably th e m o st relevant to describe their exposures.
A cum u lative sum m a ry for the low flow season of a dry year com p iles Se concentrations for each

m e dia em ployed in our analysis (water, sedim e nt, 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 m onths ) . W e assum e a particulate transform a tion of 3 X 10 3 (C2) indicative of shallow sedim e nt Bay-Delta conditions and a generic bivalve AE of 0.56 (AE2) to reflect bioaccum u lation 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 m onths). 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 seem s likely, with loss of fish and bird species. If an out-of-valley resolution to the drainage problem results in carefully m a naged discharges of Se to the Bay-Delta via the SJR (for exam ple at 3,500 lbs per six

m onths), 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 sim ilar to Se concentrations observed (and forecast) during conditions in the Bay-Delta prior to refinery cleanup. 118These 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 term s of food web exposure and effects, the Se rem oved in refinery cleanup.
Selenium contam ination docum ented from 1986 to 1996 was sufficient to threaten reproduction in key species within the Bay-Delta estuary ecosystem s and result in hum an 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 μ g Se/L (6,800 lbs per six m onths) and if Se transform a tion values or reactivity is low (C3/AE1) in the Bay-Delta; or

o the SJR discharges 3,500 lbs per six m onths and if Se transform a tion 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 seem s an unlikely scenario.

! Wet year, low and high flow seasons High flow conditions afford som e protec tion under certain forecast conditions. Under these conditions, there are som e conceivable scenarios where the potential of risk can be reduced.
Concentrations less than the threshold of effects fo r 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 m onths are released during high f l ows and reactivities are that of bed sedim e nt or lower (C2 and C3). At the lower SJR input load, a higher reactivity (C1/AE3 or AE4) also results in prey of < 10 μ g Se/g, but not at SLD input loads of 6,800 lbs or greater per six-m onth. If concentrations in the SJR are regulated under a concentration m a nagem e nt plan, increased SJR inflows will result in increased input loads to the Ba y-Delta. Under this scenario, the low flow season of a wet year m i ght be m o re vulnerable than a dr y 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 m a y not be offset as m u ch by increased flows as those that occur seasonally. Hence, m eeting a triple goal of releasing a specific load during a lim ited period of naturally high flows and keeping concentrations below a certain objective to protect against bioaccum u lation m a y not always be attainable. 119As som e forecasts show, som e releases dur ing high flows m a y carry less direct risk for fish extinctions. However, it is im portant that releases during high flows be studied carefully before it is concluded that they lower risks. The fate of Se th at enters the Bay-Delta estuary during high inflows is not fully known. For exam ple, it is not known how m u ch is retained and reacts during subsequent low flow periods or how m u ch is transported to the S outh Bay during high flows and subsequently retained (Conom os et al., 1979; 1985; Nichols et al., 1986; Pe terson et al., 1989). Also during high inflows, highly contam inated particulate m a terial from the SJ R and/or the SLD is m o st likely to add to the Se load in the estuary.

! Implications for water quality criteria for the protection of aquatic life
In m a ny forecasts, the considered load scenario results in Se concentrations in prey and predators that equal or exceed Se concentrations forecast and m easured in the Bay-Delta prior to refinery cleanup. In som e forecasts, Se concentrations in the Bay-Delta rem a ined below the 2 μ g Se/L water quality criterion proposed for the protection of aqua tic life, but those predators using the specific
bioaccum u lation pathway from sedim e nt and be nthic/suspended biom ass to bivalves were, nevertheless, im pacted. Our forecasts suggest that even at waterborne Se concentrations at the head of the estuary of 1 μ g Se/L, all risk of adverse effects cannot be elim inated.

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 m a gnitude of the

accum u lated Se reservoir in the western SJV. Calcula tions at the lower range of projections show that long-term reduction in Se discharge would not be exp ected for 63 to 304 years, if Se were disposed of at a rate of approxim a tely 42,500 lbs per year. Drai nage of wastewaters outside of the SJV m a y slow the degradation of SJV resources, but drainage al one 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

am ounts of ground water, salt, and Se that have accum u lated in the internal reservoir of the SJV m a y

m a ke m a nagem e nt of only the annual im balance of input greater than output im practical. However, forecasts of annual SJV agricultural discharges provide a basis for determ ining the upper
and lower lim its of Se discharge from the western SJ V (Tables 6 to 9; 17). Secondarily, the projections provide the basis for determ ining the m a gnitude of Se load reductions that m a y becom e necessary to achieve a specific targeted load of Se for environm ental or restoration targets or objectives. To 120narrow the range of possibilities in our analysis, agricultural inputs or discharges were divided into three groups depending upon m a nagem e nt scenarios: ! Supply-driven management. A range of 3,000 to 8,000 lbs Se per year was assum e d to address
environm ental protection via a targeted load that cannot be exceeded. For exam ple, using
different m odes of conveyance:

o Current load lim its for the Grassland subarea are from 5,661 to 6,660 lbs Se per year.
Grassland subarea loads m odeled for the SJR as part of TMDL regulation to m e et the 5

μ g Se/L concentration objective in the SJR are approxim a tely 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 environm ental review of the im pact of potential W e stlands subarea loads has been done since the ecological disaster at Kesterson National W ildlife Refuge occurred, a W e stlands subarea load estim ate as part of evidentiary hearings is 8,160 lbs Se per year (assum i ng 200,000 affected acres; drainage generation of 0.3 acre-feet per acre per year; and a Se concentration of 50 μ g Se/L) (Table 7). Thus, a load of 8,000 lbs Se per year m a y be a lower lim it 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 assum e d to address agricultural needs, to som e degree, for draining saline or waterlogged soils. In this scenario, the quality and quantity of the drainage are controlled by m a naging volum e per acre and/or quality of the drainage. For exam ple: a range of loads projected from the am ount of problem water or subsurface drainage defined by the SJV Drainage Program for year 2000 with im plem entation of the m a nagem e nt plan (dem and driven
volum e) in conjunction with a concentration of 50 μ g/L Se (controlled concentration), yields a Se load range of 19,584 to 42,704 lb Se per year (Table 6).

121 ! Demand-driven load with minimum management. A range of 45,000 to 128,000 lbs per year

seem s possible if the dem a nd f o r restoring saline soils drives drainage and neither quantity nor quality objectives can be (or are chosen to be) m e t. For exam ple, a range of loads projected
from the am ount of problem water defined by the SJV Drainage Program for year 2000 without
im plem entation of the m a nagem e nt plan (dem and driven volum e) in conjunction with a
concentration of 150 μ g/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 m odel additional probable scenarios of drainage selected for each subarea.

Implications and Monitoring Needs
Im plications for water m a nagem e nt using our approach and range of loading forecasts are:

• The m o st signif i cant im pacts of irrigation drainage disposal into the Bay-Delta will occur during low f l ow seasons and especially during low-river f l ow 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 com p rised 15 of those years. Any analysis of Se effects m u st take the
influences of variable river inflows into account.

• Selenium im pacts in the Bay-Delta also could increase if water diversions increase or if SJR
inflows increase with concom itant real-tim e discharge of Se that increases Se loading (i.e. the
Se issue and the water m a nagem e nt issues are tightly linked).

• Construction of an extension of the SLD would increase Se exposures of Bay-Delta organism s 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 problem atic if they are constant through low inflow periods, when the dilution capacity of the estuary subsides dram atically
because of diversions of freshwater inflows. Freshwater diversions, the resultant volum e of inflow, and the degree of treatm e nt of the waste are critical in determ ining the extent of the
im pact of a SLD extension.

• Treatm e nt also m a y be im portant in determ ini ng source loads im pacts. Treatm e nt technologies applied to source waters m a y affect both the con centration and speciation of the effluent. For

exam ple, a treatm e nt 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.
W e view low f l ow conditions as the bottleneck that will determ ine the ef f

ects of Se on the ecological health of the Bay-Delta. Biological dam a ge once per year can lim it populations of species with a generation tim e of m o re than a year; biological dam a ge incurred once per year can be carried
over into the rem a inder of the year. Exposures to Se are probably near their m a xim a when m i gratory species leave the estuary, enhancing risk of biologi cal dam a ge. Anim als that will be m o st vulnerable 122to 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 μ g Se/L nor the recommended USFWS criterion level of 2 μ g Se/L alone, would be sufficient to protect the estuary if Se transforms to particulate concentrations at a Kd of greater than
10 3 . 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 par ticulate 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 i m pacts, it is i m portant 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 123f l owing water system m a y be less sensitive to Se ef f

ects (especially if selenate dom inates inputs) than adjacent wetlands, the Delta or the Bay, where residence tim es and biogeochem i cal
transform a tions of selenate are m o re likely.

• Multiple-m edia guidelines provide, in com b ination, a feasible reference point for m onitoring. A
linked or com b ined approach would include all considerations that cause system s to respond differently to Se contam ination. The critical m e di a defined here are water, particulate m a terial, and prey and predator tissue. Monitoring plan com ponents necessary for a m a ss balance approach include source loads of Se; concentrations of dissolved Se and suspended Se; Se speciation in water and sedim e nt; assim ilation capacities of indicator food chain organism s; and Se concentrations in tissues of prey and pred ator species. Determ ination of transform a tion efficiency and processes that determ ine Kd’s of Se in Bay-Delta and SJR are crucial to relate
loads to bioaccum u lation, rates of transfer, and effects. Trace elem ents sequestered in bed
sedim e nts and in algal m a ts would be a part of recom m e nded m a ss balance considerations.

• Invertebrates m a y be the optim al indicator to use in m onitoring Se because they are practical to

sam p le and are m o st closely linked to predator exposure. Knowledge of optim al indicators in the Bay-Delta and SJR are necessary to fully explore feeding relationships. Resultant
correlations with Se bioaccum u lation in food webs are a part of this process.

• Determ ination of food web inter-relations will he lp identify the m o st vulnerable species. Specific protocols that include life cycles of vulnerable predators including m i gratory and

m obile species would then docum ent Se effects for the species m o st threatened.

• Little is known about Se concentrations in the Delta, yet this is the system that could be m o st im pacted 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

em phasis in CALFED’s restoration ef f

o rt. The f a te of Se in the Delta will be a key in
determ ining the extent to which Se contam ination will im pede 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 m a y occasionally be greater than the current criterion of 5

μ g/L or the proposed criterion of 2 μ g/L, it will be essential to investigate and determ ine the fate and effects of Se in this system . In short, if m a nagem e nt and regulatory m easures to restore the SJR ecological resources to their form er level of abundance are to be effective, then

124the biogeochem i stry of Se, ecology, and hydrodynam i cs in this system m u st be further investigated and understood.

• A m a ss 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 m a nagem e nt. In the past (1986 to 1995), cum u lative agricultural loading to the SJR was estim ated at approxim a tely 100,000 lbs Se (Presser and Piper, 1998). Currently, Se is discharged through Mud Slough to the SJR at the rate of approxim a tely 6,000 to 8,000 lbs per year. The ultim ate fate of Se from these past and current agricultural discharges is not known. At a m i nim u m , a m echanism for tracking Se loading via oil refineries and the SJR is needed based on SJR, Sacram ento River, and BayDelta hydrodynam i cs. Monitoring needs to m easure the on-going status of the system in term s of inputs, storage in sedim e nt, throughput s outh via the Delta-Mendota Canal and California Aqueduct, and throughput north to the Bay.

• Storm s and high f l ow years will be tim es 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 bioaccum u lation during varying conditions of flow should
be studied.

• In view of the analysis of the existing Se reser voir in the SJV, consideration of the degradation of groundwater reservoirs needs to be a factor in m a nagem e nt scenarios. Short-term

m a nagem e nt that results in m o re storage than leaching will result in m o re degradation of aquifers. Mass balance considerations should include a “storage” term , not only input and output term s. Monitoring and assessm ent of storage also will show if treating discharge on an
annual basis will suffice to m a nage the current regional im balance of water, salt, and Se.
W e have dem onstrated and thoroughly reviewed the justifications for a m e thodology that em ploys existing knowledge of each factor in a sequence of li nked processes that control ecological effects of
Se. W e have incorporated these linked processes into an internally consistent evaluation using

m u ltiple lines of evidence. Any f u ture analysis of im pacts f r om Se discharges via the SJR or a proposed SLD extension to the Bay-Delta should be at least as com p lete and could profitably build
from the fram ework presented here. For the Bay-Delta, this new tool is used in site-specfic forecasts to 125evaluate Se effects based upon the m a jor processes leading from loads through consum er organism s to predators. W e conclude that credible protective criteria need to be applicable to vulnerable food webs
and to be based on contam inant concentrations in sources such as particulate m a terial that m o st inf l uence bioavailability. Bivalves appear to be the m o st sensitive indicator of Se contam ination in the Bay-Delta.

126

### ACKNOWLEDGMENTS

W e wish to acknowledge: 1) technical and policy reviews by Marc A. Sylvester, W a ter Resources Division of the U.S. Geological Survey; 2) techni cal reviews by Steve Ham ilton, Biological Resources Division of the U.S. Geological Survey; and Joy W i ncke l of the U.S. Fish and W ildlife Service; and 3) grant review by Gail Louis and Philip W oods of the U.S. Environm ental Protection Agency. This work was perform e d with the support of a U.S. Environm ental Protection Agency interagency funding

agreem ent (EPA/IAG DW 14955347-01-0) and cooperative funding agreem ents with Contra Costa County and Contra Costa W a ter District. W e wi sh to thank Gail Louis, Eugenia McNaughton and
Michael Boots of U.S. Environm ental Protection Agency, John Kopchik of Contra Costa County, and
Richard Denton of Contra Costa W a ter District for th eir support during the preparation of our m odel.
Mark Huebner of the W a ter Resources Division pr ovided technical support with data and figures. And lastly, the long-range vision of T. John Conom os within the U.S. Geological Survey and the goals of
the W a ter Resources Division National Research Program have m a de this report possible.

127

### REFERENCES

Albers, P.H., Green, D.E., and Sanderson, C.J., 1996, Diagnostic criteria for selenium toxicosis in aquatic birds: dietary exposure, tissue concentrati ons, and m acroscopic effects: Journal of W ildlife Disease: v. 32 (3), p. 468-485.

Adam s, W

. J., Brix, K.V., Cothern, K.A., Tear, L.M., Cardwell, R.D., Fairbrother, A., and Toll, J.E., 1998, Assessm ent of selenium food chain transfer and critical exposure factors for avian wildlife species: Need for site-specific data, in Little, E.E., DeLonay, A.J., and Greenberg, B.M., eds.,
Environm ental Toxicology and Risk Assessm ent: Seventh Volum e ASTM STP 1333, Am erican Society for Testing and Materials, p. 312-342.

Anderlini, V.C., Chapm a n, J.W ., Girvin, D.C., McCorm ick, S.J., Newton, A.S., and Risebrough, R.W ., 1975, Heavy m e tal uptake study: Pollutant uptake: Dredge disposal study, San Francisco Bay and Estuary: Subm itted to the U.S. Arm y Corps of Engineers, 1975, Appendix H.

Barcellos Judgm ent, 1986, United States District Court, Eastern District of California, Barcellos and
W o lfsen, Inc., v . W e stlands W a ter District, Civ. No. F-79-106 EDP, consolidated with W e stlands
W a ter District v . United States of Am erica, Civ. No. F-81-245 EDP, Decem ber 30, 1986

Bowie, G.L., Sanders, J.G., Riedel, G.F., Gilm our, C.C., Breitburg, D.L., Cutter, G.A., and Porcella, D.B., 1996, Assessing selenium cycling and accum u lation in aquatic ecosystem s: W a ter, Air, and Soil Pollution, v. 90, p. 93–104.

Brown and Caldwell, 1986, Screening alternative geographic disposal areas, San Joaquin Valley Drainage Program , Prelim inary draft prepared fo r the U.S. Bureau of Reclam ation: Brown and Caldwell Consulting Engineers, Pleasant Hill, Calif ornia, Chapter 1-6 and 97 m a ps.

Brown, C.L., and Luom a, S.N., 1995a, Energy-related selenium and vanadium contam ination in San Francisco Bay, California-Effects on biological resources? , in Carter, L.M.H., ed., Energy and the

128Environm ent-Application of Geosciences to Deci sion-Making: Tenth V. E. McKelvey Forum on Mineral and Energy Resources: U.S. Ge ological Survey Circular 1108, p. 91-92.

Brown, C.L., and Luom a, S.N., 1995b, Use of the euryhaline bivalve Potamocorbula amurensis as a biosentinel species to assess trace m e tal contam ination in San Francisco Bay: Marine Ecology: Progress Series, v. 124, p.129-142.

Bull, W

. B., 1964, Alluvial fans and near-surface subs idence in western Fresno County, California: U.S. Geological Survey Professional Paper 437-A, 71 p.

Butler, G.W ., and Peterson, P.J., 1967, Uptake and m e tabolism of inorganic form s of selenium -75 by Spirodela oligorrhiza : Australian Journal of Biological Science, v. 20, p. 77-86.

CALFED Bay-Delta Program , 1998a, Ecosystem Rest oration Program Plan: Volum e 1, 350 p. and 1 Figure.

CALFED Bay-Delta Program , 1998b, Ecosystem Restor ation Program Plan: Volum e II, 453 p. and 19 Figures.

CALFED Bay-Delta Program , 1999a, Draft program m a tic environm ental im pact statem ent /environm ental im pact report, im pact analysis, CA LFED Bay-Delta Program , Sacram ento, California, 1200 p.

CALFED Bay-Delta Program , 1999b, Ecosystem Rest oration Program Plan: Volum e 1, Ecological attributes of the San Francisco Bay- Delta W a tershed, Revised Draft, 534 p.

CALFED Bay-Delta Program , 1999c, Ecosystem Rest oration Program Plan: Volum e 2, Ecological Managem e nt Zone Visions, Revised Drafts, 455 p.

CALFED Bay-Delta Program , 1999d, Strategic Plan fo r Ecosystem Restoration, Revised Draft, 91 p. and 3 appendices. 129(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1988, Am endm ents to the W a ter Quality Control Plan f o r the San Joaquin River Basin (5C): Calif ornia Central Valley Regional W a ter Quality Control Board, Sacram ento, Calif ornia, 61 p.

(CCVRW QCB) California Central Valley Regiona l W a ter Quality Control Board, 1990a, W a ter quality in evaporation basins used for the disposal of agricultural subsurface drainage water in the San Joaquin Valley, California, 1988 and 1989: California Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 48 p.

(CCVRW QCB) California Central Valley Regiona l W a ter Quality Control Board, 1990b, Sedim e nt quality in evaporation basins used for the disposal of agricultural subsurface drainage water in the San Joaquin Valley, California, 1988 and 1989: California Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 68 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1993, Order Nos. 93-136, -140, -142, -144, -146, -148, and –152: W a ste Di scharge Requirem e nts for Tulare Lake Drainage District: Alpaugh Group, and Lost Hills Evaporation Basins, Fresno and Kings Counties, California Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 125 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board California, 1994a, The water quality control plan (basin plan) f o r the Sacram ento River Basin and San Joaquin River Basin: third edition: Central Valley Regional W a ter Quality Control Board, Sacram ento, Calif ornia, Chapters I-V and 40 appendices.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1994b, A total

m a xim u m m onthly load m odel for the San Joaquin River: California Central Valley Regional W a ter Quality Control Board, Sacram ento, Calif ornia, 86 p.

130(CCVRW QCB) California Central Valley Regiona l W a ter Quality Control Board, 1995, The water quality control plan (basin plan) for the Tulare Lake Basin: second edition: California Central Valley Regional W a ter Quality Control Board, Fresno, California, 65 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1996a, Am endm ents to the water quality control plan f o r the Sacram ento and San Joaquin River Basins: Calif ornia Central Valley Regional W a ter Quality Control Board, Sacram ento, Calif ornia, 24 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1996b, W a ter quality of the lower San Joaquin River: Lander Avenue to Vernalis, October, 1994 to Septem ber, 1995:
Calif ornia Central Valley Regional W a ter Quality Control Board, Sacram ento, Calif ornia, 39 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1996c, Agricultural drainage contribution to water quality in the Gra ssland area of western Merced County, October, 1994 to Septem ber, 1995: California Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 62 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1996d, Staff report on control of agricultural subsurface drainage discharges: in Draf t Am endm ents to the W a ter Quality
Control Plan for the Sacram ento and San Joaquin River Basins: Sacram ento, California, 192 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1997, Order Nos.
97-226 and –263: W a ste Discharge Requirem e nts for Britz and Davenport Ranch and W e stlake Farm s Inc. Evaporation Basins, Fresno and Kings Counties: Calif ornia Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 55 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1998a, Order No.
98-171: W a ste Discharge Requirem e nts for San Luis and Delta-Mendota water authority and United States Departm e nt of the Interior, Bureau of Reclam ation, Grassland Bypass Channel Project, Fresno
and Merced Counties: Calif ornia Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 23 p. 131(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board California, 1998b, The water quality control plan (basin plan) f o r the Sacram ento River Basin and San Joaquin River
Basin: f ourth edition: Central Valley Regional W a te r Quality Control Board, Sacram ento, Calif ornia, Chapters I-V and 40 appendices.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1998c, Order Nos. 98-164, -182, and –229: W a ste discharge requirem e nts for Rainbow Ranch, Meyers Ranch, and Stone Ranch evaporation basins, Fresno and Kings Coun ties: Calif ornia Central Valley Regional W a ter Quality Control Board, Sacram ento, Calif ornia, 75 p.

(CCVRW QCB) California Central Valley Regiona l W a ter Quality Control Board, 1998d, Com p ilation of electrical conductivity, boron, and selenium water quality data for the Grassland watershed and San Joaquin River, May 1985- Septem ber 1995: Californi a Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 235 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1998e, Loads of salt, boron, and selenium in the Grassland watershed and lower San Joaquin River, October 1985 to Septem ber 1995, Raw Data Supplem ental Appendix: California Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 15 appendices.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1998f, Loads of Salt, Boron, and selenium in the Grassland W a tershed and lower San Joaquin River, October 1985 to Septem ber 1995, volum e I: load calculations: California Central Valley Regional W a ter Quality Control Board, Sacram ento, California, 51 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1998g Agricultural drainage contribution to water quality in the Grassland W a tershed of western Merced County, California: October 1995 to Septem ber 1997: Sacram ento, California, 117 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 1998h, W a ter 132quality of the lower San Joaquin River: Lander Avenue to Vernalis, October 1995 to Septem ber 1997:
Calif ornia Central Valley Regional W a ter Quality Control Board, Sacram ento, Calif ornia, 80 p.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 2000a, Draft salinity and boron basin plan am endm ent: Calif ornia Central Valley Regional W a ter Quality Control Board
Sacram ento, California, chapters 5 and 6.

(CCVRW QCB) California Central Valley Regional W a ter Quality Control Board, 2000b, Agricultural drainage contribution to water quality in the Grassland W a tershed of western Merced County, California: October 1997 to Septem ber 1998: Sacram ento, California, 63 p.

(CCVRW QCB) California Central Valley Regiona l W a ter Quality Control Board, 2000c, W a ter quality of the lower San Joaquin River: Lander Avenue to Vernalis, October 1997 to Septem ber 1998:
Sacram ento, California, 71 p.

California Code of Regulations, 1979 and as am e nded, title 22, Social Security Division 4, Minim u m standards for m a nagem e nt of hazardous and extrem ely hazardous wastes: Environm ental Health, Chapter 30, Article 66001-66699, s-161, 1121-0649.

(CDFG) California Departm e nt of Fish a nd Gam e , 1985-ongoing, W a terfowl health warnings (selenium ) Grassland area (western Merced C ounty), California Hunting Regulations: California Departm e nt of Fish and Gam e , Sacram ento, California.

(CDFG) California Departm e nt of Fish and Ga m e , 1986-ongoing, Public health advisories on fish

consum ption (selenium ) Grassland area (Merced) California Sport Fishing Regulations: California Departm e nt of Fish and Gam e , Sacram ento, California.

(CDFG) California Departm e nt of Fish and Gam e /O ffice of Environm ental Health Hazard Assessm ent (OEHHA), 1987, W a terfowl health warning (selenium ) N. W e stern Kern and S. W e stern Kings County, California Hunting Regulations: California Departm e nt of Fish and Gam e , Sacram ento, California. 133(CDFG) California Departm e nt of Fish and Gam e /Office of Environm ental Health Hazard Assessm ent (OEHHA), 1988-ongoing, W a terfowl health warning (selenium ) Suisun Bay, San Pablo Bay and San Francisco Bay, California Hunting Regulations: Califor nia Departm e nt of Fish and Gam e , Sacram ento, California.

(CDW R) California Departm e nt of W a ter Re sources, 1965a, San Joaquin Valley Drainage Investigation - San Joaquin Master Drain (Prelim inary Edition): Bulletin # 127, California Departm e nt of W a ter Resources, Sacram ento, California, 41 p.

(CDW R) California Departm e nt of W a ter Resources, 1965b, San Joaquin Valley Drainage Investigation - Appendix A - Proposed San Joaqui n Valley Drainage District Act (Prelim inary Edition): Bulletin #127, Appendix A, California Depa rtm e nt of W a ter Resources, Sacram ento, California, 25 p.

(CDW R) California Departm e nt of W a ter Resources , 1969, San Joaquin Valley Drainage Investigation - Appendix D - W a ste water quality, treatm e nt, and disposal: Bulletin # 127, Appendix D, California Departm e nt of W a ter Resources, Sacram ento, California, 57 p.

(CDW R) California Departm e nt of W a ter Resour ces, 1974, Status of San Joaquin Valley drainage problem s: Bulletin # 127-74, California Departm e nt of W a ter Resources, Sacram ento, California, 66 p.

(CDW R) California Departm e nt of W a ter Resources , 1978, A study of salinity effects of alternative San Joaquin Valley drainage discharges on the San Francisco Bay-Delta as discussed in San Joaquin Valley Interagency Drainage Program , 1979, Final Report: Agricultural drainage and salt m a nagem e nt in the San Joaquin Valley: San Joaquin Valley Inte ragency Drainage Program , Sacram ento, California, 167 p. and 8 appendices.

(CDW R) California Departm e nt of W a ter Resour ces, 1979, The California W a ter Atlas, California Departm e nt of W a ter Resources, Sacram ento, California, 118 p.

134(CDW R) California Departm e nt of W a ter Resour ces, 1982, The hydrologic-econom ic m odel of the San Joaquin Valley: Departm e nt of W a ter Resources Bulletin 214, 177 p.

(CDW R) California Departm e nt of W a ter Resour ces, 1986 to 1998, Daily weather data for station #124 Panoche, San Joaquin Valley Region, Fresno County: California Irrigation Managem e nt Inform ation System (CIMIS) clim atological database, Departm e nt of W a ter Resources, Sacram ento, California (www.ceresgroup.com /col/weather/cim i s)

(CDW R) California Departm e nt of W a ter Res ources, 1997, Tulare Basin Resources Assessm ent – Prelim inary Report, California Departm e nt of W a ter Resources, Sacram ento, California, 58 p.

(CSFBRW QCB) California San Francisco Bay Regional W a ter Quality Control Board, 1992a, Derivation of site-specific water-quality criteria for selenium in San Francisco Bay: Oakland, California, 37 p.

(CSFBRW QCB) California San Francisco Bay Re gional W a ter Quality Control Board, 1992b, Mass

em issions reduction strategy for selenium : Oakland, California, 53 p. and 1 appendix.

(CSFBRW QCB) California San Francisco Bay Re gional W a ter Quality Control Board, 1993, Mass

em issions reduction strategy for selenium : supplem ent: Oakland, California, 61 p.

(CSFBRW QCB) California San Francisco Bay Regi onal W a ter Quality Control Board, 1996, Refinery

program s to reduce m a ss loading of selenium —status report: Oakland, California, 2 p, and 3 appendices.

(CSFBRW QCB) California San Francisco Bay Regi onal W a ter Quality Control Board, 1997, Regional
Board Mem b er Issue Briefing Paper No. 1, Selenium in the bay environm ent-an overview of the
environm ental concerns, regulatory history, a nd current status: Oakland, California, 12 p.

(CSW RCB) California State W a ter Resources C ontrol Board, 1979, Com p arison of physical and

num erical m odel studies of the im pact of a San Joaquin Valley Drain on salinities in the western Delta 135as discussed in San Joaquin Valley Interagency Drainage Program , 1979, Final Report: Agricultural drainage and salt m a nagem e nt in the San Joaquin Valley: San Joaquin Valley Interagency Drainage Program , Sacram ento, California, 167 p. and 7 appendices.

(CSW RCB) California State W a ter Resources Control Board, 1985, Order No. W Q 85-1, In the m a tter of

the petition of R. J. Claus f o r the review of inaction of the Calif ornia Central Valley Regional W a ter Resources Control Board, File No. A-354, adopted 2/ 5/85: California State W a ter Resources Control Board, California, 95 p.

(CSW RCB) California State W a ter Resources Contro l Board, 1987, Regulation of agricultural drainage to the San Joaquin River, SW RCB Order No. W Q 85-1 Technical Com m ittee Report: California State
W a ter Resources Control Board, Sacram ento, California, 343 p.

(CSW RCB) California State W a ter Resources Control Board, 1994, water quality control plan for the San Francisco Bay/Sacram ento-San Joaquin Delta Es tuary: California State W a ter Resources Control Board, Sacram ento, California, 45 p.

(CSW RCB) California State W a ter Resources Control Board, 1996a, Staff report on petitions regarding Tulare Lake evaporation ponds: California State W a ter Resources Control Board,
Sacram ento, California, 7 chapters.

(CSW RCB) California State W a ter Resources Control Board, 1996b, Resolution No. 96-029,
Consideration of State W a ter Resources Control Bo ard direction regarding issues relating to an application by the U.S. Bureau of Reclam ation for a discharge perm it for the San Luis Drain:
California State W a ter Resources Control Board, Sacram ento, California, 3 p.

(CSW RCB) California State W a ter Resources Control Board, 1996c, Resolution No. 96-051, Consideration of a resolution authorizing the executiv e director to execute a contract with the U.S.
Bureau of Reclam ation and/or other responsible agencies for reim bursem e nt of State W a ter Resources Control Board costs in connection with an application for a discharge perm it for the San Luis Drain:
State W a ter Resources Control Board direction regard ing issues relating to an application by the U.S. 136Bureau of Reclam ation for a discharge perm it for the San Luis Drain: California State W a ter Resources Control Board, Sacram ento, California, 1 p.

(CSW RCB) California State W a ter Resources Contro l Board, 1997, Draft environm ental im pact report for im plem entation of the 1995 Bay/Delta water quality control plan: State W a ter Resources Control Board, Sacram ento, California, p. VIII-1 to VIII-38.

(CSW RCB) California State W a ter Resources C ontrol Board, 1999a, W a ter Right Decision 1641, In
the Matter of : Im plem entation of water quality objectives f o r the San Francisco Bay/ Sacram ento-San Joaquin Delta Estuary; a petition to change points of diversion of the Central Valley Project and the
State W a ter Project in the Southern Delta; and a petition to changes places of use and purposes of use
of

the Central Valley Project: Calif ornia Sate W a te r Resources Control Board, Sacram ento California,
Decem ber 29, 1999, 217 p.

(CSW RCB) California State W a ter Resources Cont rol Board, 1999b, Plan for California’s Non-point Source Pollution Control Program : Vols. I and II: California State W a ter Resources Control Board,
Sacram ento, California, 302 p.

(CSW RCB) California State W a ter Resources Cont rol Board, 1999c, Consolidated Toxic Hot Spots Cleanup Plan: New Series No. 8., Division of W a ter Quality, California State W a ter Resources Control Board, Sacram ento, California, 115 p.

(CSW RCB) California State W a ter Resources C ontrol Board, 1999d, W o rkshop and Progress report on San Joaquin Valley Agricultural drainage: California State W a ter Resources Control Board,
Sacram ento, California, August 4, 1999, 9 p.

Canton, S.P., and Van Derveer, W

. D., 1997, Selenium toxicity to aquatic life: An argum ent for
sedim e nt-based water quality criteria: Environm ental Toxicology and Chem istry, v. 16, p.1255-1259.

137Carlton, J.T., Thom pson, J.K., Schem e l, L.E., and Ni chols, F.H., 1990, The rem a rkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis I. Introduction and dispersal: Marine Ecology: Progress Series, v. 66, p. 81-94.

CH2M HILL, 1985, Prelim inary plan report on alternative drainage disposal facilities: prepared for
W e stlands W a ter District and U.S. Bureau of Reclam ation, 42 p.

CH2M HILL, 1988, San Joaquin Valley hydrologic and salt load budgets: San Joaquin Valley Drainage Program under U.S. Bureau of Reclam ation Contract No. 7-CS-20-05210, Order No. 8-PD20-05210/003, Modification 003, 40 p.

CH2M HILL, 1996, Kesterson Reservoir 1996 Biologi cal Monitoring Report, prepared for U.S.
Bureau of Reclam ation, Mid-Pacific Regi on, Sacram ento, California, Chapters 1-7.

CH2M HILL, 1997, Selenium in raptors from Kester son Reservoir and other areas in California: prepared for U.S. Bureau of Reclam ation, Mi d-Pacific Region, Sacram ento, California, 11 p.

CH2M HILL, 1999a, Kesterson Reservoir 1998 Biol ogical Monitoring Report: prepared for U.S.
Bureau of Reclam ation, Mid-Pacific Region, Sacram ento, California, Chapters 1-10 and 1 appendix.

CH2M HILL, 1999b, Body condition effects in Am eri can kestrel: prepared for U.S. Bureau of
Reclam ation, Mid-Pacific Region, Sacram ento, California, 12 p.

Chapm a n, P.M., 1999, Selenium – A potential tim e bom b or just another contam inant: Hum a n and Ecological Risk Assessm ent, v. 5, p. 1123-1138.

Cheng, R.T., Casulli, V., and Gartner, J.W ., 1993, Tidal, residual, intertidal m udflat (TRIM) m odel and its applications to San Francisco Bay, California: Estuarine, Coastal, and Shelf Science, v. 36, p. 235-
280.

138Clem ents, W

. H., 2000, Integrating effects of contam inan ts across levels of biological organization: an overview: Journal of Aquatic Ecosystem Stress and Recovery, v. 7, p. 113-116.

Cleveland, L., Little, E.E., Buckler, D.R., and W i edm e yer, R.H., 1993, Toxicity and bioaccum ulation
of

waterborne and dietary selenium in juvenile bluegill ( Lepomis macrochirus ): Aquatic Toxicology, v. 27, p. 265-280.

Cloern, J.E., and Nichols, F.H., eds., 1985, Tem poral dynam i cs of an estuary: San Francisco Bay: Boston, Dr. W

. Junk Publishers, 237 p.

Conom os, T.J., 1979, San Francisco Bay: The Urbanized Estuary – Investigations into the natural history of San Francisco Bay and Delta with refe rence to the influence of Man: Pacific Division
Am erican Association of the Advancem ent of Science, San Francisco, California, 493 p.

Conom os, T.J., Sm ith, R.E., Peterson, D.H., Hager, S.W ., and Schem e l, L.E., 1979, Processes affecting seasonal distributions of water properties in the San Francisco Bay Estuarine System , in Conom os, T.J., ed., San Francisco Bay: The Urbanized Estuary – Investigations into the natural history of San Francisco Bay and Delta with reference to the influence of Man: Pacific Division Am erican
Association of the Advancem ent of Science, San Francisco, California, p. 115-142.

Conom os, T.J., Sm ith, R.E., and Gartner, J.W ., 1985, Environm ental setting of San Francisco Bay in Cloern, J.E., and Nichols, F.H., eds., Tem poral dynam i cs of an estuary: San Francisco Bay: Boston, Dr.
W

. Junk Publishers, p. 1-12.

Contra Costa County, Contra Costa County W a ter Agency, Contra County W a ter District, Natural Resources Defense Council, and the Bay Institute, 1997, United States District Court for the Eastern
District of California DC Nos. CV-88-634 OW W and CV-F-91-048 OW W , Response of intervenorsappellants to the joint m o tion of W e stlands and the United States to dism iss without prejudice to
reinstatem ent: United States Court of Appeals for the Ninth Circuit, Nos. 95-15300 and 95-16641, August 4, 1997, 5 p.

139Cooke, T.D., and Bruland. K.W ., 1987, Aquatic chem istr y of selenium : Evidence of biom ethylation:
Environm ental Science and Technology, v. 21, p. 1214 - 1219.

Coyle, J.J., Buckler, D.R., Ingersoll, C.G., Fa irchild, J.F., and May, T.W ., 1993, Effect of dietary
selenium on the reproductive success of bluegill ( Lepomis macrochirus ): Environm ental Toxicology
and Chem istry, v. 12, p. 551-565.

Cum b ie, P.M., and Van Horn, S.L., 1978, Selenium accum u lation associated with fish m o rtality and reproductive failure, Proceedings of the Annual Confer ence of the Southeastern Association of Fish
and W ildlife Agencies, v. 32, p. 612-624.

Cutter, G.A., 1982, Selenium in reducing waters: Science, v. 217, p. 829 - 831.

Cutter, G.A., 1989, The estuarine behavior of selenium in San Francisco Bay: Estuarine, Coastal, and Shelf Science, v. 28, p. 13-34.

Cutter, G.A., and Bruland, K.W ., 1984, The m a rine bi ogeochem i stry of selenium : A re-evaluation:
Lim nology and Oceanography, v. 29, p. 1179-1192.

Cutter, G.A., and San Diego-McGlone, M.L.C., 1990, Te m poral variability of selenium fluxes in San Francisco Bay: The Science of the Total Environm ent, v. 97/98, p. 235-250.

Davis, G.H., and Poland, J.F., 1957, Ground-water c onditions in the Mendota-Huron Area, Fresno and Kings Counties, California: U.S. Geologi cal Survey W a ter-Supply Paper 1360-G, 588 p.

Davis, J.A., Gunther, A.J., Richardson, B.J., O’C onnor, J.M., Spies, R.B., W y att, E., Larson, E., and Meiorin, E.C., 1991, San Francisco Estuary Project: St atus and trends report on pollutants in the San Francisco Estuary, San Francisco Bay-Delta Aquatic Habitat Institute. 240 p. and 3 appendices.

140Davis, et al., 1997, Contam inant concentrations in fish from San Francisco Bay, 1997: sum m a ry: Regional Monitoring Program 1997 Annual Report, San Francisco Estuary Institute, Richm ond, California, p. 240-247.

DeForest, D.K., Brix, K.V., and Adam s, W

. J., 1999, Critical review of proposed residue-based
selenium toxicity thresholds for freshwater fi sh: Hum a n and Ecological Risk Assessm ent, v. 5, p.
1187–1228.

Deverel, S.J., and Gallanthine, S.K., 1989, Relation of salinity and selenium in shallow ground water to hydrologic and geochem i cal processes, western San Joaquin Valley, California: Journal of Hydrology, v. 109, p. 125-149.

Deverel, S.J., Gilliom , R.J., Fujii, Roger, Izbicki, J.A., and Fields, J.C., 1984, Areal distribution of
selenium and other inorganic constituents in shallow ground water of the San Luis Drain Service Area, San Joaquin Valley, California: Prelim inary St udy: U.S. Geological Survey W a ter-Resources Investigations Report 84-4319, 67 p.

Dinar, A., and Zilberm a n, D., eds., 1991, The econom ics and m a nagem e nt of water and drainage in agriculture: Boston, Kluwer Academ ic Publishers, 946 p.

Dowdle, P.R., and Orem land, R.S., 1999, Microbial oxidati on of elem ental selenium in soil slurries and
bacterial cultures: Environm ental Science and Technology, v. 32, p. 3749-3755.

Dubrovsky, N.M., Kratzer, C.R., Brown, L.R., Gronbe rg, J.M., Burow, K.R., 1998, W a ter-quality in the San Joaquin-Tulare Basins, California, 1992- 95: U.S. Geological Survey Circular 1159, 38 p.

EA Engineering, Science, and Technology, 1999, Environm ental im pact statem ent/environm ental
im pact report for m eeting flow objectives for the San Joaquin River Agreem ent, 1999-2010: prepared
for U.S. Bureau of Reclam ation, Mid-Pacific Re gion, Sacram ento, California and San Joaquin River Group Authority: Modesto, California, Chapters 1-6 and 8 appendices.

141Eisler, R., 2000, Chapter 31. (Selenium ) , in Handbook of Chem ical Risk Assessm ent: Health Hazards
to Hum a ns, Plants, and Anim als: Volum e 3: Metalloids, Radiation, Cum u lative Index to Chem icals and Species: Boca Raton, Lewis Publishers, p.1649-1705.

Engberg, R.A., W e stcot, D.W ., Delam o re, M., and Holz, D.D., 1998, Federal and state perspectives on regulation and rem e diation of irrigation-induced selenium problem s, in Frankenberger, W

. T., Jr., and Engberg, R.A., eds., Environm ental Chem istry of Selenium : New York, Marcel Dekker Inc., p. 153-
182.

Environm ent Canada/Health Canada, 1995, Canadian water guidelines. Sum m a ry of guidelines for water quality in Canada, 1995: Departm e nt of Supply and Services, Ottawa, Canada.

Environm ental Defense Fund, 1994, Plowing new ground, using econom ic incentives to control water pollution from agriculture: Environm ental Defense Fund, Oakland, California, 136 p.

Fairey, R., Taberski, K., Lam e rdin, S., Johnson, E., Clark, R.P., Downing, J.W ., Newm an, J., and Petreas, M., 1997, Organochlorines and other environm ental contam inants in m u scle tissues of sportfish collected from San Francisco Bay: Marine Pollution Bulletin, v. 34, p 1058-1071.

Fan, A.M., Book, S.A., Neutra, R.R., and Epstein, D.M., 1988, Selenium and hum an health
im plications in California’s San Joaquin Valley: Journal of Toxicology and Environm ental Health, v. 23, p. 539-559.

Fan, T. W

- M., and Higashi, R.M., 1998, Biochem i cal fate of selenium in m i crophytes: Natural
biorem ediation by volatilization and sedim e ntation in aquatic environm ents, in Frankenberger, W

. T., Jr., and Engberg, R.A., eds., Environm ental Chem istr y of Selenium : New York, Marcel Dekker Inc., p. 545-564.

Flury, M., Frankenburger, W

. T., Jr., and Jury, W

. A., 1997, Long-term depletion of selenium from
Kesterson dewatered sedim e nts: The Science of the Total Environm ent, v. 198, p. 259-270.

142Fowler, S.W ., and Benayoun, G., 1976, Influence of e nvironm ental factors on selenium flux in two

m a rine invertebrates: Marine Biology, v. 37, p. 59–68.

Frankenberger, W

. T., Jr., and Benson, S., eds., 1994, Se lenium in the Environm ent: New York, Marcel Dekker Inc., 456 p.

Frankenberger, W

. T., Jr. and Engberg, R.A., eds ., 1998, Environm ental Chem istry of Selenium : New York, Marcel Dekker Inc., 713 p.

Fujii, R., and Swain, W

. C., 1995, Areal distribution of selected trace elem ents, salinity, and m a jor ions in shallow ground water, Tulare Basin, southern Sa n Joaquin Valley, California: U. S. Geological Survey W a ter-Resources Investigations Report 95-4048, 67 p.

Gaines, R.W ., 1988, W e st San Joaquin Valley agri cultural setting: San Joaquin Valley Drainage Program , Sacram ento, California, 75 p.

Gilliom , R.J., Belitz, K., Heim es, F.J., Dubrovsky, N.M., Deverel, S.J., Fio, J.L., Fujii R., Clifton, D.G., 1989, Prelim inary Assessm ent of sources, distribution, and m obility of selenium in the San Joaquin Valley, California: U.S. Geological Surv ey W a ter-Resources Investigations Report 88-4186, 129 p.

Gilm er, D.S., Miller, M.R., Bauer, R.D., and LeDonne, J.R., 1982, California’s Central Valley wintering waterfowl: concerns and challenges: Tr ansactions of the North Am erican W ildlife and Natural Resources Conference, v. 47, p. 441-452.

Goede, A.A., 1994, The possible role of selenium in antioxidation in m a rine waters: a prelim inary study: The Science of the Total Environm ent, v. 144, p. 241-246.

Goettl, J.P., and Davies, P.H., 1978, W a ter Polluti on studies: Federal Aid Project F-33-R-13, Colorado
Division of W ildlife, Fort Collins, Colorado.

143(GAF) Grassland Area Farm ers, 1997, Sum m a ry of Grassland Basin Drainers drainage reduction activities: Hanford, California, Sum m e rs Engineering, Inc., 16 p.

(GAF) Grassland Area Farm ers and San Luis Delta-Mendota W a ter Authority, 1998a, Long-term drainage m a nagem e nt plan for the Grassland Drainage Area: Hanford, California, Sum m e rs Engineering, Inc., 32 p.

(GAF) Grassland Area Farm ers, 1998b, Calculation of partitioning of drainage flows and selenium loads for water year 1998 and base period (W Y 1986 –W Y 1994): Hanford, California, Sum m e rs Engineering, Inc., 15p. and 8 attachm e nts.

Grober, L.F., 1996, Sources and circulation of salt in the San Joaquin River Basin, in Bathala, C., ed., Proceedings of the North Am erican W a ter and E nvironm ental Congress 1996: Am erican Society of Civil Engineers, Environm ental Engineer ing Division, Orange, California, p. 54-59.

Ham ilton, S.J., 1998, Selenium effects on endangered fish in the Colorado River basin, in Frankenberger, W

. T., Jr., and Engberg, R.A., eds., Environm ental Chem istry of Selenium : New York, Marcel Dekker Inc., p. 297-313.

Ham ilton, S.J., 1999, Hypothesis of historical eff ects from selenium on endangered fish in the
Colorado River Basin: Hum a n and Ecological Risk Assessm ent, v. 5, p. 1153-1180.

Ham ilton, S.J., Buhl, K.J., Bullard, F.A., and McDona ld, S.F., 1996, Evaluation of toxicity to larval
razorback sucker of selenium -laden food orgam i sm s from Ouray NW R on the Green River, Utah: National Biological Survey, Yankton, South Dakota, Final Report, Recovery Im plem entation Program for the Endangered Fishes of the Upper Colorado River Basin, Denver, Colorado.

Ham ilton, S.J., Buhl, K.J., Faerber, N.L., W i edm e yer, R.H., and Bullard, F.A., 1990, Toxicity of organic selenium in the diet to Chinook salm on: Environm ental Toxicology and Chem istry, v. 9, p347-
358.

144Ham ilton, S.J., Holley, K.M., Buhl, K.J., Bullard, F.A., W e ston, L.K., and McDonald, S.F., 2000b, The
evaluation of contam inant im pacts on razorback sucker held in flooded bottom l and sites near Grand Junction, Colorado-1996: Draft report to the Recovery Im plem entation Program for the Endangered Fish Species of the Upper Colorado River Basin, CO: U.S. Geological Survey, Yankton, South Dakota, 351 p.

Ham ilton, S.J., and Lem l y, A.D., 1999, W a ter-sedim ent controversy in setting environm ental standards
for selenium : Ecotoxicology and Environm ental Safety, v. 44, p. 227-235.

Ham ilton, S.J., Muth, R.T., W a dell, B., and May, T.W ., 2000a, Hazard assessm ent of selenium and
other trace elem ents in wild larval razorback sucker from the Green River, Utah: Ecotoxicology and
Environm ental Safety, v. 45, p. 132-147.

Hanna, G.P., Kipps, J., and Owens, L.P., 1990, Agricu ltural drainage treatm e nt technology review: San Joaquin Valley Drainage Program , Sacram ento California, Chapters 1-15.

Hansen, D., Duda, P.J., Zayed, A.D.L., and Te rry, N., 1998, Selenium rem oval by constructed wetlands: Role of biological volatilization: Environm ental Science and Technology, v. 32, p. 591-597.

Harvey, T.E., Miller, K.J., Hothem , R.L., Rauzon, M.J., Page, G.W ., and Keck, R.A., 1992, Status and trends report on wildlife of the San Francisco Estuary: United States Fish and W ildlife Service, 283 p., 2 appendices, and recom m e ndations.

Haygarth, P.M., 1994, Global im portance and global cycling of selenium , in Frankenberger, W

. T., Jr., and Benson, S., eds., Selenium in the Environm ent: New York, Marcel Dekker Inc., p. 1-27.

Heinz, G.H., 1996, Selenium in birds, in Beyer, W

. N., Heinz, G.H., and Redm on-Norwood, A.W ., eds.,
Environm ental contam inants in wildlif e: interpreting tissue concentrations, New York, Lewis Publishers, p. 447-458.

145Heinz, G.H., and Fitzgerald, M.A., 1993, Overwinter survival of m a llards fed selenium : Archives of
Environm ental Contam ination and Toxicology, v. 25, p. 90-94.

Heinz, G.H., Hoffm an, D.J., and Gold, L.G., 1989, Im paired reproduction of m a llards fed an organic
form of selenium : Journal of W ildlife Managem e nt, v. 53, p. 418-428.

Henderson, J.D., Maurer, T.C., and Schwarzbach, S. E., 1995, Assessing selenium contam ination in two San Joaquin Valley, California sloughs: an update of m onitoring for interim re-use of the San Luis
Drain: U.S. Fish and W ildlife Service, Regi on 1, Division of Environm ental Contam inants,
Sacram ento, California 18 p.

Henny, C.J., Rudis, D.D., Roffe, T.J., and Robinson-W ilson, E., 1995, Contam inants and sea ducks in
Alaska and the circum polar region: Environm ental Health Perspectives, v. 103, p. 41-49.

Hilton, J.W ., Hodson, P.V., and Slinger, S.J., 1980, The requirem e nt and toxicity of selenium in rainbow trout ( Salmo gairdneri ): Journal of Nutrition, v. 110, p. 2527-2535.

Hodson, P.V., and Hilton. J.W ., 1983, The nutritional requi rem e nts and toxicity to fish of dietary and
waterborne selenium : Ecological Bulletins No. 35, in Hallberg, R., ed., Proceedings of the 5 th International Sym posium on Environm ental Biogeochem i stry, ISEB, Stockholm , Sweden, p. 335–340.

Hollibaugh, J.T., ed., 1996, San Francisco Bay: The Ecosystem , Further Investigations into the Natural History of San Francisco Bay and Delta with Refere nce to the Influence of Man: Pacific Division of
the Am erican Association for the Advancem ent of Science, Altona, Manitoba, Friesen Printers, 542 p.

Hornberger, M.I., Luom a, S.N., van Geen, A., Fulle r, C., and Anim a, R., 1999, Historical trends of

trace m e tals in the sedim e nts of San Francisc o Bay, California: Marine Chem istry, v. 64, p. 39-55.

Horner, G.L., ed., 1986, Decision criteria for residuals m a nagem e nt in agriculture: Proceedings of conference on long-term residuals m a nagem e nt issues : The Agricultural Issues Center, The Giannini

146Foundation of Agricultural Econom ics, and the Kear ney Foundation of Soil Science, University of California, 252 p.

Hothem , R.L., Lonzarich, D.G., Takekawa, J.E., and Ohlendorf, H.M., 1998, Contam inants in wintering canvasbacks and scaups from San Franci sco Bay, California: Environm ental Monitoring and
Assessm ent, v. 50, p. 67-84.

Hug, P., Fletcher, B.B., and Trott, S.S., 2000, Opinion of Judge Hug and Judge Trott (dissent) in appeal of Firebaugh Canal v USA 9516641, Office of the Circuit Executive, U.S. Court of Appeals for the Ninth Circuit, Fresno, California, 15 p.

Hydroscience, Inc., 1977, Assessm ent of water quality im pacts: alternatives for m a nagem e nt of San Joaquin Valley agricultural drainage as discussed in San Joaquin Valley Interagency Drainage Program , 1979, Final Report: Agricultural drainage and salt m a nagem e nt in the San Joaquin Valley: San Joaquin Valley Interagency Drainage Program , Sacram ento, California, 167 p. and 7 appendices.

Johns, C., Luom a, S.N., and Eldrod, V., 1988, Seleni um accum u lation in benthic bivalves and fine
sedim e nts of San Francisco Bay, the Sacram ento-San Jo aquin Delta and selected tributaries: Estuarine, Coastal, and Shelf Science, v. 27, p. 381-396.

Jones and Stokes Associates, Inc., 1986a, Draft Environm ental Im pact Statem ent: Contingency

program for W e stlands W a ter District drainage pr oposal project: U.S. Bureau of Reclam ation, MidPacific Region, Sacram ento, California, 175 p. and 2 appendices.

Jones and Stokes Associates, Inc., 1986b, Final Environm ental Im pact Statem ent: Contingency

program for W e stlands W a ter District drainage di sposal project: U.S. Bureau of Reclam ation, MidPacific Region, Sacram ento, California, 160 p., and 1 appendix.

Karkoski, J, 1996, Dynam i c versus quasi-static effluent lim its, in Bathala, C., ed., Proceedings of the
North Am erican W a ter and Environm ental Congress 1996: Am erican Society of Civil Engineering and
Environm ental Engineering Divi sion, Orange California, p. 59-64.
147Kohlhorst, D.W ., Botsford, L.W ., Brennan, J.S., a nd Cailliet, G.M., 1991, Aspects of the structure and dynam i cs of an exploited central California population of white sturegon ( Acipenser transmontanus ),
in W illiot, P., ed., Acipenser: Paris, Cem a gref Publishers, p. 277-293.

Kratzer, C.R., Saleh, D.K., and Zam o ra, C., in press, Selenium and sedim e nt loads in storm runoff in Panoche Creek at interstate five, California, water years 1998 through 2000, U.S. Geological Survey
W a ter Resources Investigations Report.

Kroll, K.J., and Doroshov, S.I., 1991, Vitellogen: pot ential vehicle for selenium bioaccum ulation in oocytes of the white sturgeon ( Acipenser transmontanus ), in W illiot, P., ed., Acipenser: Paris,
Cem a gref Publishers, p. 99-106.

Lem l y, A.D., 1982, Response of juvenile centrarchids to sublethal concentrations of waterborne
selenium : I. Uptake, tissue distribution, a nd retention: Aquatic Toxicology, v. 2, p. 235-252.

Lem l y, A.D., 1985, Toxicology of selenium in a freshwat er reservoir: Im plications for environm ental hazard evaluation and safety: Ecotoxico logy and Environm ental Safety, v.10, p. 314-338.

Lem l y, A.D., 1993a, Guidelines for evaluating selenium data from aquatic m onitoring and assessm ent studies: Environm ental Monitoring and Assessm ent, v. 28, p. 83-100.

Lem l y, A.D., 1993b, Metabolic stress during winter increas es the toxicity of selenium to fish: Aquatic Toxicology, v. 27, p. 133-158.

Lem l y, A.D., 1993c, Teratogenic effects of selenium in natural populations of freshwater fish: Ecotoxicology and Environm ental Safety, v. 26, p. 181-204.

Lem l y, A.D., 1995, A protocol for aquatic hazar d assessm ent of selenium : Ecotoxicology and
Environm ental Safety, v. 32, p. 280-288.

148Lem l y, A.D., 1996a, Assessing the toxic threat of sele nium to fish and aquatic birds: Environm ental Monitoring and Assessm ent, v. 43, p.19-35.

Lem l y, A.D., 1996b, Evaluation of the hazard quotient m e thod for risk assessm ent of selenium : Ecotoxicology and Environm ental Safety, v. 35, p. 156-162.

Lem l y. A.D., 1996c, W i nter Stress Syndrom e: An im portant consideration for hazard assessm ent of aquatic pollutants: Ecotoxicology and Environm ental Safety, v. 34, p. 223-227.

Lem l y, A.D., 1997a, A teratogenic deform ity index for evaluating im pacts of selenium on fish populations: Ecotoxicology and Environm ental Safety, v. 37, p. 259-266.

Lem l y, A.D., 1997b, Ecosystem recovery following selenium contam ination in a freshwater reservoir: Ecotoxicology and Environm ental Safety, v. 36, p. 275-281.

Lem l y, A.D., 1997c, Environm ental hazard of selenium in the Anim as La Plata water developm ent project: Ecotoxicology and Environm ental Safety, v. 37, p. 92-96.

Lem l y, A.D. 1997d. Environm ental im plications of excessive selenium : Biom edical and
Environm ental Sciences, v. 10, p. 415-435.

Lem l y, A.D., 1998a, Pathology of selenium poisoning in fish, in Frankenberger, W

. T., Jr., and Engberg, R.A., eds., Environm ental Chem istry of Selenium : New York, Marcel-Dekker Inc., p. 281-
296.

Lem l y, A.D., 1998b, A position paper on selenium in ecotoxicology: a procedure for deriving sitespecific water quality criteria: Ecotoxicol ogy and Environm ental Safety, v. 39, p. 1-9.

Lem l y, A.D., 1999a, Selenium im pacts on fish: An insidious tim e bom b: Hum a n and Environm ental
Risk Assessm ent, v. 5, p. 1123-1138.

149Lem l y, A.D., 1999b, Selenium transport and bioaccum u lation in aquatic ecosystem s: a proposal for water quality criteria based on hydrological units: Ec otoxicology and Environm ental Safety, v. 42, p.
150-156.

Linville, R., and Luom a, S.N., in press, Selenium in the invasive bivalve Potamocorbula amurensis in the San Francisco Bay-Delta: Spatial distribution, tem poral variability, and com p arisons to other species: Aquatic Toxicology.

Lonzarich, D.G., Harvey, T.E., and Takekawa, J.E., 1992, Trace elem ent and organochlorine concentrations in California clapper rail (Rallus longirostris obsoletus) eggs : Archives of
Environm ental Contam ination and Toxicology, v., 23, p 147-153.

Luom a, S.N., 1996, The developing fram ework of m a ri ne ecotoxicology: Pollutants as a variable in

m a rine ecosystem s? : Journal of Experim e ntal Marine Biology and Ecology, v. 200, p. 29-55.

Luom a, S.N., and Linville, R., 1997, Selenium trends in North San Francisco Bay: Interagency Ecological Program for the Sacram ento-San Joaquin Estuary Newsletter, v. 10, p. 25-26.

Luom a, S.N., and Fisher, N., 1997, Uncertainties in assessing contam inant exposure from sedim e nts, in Ingersoll, C., Dillon, T., and Biddinger, G., eds., Ecological Risk Assessm ents of Contam inated
Sedim e nts, Pensacola, SETAC Press, p. 211-239.

Luom a, S.N., Johns, C., Fisher, N., Steinberg, N.A., Orem land, R.S., and Reinfelder, J.R., 1992,
Determ ination of selenium bioavailability to a benthic bivalve f r om particulate and solute pathways:
Environm ental Science and Technology, v. 26, p. 485-491.

Luom a, S.N., Clem ents, W ., DeW itt, T, Gerritsen, J., Jepson, P., Hatch, A., Reynoldson, T., and Thom , R., in press, Role of environm ental variability in evaluating stressor ef f

ects: in Baird D. and Burton, A., eds., Ecological com p lexity: new direc tion for assessing stress: SETAC Press.

150Maier, K.J., Foe, C.G., and Knight, A.W ., 1993, Com p arative toxicity of selenate, selenite, seleno-DLm e thionine, and seleno-DL-cysteine to Daphia Magna : Environm ental Toxicology and Chem istry, v. 12, p. 755-763.

Maier, K.J., and Knight, A.W ., 1994, Ecotoxicology of selenium in freshwater system s: Reviews of
Environm ental Contam ination, and Toxicology, v. 134, p. 31-48.

Martens, D.A., and Suarez, D.L., 1997, Selenium speciation of soil/sedim ent determ ined with sequential extractions and hydride generation atom ic absorption spectrophotom etry: Environm ental Science and Technology, v. 31, p. 133–139.

McGuire, D.J., 1988, Stratigraphy, depositional history, and hydrocarbon source-rock potential of the upper Cretaceous-lower Tertiary Moreno Form ation, cen tral San Joaquin basin, California: PhD thesis: Stanford University, Stanford, California, 240 p.

Measures, C.I., and Burton, J.D., 1978, Behaviour and speciation of dissolved selenium in estuarine waters: Nature, v. 273, p. 293-295.

Mendenhall, W

. C., Dole, R.B., and Stabler, H., 1916, Ground W a ter in San Joaquin Valley, California: U.S. Geological Survey W a ter-Supply Paper 398, 310 p.

Milam , R.W ., 1985, Biostratigraphy and sedim e ntation of the Eocene and Oligocene Kreyenhagen
Form ation, central California: PhD thesis: Stan ford University, Stanford, California, 240 p.

Monroe, M.W ., Kelly, J., and Lisowski, N., 1992, San Francisco Estuary Project: State of the Estuary– A report on conditions and problem s in the San Franci sco Bay/Sacram ento-San Joaquin Delta Estuary: Association of Bay Area Governm e nts, 270 p.

Monsen, N., 2000, A study of subtidal transport in Suisun Bay and the Sacram ento-San Joaquin delta, California: PhD thesis: Stanford University, Stanford, California.

151Montgom ery-W a tson, 1993, Environm ental use of reclaim e d water in the San Joaquin Valley: San Francisco, Montgom ery-W a tson, 226 p. and 11 appendices.

Moyle, P.B., Brown, L.R., and Herbold, B, 1986, Fina l report on developm ent and prelim inary tests of indices of biotic integrity for California: Final re port to the U. S. Environm ental Protection Agency,
Environm ental Research Laboratory, Corvallis, Oregon.

Myneni, S.C.B., Tokunaga, T.K., and Brown, G.E., Jr., 1997, Abiotic selenium redox transform a tions in the presence of Fe (II, III) oxides: Science, v. 278, p. 1106-1109.

National Research Council, 1976, Selenium : Medical and biological effects of environm ental pollutants: W a shington, D.C., National Academ y of Sciences Press, 203 p.

National Research Council, 1989, Irrigation-induced wate r quality problem s: W h at can be learned from the San Joaquin Valley experience: W a shington, D.C., National Academ y Press, 157 p.

Natural Resources Defense Council et al., 1988, 1989, 1992, 1999, v U.S Bureau of Reclam ation, U.S. Departm e nt of the Interior, and Friant W a ter User s Authority: United States District Court, Eastern District of California, Case No. Civ-S-88-1658.

Nichols, F.H., Cloern, J.E., Luom a, S.N., and Pe terson, D.H., 1986, The m odification of an estuary: Science, v. 231, p. 567-573.

Nichols, F.H., Thom pson, J.K., and Schem e l, L.E ., 1990, Rem a rkable invasion of San Francisco Bay (California, U.S.A.) by the Asian clam Potamocorbula amurensis . II. Displacem ent of a form er

com m unity: Marine Ecology Progress Series, v. 66, p. 95-101.

Nigro, M., and Leonzio, C., 1996, Intracellular storage of m e rcury and selenium in different m a rine invertebrates: Marine Ecology: Progress Series, v.135, p. 137–143.

152O’Toole, D., and Raisbeck, M.F., 1998, Magic num bers, elusive lesions: Com p arative pathology and toxicology of selenosis in waterfowl and m a m m a lian species, in Frankenberger, W

. T., Jr., and Engberg, R.A., eds., Environm ental Chem istry of Selenium , New York, Marcel Dekker Inc., p. 355-
398.

Ogden, G.R., 1988, Agricultural land use and wildlife in the San Joaquin Valley 1769-1930: an overview: San Joaquin Valley Drainage Program , Sacram ento California, 163 p.

Ohlendorf, H.M., 1989, Bioaccum u lation and effects of selenium in wildlife, in Jacobs, L.W ., ed.,
Selenium in Agriculture and the Environm ent, Special Publication No. 23, Soil Science Society of
Am erica, Madison, W I ., p.133-177.

Ohlendorf, H.M., Hoffm an, D.J., Saiki, M.K., and Aldrich, T.W ., 1986, Em bryonic m o rtality and
abnorm a lities of aquatic birds: apparent im pacts by selenium from irrigation drainwater: The Science
of the Total Environm ent, v. 52, p. 49-63.

Ohlendorf, H.M., Hothem , R.L., and W e lsh, D., 1989a, Nest success, cause-specific nest failure, and hatchability of aquatic birds at selenium -contam inated Kesterson Reservoir, Calif ornia and a ref e rence site: Condor, v. 91, p. 787-796.

Ohlendorf, H.M., Lowe, R.W ., Harvey, T.E., and Kelly, P.R, 1989c, Selenium and heavy m e tals in San Francisco Bay diving ducks: Journal of W ildlife Managem e nt, v. 50, p. 64-71.

Ohlendorf, H.M., and Marois, K.C., 1990, Organochlorin es and selenium in California night-heron and egret eggs: Environm ental Monitoring and Assessm ent, v. 15, p. 91-104.

Ohlendorf, H.M., Marois, K.C., Lowe, R.W ., Harvey, T.E., and Kelly, P.R., 1989b, Environm ental

contam inants and diving ducks in San Francisco Bay, in Howard, A., ed., Selenium and agricultural drainage: im plications for San Francisco Bay and the California environm ent, Proceedings of the
Fourth Selenium Sym posium , March 21, 1987, Bay Institute of San Francisco, Sausalito, California, p.
61-69. 153Orem land, R.S., Hollibaugh, J.T., Maest, A.S., Presser, T.S., Miller, L.G., and Culbertson, C.W ., 1989,
Selenate reduction to elem ental selenium by anaerobic bacteria in sedim e nts and culture: biogeochem i cal significance of a novel, sulfate-inde pendent respiration: Applied and Environm ental Microbiology, v. 55, p. 2333-2343.

Outridge, P.M., Scheuham m e r, A.M., Fox, G.A., Br aune, B.M., W h ite, L.M., Greegorich, L.J., and Keddy, C., 1999, An assessm ent of the potential hazards of environm ental selenium for Canadian
water birds: Environm ental Reviews, v.7, 81-96.

Paulsson, K., and Lundbergh, K., 1991, Treatm e nt of m e rc ury contam inated fish by selenium addition:
W a ter, Air, and Soil Pollution, v. 56, p. 833–841.

Peterson, D.H., Cayan, D.R., Festa, J.F., Nichols, F.H., W a lters, R.A., Slack, J.V., Hager, S.E., and
Schem e l, L.E., 1989, Clim ate variability in an estuar y: effects of riverflow on San Francisco Bay: Geophysical Monograph 53, Am eri can Geophysical Union, p. 419-445.

Peterson, J.A., and Nebeker, A.V., 1992, Estim ation of waterborne selenium concentrations that are toxicity thresholds for wildlife: Archives of Environm ental Contam ination and Toxicology, v. 23, p.
154-162.

Phillips, D.J.H., and Rainbow, P.S., 1993, Biom onitoring of Trace Aquatic Contam inants: London, Elsevier Applied Science, 371 p.

Piper, D.Z., Skorupa, J.P., Presser, T.S., Hardy, M.A., Ham ilton, S.J., Huebner, M., and Gulbrandsen, R.A., 2000, The Phosphoria Form ation at the Hot Springs Mine in southeast Idaho: a source of
selenium and other trace elem ents to surface wa ter, groundwater, vegetation, and biota: U.S. Geological Survey Open-File Report 00-020, 73 p.

Porgans, P., Carter, L, U.S. Fish and W ildlife Service, Bay Institute, and other environm ental groups, 1993, Petition to review of action of the Californi a Regional W a ter Quality Control Board, Central 154Valley Region, in adopting waste discharge requirem e nts and certifying environm ental im pact reports for 14 Tulare Lake Basin agricultural discha rgers: File Nos. A-858, A-858(a), and A-858(b)

Presser, T.S., 1994a, The Kesterson effec t: Environm ental Managem e nt, v. 18, p. 437-454.

Presser, T.S., 1994b, Geologic origin and pathways of selenium from the California Coast Ranges to the west-central San Joaquin Valley, in Frankenberger, W

. T., Jr., and Benson, S., eds., Selenium in the
Environm ent: New York, Marcel Dekker Inc., p. 139-155.

Presser, T.S., 1999, Selenium pollution, in Alexander, D.E., and Fairbridge, R.W ., eds., Encyclopedia
of environm ental science: Boston, Kluwer Academ ic Publishers, p. 554-556.

Presser, T.S., and Barnes, I., 1984, Selenium concentrati ons in waters tributary to and in the vicinity of
the Kesterson National W ildlife Refuge, Fresno and Merced Counties, California: U.S. Geological Survey W a ter Resources Investigations Report 84-4122, 26 p.

Presser, T.S., and Barnes, I, 1985, Dissolved constituents including selenium in the vicinity of the
Kesterson National W ildlife Refuge and the west Gr assland, Fresno and Merced Counties, California: U.S. Geological Survey W a ter Resources Investigations Report 85-4220, 73 p.

Presser, T.S., and Ohlendorf, H.M., 1987, Biogeochem i cal cycling of selenium in the San Joaquin Valley, California, USA: Environm ental Managem e nt, v. 11, p. 805-821.

Presser, T.S., and Piper, D.Z., 1998, Mass balance approach to selenium cycling through the San Joaquin Valley, sources to river to bay, in Frankenberger, W

. T., Jr., and Engberg, R.A., eds.,
Environm ental Chem istry of Selenium : New York, Marcel Dekker Inc., p. 153-182.

Presser, T.S., Sylvester, M.A., and Hoffm an, R.J., 1996, Review of the Grassland Bypass Channel Project Monitoring Program , Part I: Executive Sum m a ry and Part II Review of the Grassland Bypass Channel Project Monitoring Plan and Quality Assurance Project Plan: U.S. Geological Survey
Adm i nistrative Report, 111 p. and 5 appendices. 155Presser, T.S., Sylvester, M.A., and Low, W

. H., 1994, Bioaccum u lation of selenium from natural geologic sources in the western United States and its potential consequences: Environm ental Managem e nt, v. 18, p. 423-436.

Presser, T.S., Swain, W

. C., Tidball, R.R., and Severson, R.C., 1990, Geologic sources, m obilization, and transport of selenium from the California Co ast Ranges to the western San Joaquin Valley: a reconnaissance study: U.S. Geological Survey W a ter-Resources Investigations Report 90-4070, 66p.

Prokopovich, N.P., 1989, Irrigation history of the west- central San Joaquin Valley: San Joaquin Valley Drainage Program , Sacram ento California, 73 p.

Reinfelder, J.R., and Fisher, N.S., 1991, The assim ilation of elem ents ingested by m a rine copepods: Science, v. 251, p. 794-796.

Reinfelder, J.R., W a ng, W

- X., Luom a, S.N., and Fi sher, N.S., 1997, Assim ilation efficiencies and
turnover rates of trace elem ents in m a rine bivalves: a com p arison of oysters, clam s, and m u ssels: Marine Biology, v. 129, p. 443-452.

Reinfelder, J.R., Fisher, N.S., Luom a, S.N., Nichols, J.W ., and W a ng, W

- X., 1998, Trace elem ent trophic transfer in aquatic organism s: a critique of the kinetic m odel approach: The Science of the Total
Environm ent, v. 219 p.117-135.

Renner, R., 1998, EPA decision to revise selenium standard stirs debate: Environm ental Science and Technology, vol. 32, p. 350A.

Riedel, G.F., and Sanders, J.G., 1998, Trace elem ent sp eciation and behavior in the tidal Delaware River: Estuaries, v. 21, p. 78-90.

Risebrough, R.W ., Chapm a n, J.W ., Okazaki, R.K., and Schm idt, T.T., 1977, Toxicants in the San Francisco Bay and Estuary: Associati on of Bay Area Governm e nts Report, 108 p. 156Saiki, M.K., 1986, Concentrations of selenium in aquatic food-chain organism s and fish exposed to agricultural tile drainage water, in Howard, Alice, ed., Selenium and agricultural drainage:
Im plications for San Francisco Bay and the Ca lifornia environm ent: Proceedings of the Second
Selenium Sym posium , March 23, 1985: Berkeley, Ca lifornia: The Bay Institute of San Francisco, Tiburon, California, p. 25-33.

Saiki, M.K., and Palawski, D.U., 1990, Selenium and ot her elem ents in juvenile striped bass from the San Joaquin Valley and San Francisco estuary, Califor nia: Archives of Environm ental Contam ination and Toxicology, v. 19, p. 717-730.

Saiki, M.K., Jennings, M.R., and Ham ilton, S.J., 1991, Prelim inary assessm ent of the effects of
selenium in agricultural drainage on fish in the San Joaquin Valley, in Dinar, A., and Zilberm a n, D., eds., The econom ics and m a nagem e nt of water and drainage in agriculture: Boston, Kluwer Academ ic Publishers, p. 369-385.

Saiki, M.K., and Lowe, T.P., 1987, Selenium in aquatic organism s from subsurface agricultural drainage water, San Joaquin Valley, California: Archives of Environm ental Contam ination and Toxicology, v. 16, p. 657-670.

San Francisco Estuary Institute, 1993, San Francisco Estuary Regional Monitoring Program for Toxic Substances: San Francisco Estuary Institute, Oakland, California, 229 p.

San Francisco Estuary Institute, 1994, San Francisco Estuary Regional Monitoring Program for Toxic Substances: San Francisco Estuary Institute, Oakland, California, 339 p.

San Francisco Estuary Institute, 1995, San Francisco Estuary Regional Monitoring Program for Toxic Substances: San Francisco Estuary Institute, Oakland, California, 380 p.

San Francisco Estuary Institute, 1996, San Francisco Estuary Regional Monitoring Program for Toxic Substances: San Francisco Estuary Institute, Oakland, California, 310 p. 157San Francisco Estuary Institute, 1999, Contam inant c oncentrations in fish from San Francisco Bay, 1997, San Francisco Estuary Institute, Oakland, California, 65 p.

San Francisco Estuary Project, 1991, Status and trends report on wetlands and related habitats in the San Francisco Estuary, San Francisco Estuary Proj ect, Oakland, California, 209 p. and 5 appendices.

San Francisco Estuary Project, 1992, The effects of land use change and intensification on the San Francisco Estuary, San Francisco Estu ary Project, Oakland, California, 157 p.

San Francisco Estuary Project, 1999, Bay-Delta environm ental report card, com p rehensive
conservation and m a nagem e nt plan im plem en tation progress 1996-1999: San Francisco Estuary Project, Oakland, California, 28 p.

San Joaquin River Exchange Contractors W a ter Aut hority (Central California Irrigation District, San
Luis Canal Com p any, Colum b ia Canal Com p any, and Firebaugh Canal W a ter District), 1999, Phase 5 closing brief in the California State W a ter Resour ces Control Board Bay-Delta W a ter Rights Hearings,
State W a ter Resources Control Board, Sacram ento, California, 44 p.

(SJV Drainage Im plem entation Program ) San Jo aquin Valley Drainage Im plem entation Program , 1991, A strategy for im plem entation of the m a nagem e nt plan for agricultural subsurface drainage and related problem s on the westside San Joaquin Valle y: San Joaquin Valley Drainage Im plem entation Program , California Departm e nt of W a ter Resources, Sacram ento, California, 80 p.

(SJV Drainage Im plem entation Program ) San Jo aquin Valley Drainage Im plem entation Program , 1998, Drainage Managem e nt in the San Joaquin Valle y - A status report: San Joaquin Valley Drainage
Im plem entation Program , California Departm e nt of W a ter Resources, Sacram ento, California, 65 p.

(SJV Drainage Im plem entation Program ) San Jo aquin Valley Drainage Im plem entation Program , 1999a, Drainage water treatm e nt technical com m itt ee final report: The San Joaquin Valley Drainage
Im plem entation Program and the University of California Salinity/Drainage Program , 41 p. 158(SJV Drainage Im plem entation Program ) San Jo aquin Valley Drainage Im plem entation Program , 1999b, Land retirem ent technical com m ittee final report: The San Joaquin Valley Drainage
Im plem entation Program and the University of California Salinity/Drainage Program , 120 p.

(SJV Drainage Im plem entation Program ) San Jo aquin Valley Drainage Im plem entation Program , 1999c, River discharge technical com m ittee fina l report: The San Joaquin Valley Drainage
Im plem entation Program and the University of California Salinity/Drainage Program , 111 p.

(SJV Drainage Im plem entation Program ) San Jo aquin Valley Drainage Im plem entation Program , 1999d, Evaporation ponds technical com m ittee fina l report: The San Joaquin Valley Drainage
Im plem entation Program and the University of California Salinity/Drainage Program , 77 p.

(SJV Drainage Program ) San Joaquin Valley Drainage Program , 1989, Prelim inary planning alternatives for solving agricultural drainage and drainage-related problem s in the San Joaquin Valley: San Joaquin Valley Drainage Program , Sacr am ento California, 337 p. and 56 figures.

(SJV Drainage Program ) San Joaquin Valley Dr ainage Program , 1990a, A m a nagem e nt plan for agricultural subsurface drainage and related problem s on the westside San Joaquin Valley: San Joaquin Valley Drainage Program , Sacram ento, California, 183 p.

(SJV Drainage Program ) San Joaquin Valley Drai nage Program , 1990b, Fish and W ildlife Resources and Agricultural drainage in the San Joaquin Valley, California, Volum e s I and II: San Joaquin Valley Drainage Program , Sacram ento, California, 878 p., 2 appendices.

(SJV Interagency Drainage Program ) San Joa quin Valley Interagency Drainage Program , 1979a,
Recom m e nded Plan for com p letion of the Valley Drain, in Final Report: Agricultural drainage and salt

m a nagem e nt in the San Joaquin Valley: San Joaquin Valley Interagency Drainage Program , Sacram ento, California, Part I, Chapters 1-13 and 7 appendices.

159(SJV Interagency Drainage Program ) San Joaqui n Valley Interagency Drainage Program , 1979b, First stage environm ental im pact report for com p letion of the Valley Drain, in Final Report: Agricultural drainage and salt m a nagem e nt in the San Joaquin Valley: San Joaquin Valley Interagency Drainage Program , Sacram ento, California, Part II, Chapters 14-20 and 7 appendices.

Santolo, G.M., Yam a m o to, J.T., Pisenti, J.M., and W ilson, B.W ., 1999, Selenium accum u lation and effects on reproduction in captive Am erican kestrels fed seleno-m e thionine: Journal of W ildlife Managem e nt, v. 63, p. 502-511.

Schlekat,C.E., Lee, B-G, and Luom a, S.N., in pr ess (a), Dietary m e tals exposure and toxicity by aquatic organism s: Im plications for ecological risk assessm ent, in Newm an, M., ed., Coastal and
Estuarine Risk Assessm ent.

Schlekat, C.E., Luom a, S.N., Dowdle, and Orem land, R.S., in press (b), Bioavailability of particleassociated selenium to the bivalve Potam o corbul a am urensis: Environm ental Science and Technology.

Seiler, R.L., Skorupa, J.P., and Peltz, L.A., 1999, Areas susceptible to irrigation-induced selenium

contam ination of water and biota in the western United States: U.S. Geological Survey Circular 1180, 36 p.

Shacklette, H.T., and Boerngen, J.G., 1984, Elem ent concentrations in soils and other surficial

m a terials of the conterm i nous United States: U. S. Geological Survey Professional Paper 1270, 105 p.

Shrift, A., 1964, A selenium cycle in nature? : Nature, v. 201, p. 1304-1305.

Skorupa, J.P., 1998a, Selenium poisoning of fish and w ildlife in nature: lessons from twelve real-world

exam ples, in Frankenberger, W

. T., Jr., and Engberg, R.A., eds., Environm ental Chem istry of Selenium : New York, Marcel Dekker Inc., p. 315-354.

Skorupa, J.P., 1998b, Constituents of concern: selenium , in Guidelines f o r interpretation of the biological ef f

ects of selected constituents in biota, water, and sedim e nt, National Irrigation W a ter 160Quality Program Inform ation Report No. 3: U.S. Departm e nt of the Interior, W a shington, DC, p. 139-
184.

Skorupa, J.P., 1998c, Risk assessm ent for the biota database of the National Irrigation W a ter Quality Program , National Irrigation W a ter Quality Program , U.S. Departm e nt of the Interior, W a shington, DC, 151 p.

Skorupa, J.P., 1999, Beware m i ssing data and undernourished statistical m odels: com m e nt on Fairbrother et al.’s crtical evaluation: Hum a n and Ecological Risk Assessm ent, v. 5 (6), p. 1255-1262.

Skorupa, J.P., and Ohlendorf, H.M., 1991, Contam inants in drainage water and avian risk threshold, i n Dinar, A., and Zilberm a n, D., eds., The econom ics and m a nagem e nt of water and drainage in agriculture: Boston, Kluwer Academ ic Publishers, p. 345-368.

Stadtm an, T.C., 1974, Selenium biochem i stry: Science, v. 183, p. 915-922.

Stanley, T.R., Sm ith, G.J., Hoffm an, D.J. , Hoffm a n, D.J., Heinz, G.H., and Rosscoe, R., 1996, Effects
of boron and selenium on m a llard reproduction and duckling growth: Environm ental Toxicology and
Chem istry, v. 15, p. 1124–1132.

Stevens, C.J., and Bensing, D., (U.S. Attorneys) , 1994, Federal defendants’ proposed finding of fact and conclusions law: United States District Court, Eastern District of California, Sum n er Peck Ranch Inc., et al. v United States of Am erica, et al., Ci v. Nos, F-88-634 OW W , F-91-048 OW W , and F-92-
5554 OW W , October 12, 1994, 54 p.

Takayanagi, K., and Cossa, D., 1985, Speciation of dissolved selenium in the upper St. Lawrence Estuary, in Sigleo, A.C., and Hattori, A., eds., Marine and Estuarine Geochem i stry: Chelsea, Michigan, Lewis Publishers, p. 275-284.

Takayanagi, K., and W ong, G.T.F., 1984, Total selenium and selenium (IV) in the Jam e s River Estuary and southern Chesapeake Bay: Estuarine, Coastal, and Shelf Science, v.18, p. 113-119. 161Thom pson, B., Hoenicke, R., Davis, J.A., and Gunther, A., 2000, An overview of contam inant-related issues identified by m onitoring in San Francisco Bay: Environm ental Monitoring and Assessm ent, v. 64, p. 409-419.

Thom pson-Eagle, E.T., and Frankenburger, W

. T., Jr ., 1992, Biorem ediation of soils contam inated with
selenium : Advances in Soil Science, v. 17, p. 261-310.

Tidball, R.R., Severson, R.C., McNeal, J.M. a nd W ilson, S.A., 1989, Distribution of selenium ,

m e rcury, and other elem ents in soils of the San Joaquin Valley and parts of the San Luis Drain Service Area, California, in Howard, A., ed., Selenium and agricultural drainage: im plications for San Francisco Bay and the California environm ent: Proceed ings of the Third Selenium Sym posium , March 15, 1986, Berkeley, California: The Bay Institute of San Francisco, Sausalito, California, p. 71-82.

Tidball, R.R., Severson, R.C., Gent, C.A., and Riddle, G.O., 1986, Elem ent associations in soils of the San Joaquin Valley, California: U.S. Geol ogical Survey Open-File Report 86-583, 15 p.

Tokunaga, T.K., Brown, G.E., Jr., Pickering, I.J ., Sutton, S.R., and Bajt, S., 1997, Selenium redox reactions and transport between ponded waters and sedim e nts: Environm ental Science and Technology, v. 31, p. 1419-1425.

Tokunaga, T.K., Pickering, I.J., and Brown, G.E ., Jr., 1996, Selenium transform a tions in ponded
sedim e nt: Soil Science Society of Am erica Journal, v. 60, p. 781-790.

Tokunaga, T.K., Sutton, S.R., Bajt, S., Nuessle, P., and Shea-McCarthy, G., 1998, Selenium diffusion
and reduction at the water- sedim e nt boundary: Micro-XANES spectroscopy of reactive transport:
Environm ental Science and Technology, v. 32, p. 1092-1098.

Trelease, S.F., and Beath, O.A., 1949, Selenium : Its ge ological occurrence and its biological effects in relation to botany, chem istry, agriculture, nutriti on, and m e dicine: New York, Trelease and Beath, 292

p. 162Trinity County, California, 1999, Phase 5 closing brief in the California State W a ter Resources Control Board Bay-Delta W a ter Rights Hearings, State W a ter Resources Control Board, Sacram ento, California, 8 p.

(USBR) United States Bureau of Reclam ation, 1955, A Report on the Feasibility of W a ter Supply Developm ent, San Luis Unit, Central Valley Project , California: U.S. Bureau of Reclam ation, MidPacific Region, Sacram ento, California, 90 p. as discussed in U.S. Bureau of Reclam ation, 1978, Special Task Force report on the San Luis Unit as required by Public Law 94-46, Central Valley Project, California: U.S. Bureau of Reclam ati on, Mid-Pacific Region, Sacram ento, California, 331 p.
and 11 m a ps.

(USBR) United States Bureau of Reclam ation, 1962, Definite plan report, San Luis Unit, Central Valley Project, California: U.S. Bureau of Reclam ation, Mid-Pacific Region, Sacram ento, California,
as discussed in U.S. Bureau of Reclam ation, 1978, Special Task Force report on the San Luis Unit as required by Public Law 94-46, Central Valley Project, California: U.S. Bureau of Reclam ation, MidPacific Region, Sacram ento, California, 331 p. and 11 m a ps.

(USBR) United States Bureau of Reclam ation, 1978, Sp ecial Task Force report on the San Luis Unit as required by Public Law 94-46, Central Valley Project, California: U.S. Bureau of Reclam ation, MidPacific Region, Sacram ento, California, 331 p. and 11 m a ps.

(USBR) United States Bureau of Reclam ation, 1981, U. S. Bureau of Reclam ation Project Data: U.S.
Governm e nt Printing Office, Denver CO, 1463 p.

(USBR) United States Bureau of Reclam ation, 1983, Estim ate of drainage quantity and quality, San Luis Drain, 1995 to 2095: U.S. Bureau of Reclam a tion, Mid-Pacific Region, Sacram ento, California, 10 p.

163(USBR) United States Bureau of Reclam ation, 1984a, Central Valley Project, U.S. Bureau of
Reclam ation Map No. 214-208-5133: U.S. Bureau of Reclam ation, Mid-Pacific Region, Sacram ento, California, 2 p.

(USBR) United States Bureau of Reclam ati on, 1984b, San Luis Unit, Central Valley Project - California; Report of waste discharge estuarine disposal: Toxicity Bioassays; Volum e 1 Main Report - Aquatic bioassays for the San Luis Drain, Centra l Valley Project, California: U.S. Bureau of
Reclam ation, Mid-Pacific Region, Sacram ento, California. 205 p.

(USBR) United States Bureau of Reclam ation, 1984c, San Luis Unit, Central Valley Project - California; Report of waste discharge estuarine di sposal: Toxicity Bioassays; Volum e 2 Appendixes - Aquatic bioassays for the San Luis Drain, Centra l Valley Project, California: U.S. Bureau of
Reclam ation, Mid-Pacific Region, Sacram ento, California, 231 p.

(USBR) United States Bureau of Reclam ati on, 1984d, San Luis Unit, Central Valley Project - California; Report of waste discharge estuarine disposal: Toxicity Bioassays: Volum e 3 Supplem entary Inform ation - Additional inform ation and clarification: aquatic bioassays for the San Luis Drain, Central Valley Project, California: U.S. Bureau of Reclam ation, Mid-Pacific Region, Sacram ento, California, 32 p.

(USBR) United States Bureau of Reclam ation, 1984e, San Luis Unit, Central Valley Project - California; Report of waste discharge estuarine disposal: Macroalgae biostim ulation; Field and bioassay studies on the im pact of San Luis Drain water on estuarine m acroalgae: U.S. Bureau of
Reclam ation, Mid-Pacific Region, Sacram ento, California, 67 p.

(USBR) United States Bureau of Reclam ation, 1984f, San Luis Unit, Central Valley Project - California, Report of waste discharge estuarine di sposal: Phytoplankton m odeling; Analysis of the effects of the proposed San Luis Drain on the receivi ng water of the western Delta - Suisun Bay: U.S.
Bureau of Reclam ation, Mid-Pacific Region, Sacram ento, California, 270 p.

164(USBR) United States Bureau of Reclam ati on, 1984g, San Luis Unit, Central Valley Project - California, Report of waste discharge estuarine disposal: Dispersion of drainage effluent; San Francisco Bay - Delta Model - San Luis Drain outfall dye dispersion tests: U.S. Bureau of
Reclam ation, Mid-Pacific Region, Sacram ento, California, 117 p.

(USBR) United States Bureau of Reclam ati on, 1984h, San Luis Unit, Central Valley Project - California, Report of waste discharge estuarine di sposal: Benthic and sedim e nt trace elem ents: Trace

m e tals in Suisun Bay, California: A prelim inary report: [U.S. Geological Survey W a ter- Resources Investigations Report 84-4170]: U.S. Bureau of Reclam ation, Mid-Pacific Region, Sacram ento, California, 35 p.

(USBR) United States Bureau of Reclam ation, 1986, Fi nal environm ental im pact statem ent, Kesterson
program : alternative cleanup actions and future use of Kesterson Reservoir and the San Luis Drain,
Volum e s I and II. U.S. Bureau of Reclam ation, Mi d-Pacific Region, Sacram ento, California, Chapters 1-7 and 1-10 and appendix I.

(USBR) United States Bureau of Reclam ation, 1992, San Luis Unit Drainage Program , Central Valley Project, California: Draft Environm ental Im pact Study, U.S. Bureau of Reclam ation, Mid-Pacific Region, Sacram ento, California, 290 p.

(USBR) United States Bureau of Reclam ation, 1995, Finding of No Significant Im pact and Supplem ent Environm ental Assessm ent, Grassland Bypass Channe l Project, Interim use of a portion of the San Luis Drain for conveyance of drainage water through the Grassland W a ter District and adjacent
Grassland Areas: U.S. Bureau of Reclam ation Mi d-Pacific Region, Sacram ento, California, 36 p. and appendices.

(USBR, et al.) United States Bureau of Reclam ation, et al., 1996, Com p liance m onitoring program for use and operation of the Grassland Bypass Project: U.S. Bureau of Reclam ation Mid-Pacific Region,
Sacram ento, California, 53 p. and 2 appendices.

165(USBR, et al.) United States Bureau of Recl am ation, et al., 1998, Grassland Bypass Project annual report, October 1, 1996 through Septem ber 30,1997: U.S. Bureau of Reclam ation, Mid-Pacific Region,
Sacram ento, California, Chapters A-H.

(USBR et al.) United States Bureau of Reclam ation, et al., 1999, Grassland Bypass Project annual report, October 1, 1997 through Septem ber 30,1998: U.S. Bureau of Reclam ation, Mid-Pacific Region,
Sacram ento, California, 135 p.

(USBR et al.) United States Bureau of Reclam ation, et al., 2000, Grassland Bypass Project annual report, 1998-1999: U.S. Bureau of Reclam ation, Mi d-Pacific Region, Sacram ento, California, 136 p.
and errata.

United States Departm e nt of the Interior Interagency Land Retirem ent Team , 1999, Final
Environm ental Assessm ent: Central Valley Project Im provem e nt Act (CVPIA), Land Retirem ent Program , Dem onstration Project: Bureau of Reclam ation, U.S. Fish and W ildlife, Bureau of Land Managem e nt, 127 p. and 7 appendices.

United States Departm e nt of the Interior National Irrigation W a ter Quality Program , 2000: National Irrigation W a ter Quality Program , Denver, Colorado, 15 p.

(USEPA) United States Environm ental Protection Agency, 1980, Am bient water quality criteria for
selenium : NTIS, PB81-117814, 123 p.

(USEPA) United States Environm ental Protection Agency, 1987, Am bient water quality criteria for
selenium —1987: Publication EPA-440/5-87-006: U.S. Environm ental Protection Agency, Office of
W a ter Regulations and Standards, W a shington, D.C., 121 p.

(USEPA) United States Environm ental Protection Agency, 1992, Rulem a king: water quality standards:
establishm ent of num eric criteria for priority toxic pollutants: States' com p liance: Final Rule, 57 FR 60848 (Decem ber 22, 1992).

166(USEPA) United States Environm ental Protec tion Agency, 1997 and am ended 2000, Proposed and
f i nal rule f o r the prom ulgation of water quality standards: establishm ent of num eric criteria f o r priority toxic pollutants for the state of California: 62 FR 42159 (August 5, 1997) and 65 FR 31682 (May 8, 2000).

(USEPA) United States Environm ental Protection Agency, 1998, Report on the peer consultation workshop on selenium aquatic toxicity and bioaccu m u lation: United States Environm ental Protection Agency, W a shington, D.C., 59 pp., 6 appendices.

(USEPA) United States Environm ental Protection Agency, 2000, Revisions to the water quality planning and m a nagem e nt regulation and revisions to the National Pollutant Discharge Elim ination System Program in support of revisions to the W a ter Quality Planning and Managem e nt Regulation (regarding establishm ent of Total Maxim u m Daily Loads (TMDLs): Final Rules: 40 CFR Part 9 et al., Federal Register, v. 65, p. 43586-43670.

(USFW S) United States Fish and W ildlife Service, 1990, Effects of irrigation drainwater contam inants on wildlife, U.S. Fish and W ildlife Service, Laurel, Maryland, 542 p.

(USFW S) United States Fish and W ildlife Service, 1995, Sacram ento-San Joaquin Delta Native Fishes Recovery Plan: U.S. Fish and W ildlife Service, Portland, Oregon, 195 p.

(USFW S) United States Fish and W ildlife Service and National Marine Fisheries Service, 1998 and

am ended 2000, Biological opinion on USEPA’s proposed rule for the prom ulgation of water quality
standard: establishm ent of num eric criteria f o r priority toxic pollutants for the state of California: U.S.
Fish and W ildlife Service and National Marine Fisheries Service, 260 p.

(USGS) United States Geological Survey, 1999, W a te r resources data, California, water year 1998, southern Central Valley and the Great Basin from W a lker River to Truckee River: U. S. Geological Survey W a ter-Data Report, CA-98-3, v. 3, p. 294-295.

167United States House of Representatives Com m ittee on Natural Resources and Subcom m ittee on Oversight and Investigation, 1993, Oversight hear ing (Chairm a n Representative George Miller) on agricultural drainage issues in the Central Va lley, California, October 26, 1993: Serial No. 103-54,
U.S. Governm e nt Printing Office, W a shington, DC, 101 p. and appendices.

United States House of Representatives Com m ittee on Resources and Subcom m ittee on W a ter and Power, 1999, Record of oversight field hearing (Chairm a n Representative John Doolittle) to exam ine agricultural drainage issues associated with the California Central Valley, August 19, 1999, Clovis,
California.

Urquhart, K.A.F., and Regalado, K., 1991, Seleni um Verification Study, 1988–1990: California State
W a ter Resources Control Board Report 91-2-W Q W R , Sacram ento, California, 94 p. and 7 appendices.

URS Griener W oodward Clyde, 2000, San Joaquin Rive r riparian habitat restoration program , 2000 pilot project, environm ental assessm ent and initial study, prepared for the U.S. Bureau of Reclam ation,
Sacram ento, CA and Friant W a ter Users Authority, Lindsay, California, chapters 1-5, and appendices
A-C.

Velinsky, D.J., and Cutter, G.A., 1991, Geochem i stry of selenium in a coastal salt m a rsh: Geochim i ca et Cosm ochim i ca Acta, v. 55, p.179–191.

Vencil, B., 1986, The Migratory Bird Treaty Ac t-protecting wildlife on our national refuges— California’s Kesterson Reservoir, a case in point: Natural Resources Journal, v. 26, p. 609-627.

W a lters, R.A., Cheng, R.T., and Conom os, T.J., 1985, Tim e s scales of circulation and m i xing processes of San Francisco Bay waters: Hydrobiologia, v. 129, p. 13-36.

W a ng, W

. -X., Fisher, N.S., and Luom a, S.N., 1996, Kinetic determ inations of trace elem ent bioaccum u lation in the m u ssel Mytilus edulis : Marine Ecology: Progress Series, v. 140, p. 91-113.

168W a nger, Oliver, U.S. District Judge (i.e., W a nger Decision), 1994, Finding of Fact and Conclusions of Law: United States District Court, Eastern District of California, Sum n er Peck Ranch Inc., et al. v Bureau of Reclam ation, et al., and Firebaugh Canal Com p any and Central California Irrigation District

v . United States of Am erica (W estlands W a ter Di strict-in-intervention): Civ. No, F-91-048 OW W and CV-F-88-634, Decem ber 16, 1994 as m odified February 6, 1995, partial judgm ent March 10, 1995, 48

p.

W e stcot, D.W ., Karkoski, J., and Schangl, R., 1996, Non-point source policies for agricultural drainage, in Bathala, C., ed., Proceedings of the North Am erican W a ter and Environm ental Congress
1996. Am erican Society of Civil Engineering a nd Environm ental Engineering Division, Orange California, p. 83-88.

(W W D ) W e stlands W a ter District, 1996, Statem ent subm itted by W

. R. Johnston concerning current
estim ates of the W e stlands W a ter District drainage problem , April 4, 1996: W e stlands W a ter District, Fresno, California, 56 p.

(W W D ) W e stlands W a ter District, 1998, W e stlands Subarea Report: W e stlands W a ter District, Fresno, California, 56 p.

W h ite, J.R., Hofm ann, P.S., Ham m ond, D., and Baum gartner, S., 1987, Selenium Verification Study:
1986: California State W a ter Resources Contro l Board, Sacram ento, 79 p. and 9 appendices.

W h ite. J.R., Hofm ann, P.S., Ham m ond, D., and Baum gartner, S., 1988, Selenium Verification Study:
1986-1987: California State W a ter Resources Contro l Board, Sacram ento, 60 p. and 8 appendices.

W h ite, J.R., Hofm ann, P.S., Urquhart, K.A.F., Ham m ond, D., and Baum gartner, S., 1989, Selenium Verification Study: 1987-88: California State W a te r Resources Control Board, Sacram ento, 81p. and 11 appendices.

W ilber, C.G., 1983, Selenium , A potential environm ental poison and a necessary food constituent: Springfield, Ill., Charles C. Thom as Publishers, 126 pp. 169W illey, Z., 1990, Environm ental quality and agricultural irrigation-reconciliation through econom ic
incentives in Tanji, K.E., ed., Agriculture Salinity Assessm ent and Managem e nt: Am erican Society of Civil Engineers, New York, p. 561-583.

W oock, S.E., Garrett, W

. R., Partin, W

. E., and Bryson, W

. T., 1987, Decreased survival and teratogenesis during laboratory selenium exposures to bluegill, Lepomis macrochirus , Bulletin of
Environm ental Contam ination and Toxicology, V. 39, p.998-1005.

W r ench, J.J., 1978, Selenium m e tabolism in the m a rine phytoplankters Tetraselmis tetrathele and
Dunaliella minuta : Marine Biology, v. 49, p. 231-236.

W r ench, J.J., and Cam pbell, N.C., 1981, Protein bound selenium in som e m a rine organism s: Chem osphere, v. 10, p. 1155-1161.

W r ench, J.J., and Measures, C.I., 1982, Tem poral variations in dissolved selenium in a coastal ecosystem : Nature, v. 299, p. 431-433.

Zawislanski, P.T., and McGrath, A.E., 1997, Selenium cycling in estuarine wetlands: overview and
new results from the San Francisco Bay, in Frankenberger, W

. T., Jr., and Engberg, R.A., eds.,
Environm ental Chem istry of Selenium : New York, Marcel Dekker Inc., p. 223–242.

Zhang, Y-Q., and Moore, J.N., 1996, Selenium frac tionation and speciation in a wetland sedim e nt: Environm ental Science and Technology, v. 30, p. 2613-2619.

Zhang, Y-Q., and Moore, J.N., 1997a, Reduction potential of selenate in wetland sedim e nt: Journal of
Environm ental Quality, v. 26, p. 910-916.

Zhang, Y-Q., and Moore, J.N., 1997b, Controls on se dim e nt distribution in wetland sedim e nt, Benton Lake, Montana: W a ter, Air, and Soil Pollution, v. 97, p. 323-340.

170Zhang, Y-Q., and Moore, J.N., 1997c, Interaction of selenate with a wetland sedim e nt: Applied
Geochem i stry, v. 12, p. 685-691.

Zhang, Y-Q., and Moore, J.N., 1997d, Environm enta l conditions controlling selenium volatilization
from a wetland system : Environm ental Science and Technology, v. 31, p. 511-517.

171

## FIGURES

### Coal Oil Phosphorite Soils and Alluvium

Power Generation Mining Refining Irrigation

Ash, Flue Gas Scrubbing Wastewater

Subsurface drainage

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 depos its, anthropogenic activities, receiving water bodies, and biota at risk



### .Figure 2. Conceptual model describing linked factors that determine the e ffects of selenium on ecosystems. The sequence of relations lin ks 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 ter m explicitly in reference to particulate/invertebrate bioaccumul ation.



### 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

effectsS a

c r

S a n J o a q u i n R

. G r i z z l y B a y S u i s u n B a y
C

a r q i n e z S t r a i t
S a n P a b l o B a y

C e n t r a l B a y

S o u t h B a y

C o y o t e C r

. ** R** **o d**  **e o**  **B e**  **n i**  **c i**  **a**

**M a**  **r t**  **i n**  **e z**  **P i**  **t t**  **s b**  **u r**  **g**

**S a**  **n F**  **r a**  **n c**  **i s**  **c o** 

C o

y o t e P t

. **B e**  **r k**  **e l**  **e y** 

**1 0**  **m 1**  **0**

**m**

**S a**  **n J**  **o s**  **e** a m

e n t o

R

. **R i**  **o V**  **i s**  **t a** 

D e l t a

P a c i f i c O c e a n

1 2 2 **°** 3 0 '

3 8 **°** 0 0 '

3 7 **°** 3 0 ' 1 2 2 **°** 0 0 '

**O a**  **k l**  **a n**  **d**

0 2 0 K M 0 2 0 M I **C h**  **i p**  **p s**  **I s**  **l a**  **n d** 

P r o p o s e d S a n L u i s D r a i n ( n o r t h e r n s e g m e n t )

O i l r e f i n e r i e s

1 0

1 0

Figure 4. Map of the San Francisco Bay-Delta Estuary including the locations of oil refineries (filled circles) in the North Bay and the location of the proposed northern segment of the San Luis Drain. The North Bay includes Suisun Bay and San Pablo Bay. Adapted from Conomos et al., 1985.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 NevadaExistingSan Luis DrainFriantKern CanalCoast RangesPotentialSan Luis DrainExtensionPotentialSan Luis DrainExtension

Kesterson N.W.R Freeport

Suisun Bay 

## San Francisco Bay

- Estuary System

Clifton Court Forebay Tracy PumpsPacificOcean 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 Rive r. An extension of the San Luis Drain would provide a constructed outlet for agricultu ral drainage from the San Joaquin Valley to the Bay

- Delta. Filled circles show locations of five major oil refineries. E nlarged arrows are for emphasis and are not representational of flow. N ot to scale.



## San Joaquin River

San Luis Drain RECYCLE 

### N

North Bay Sacramento

- San Joaquin Delta Central Bay Honker Bay Grizzly Bay

RIVER Grassland Grassland wetlands Contra Costa Canal Delta Pumps

Bypass

1981 to 1986 connection currently, no discharge Friant DamSelenium Concentration



# Water Flux Load

Concentration

El Nino summer fallSelenium 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 schemati c representation from current data depicts the effects of a large reservoir of Se on s ubsurface 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 fr om 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 ec ological 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 200000Cubic 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 25000Cubic 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 200000Cubic 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 25000Cubic 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 0.3Selenium (mg/L)



## 0 5 10 15 20 25 30 35 

# Salinity ( psu ) Selenium Dilution in Bay

- Delta Existing Conditions: Annual average

Sacramento River endmember Seawatr endmember Regional Se bsine Mixig Landward Suisun Bay Carquinez Strait San PabloBay Composite freshwater endmmber (i.e. athad of estuary) 17.5 psu Seaward Figure 11.Hypotheical dilution profiles for Sein theBay/Del t. The rgional bseine profile shows Se concentrations thru gh thesuary s concentrations n theSacrmento River arediluted by concentrat ions thePacific Ocean asidcte by salinties (practical sintyunits, p ). The xample mixing profile shows the Seconcetration n ahypot eical averg feshwater ndmmber as it is dlutedby concentrations the Pacific Ocean. This was calculated from loads n volumes in the Sacramento Rivera t 20 MAF perya plus refinery inputs of apprximately 4,000 lbs Seper ya(typical ofawet yarpior to 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 concentrati ons through the estuary as concentrations in the Sacramento River are dilute d by concentrations in the Pacific Ocean as indicated by salinit ies (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 a t 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 0.30Se (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 Bay

Delta, comparing high and low flow seasons in 1986 (4/86 and 9/8 6) 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 9Particulate Se (μg/g) 

# Se Particulate Concentrations vs. Salinity

Figure 13 . Particulate selenium profiles as a function of salinity (pract ical 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 F M A M J J A S O N D 95 J F M

A M J J A S O N D 96 J F M

A M J 97 0 5 10 15 20 25Se Concentration (μg/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.

### 3 8 **°** 0 0 ’ 1 2 2 **°** 3 0 ’ 1 2 2 **°** 1 5 ’ 1 2 2 **°** 0 0 ’



# S u i s u n B a y
C

a r q u i n e z S t

r

a i t

5 m i 8 k m 0 0 

# S a n P a b l o B a y 4

. 0 8

. 1 1 4

. 1 8

. 0 1 4

. 0 2 0

. 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 1 0

. 3 1 0

. 0

8

. 9

2 0

. 0 6

. 7 6

. 1 8

. 2

5

. 7

1 6

. 8 1 1

. 0

F i g u r e 1 6

. S e l e n i u m c o n c e n t r a t i o n s i n r e p l i c a t e c o m p o s i t e s a m p l e s o f P o t a m o c o r b u l a
a m u r e n s i s a t 2 2 l o c a t i o n s i n t h e B a y
- D e l t a d u r i n g O c t o b e r 1 9 9 6

. B i v a l v e s e l e n i u m
c o n c e n t r a t i o n s a r e g i v e n i n **μ** g S e / g , d ry w e i g h t

.

### English Sole Herring LF Smelt

No. Anchovy STR Flounder SPK Sanddab

PS Sculpin

YF Goby WHT Sturgeon Fish Species 

## 0 3 6 9 12 15Selenium (μg/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 Anchovy English Sole Sanddab Sturgeon

** includes San Pablo, Suisun, Grizzly and Honker Bays Figure 17 . Selenium concentrations in fish samples collected from the Nor th 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 1.4Composite FW endmember (μg/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 

### 5Composite FWendmember, (μg/L Se)

0 2400 4800 7200 9600 12000Se 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 μ g Se/L; San Luis Drain at 62.5 μ g Se/L) contrasted to input concentrations and loads of selenium

.

## 0

1 2 3 4 5Composite FWendmember, (mg/L Se)



## 0 5 10 15 20 25 30 35 

# Salinity ( psu ) October 1997 (wet year) Forecast SLD extension or SJR conveyance Seawatr endmember Regional Se bsine Mixig Landward Suisun Bay Carquinez Strait San PabloBay Composite freshwater endmmber (i.e. athad of estuary) 17.5 psu Seaward Figure 11.Hypotheical dilution profiles for Sein theBay/Del t. The rgional bseine profile shows Se concentrations thru gh thesuary s concentrations n theSacrmento River arediluted by concentrat ions thePacific Ocean asidcte by salinties (practical sintyunits, p ). The xample mixing profile shows the Seconcetration n ahypot eical averg feshwater ndmmber as it is dlutedby concentrations the Pacific Ocean. This was calculated from loads n volumes in the Sacramento Rivera t 20 MAF perya plus refinery inputs of apprximately 4,000 lbs Seper ya(typical ofawet yarpior to refinry cleanup).



## Carquinez Strait (17.5 psu )

Figure 21

. D ilution 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 μ g Se/L and for a SLD extension at 62.5 μ g Se/L. 

## SLD input (62.5 μ g/L)

SJR input (2 μ g/L) SJR input (1 μ g/L)

## 0

5 10 15 20 25Composite FWendmember(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

. F orecasts 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 dr y 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 50000Se 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 , m g/L Se (low flow season, head of estuary)

10

8 5 4

3

2

1

0.3 

## Dry year 1.3 MAF

Wet year 2.3 MAF

Figure 23

. C alculation of eight composite freshwater endmember selenium concentrations as derived from different combinations of total input load and total river inflow. River inflows are t he composited mass of water that reaches the estuary in a six

- month period. The range of inflows and input loads are typical of dif ferent 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 (

μ g/L) 0 1 2 3 

### September 1996 October 1996

7 8Particulate 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 10 3 and 1 X 10 4 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 4.00Particulate 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 (sa linity, psu = 0) to seaward (salinity, psu = 35) in the Bay

Delta. Three different Kd’s forecast three different trend lines for particulate concentrati ons using dissolved Se concentrations ( Figure 24 ). The observed October 1996 particulate data is superimposed o n the projections.

## 0 2 4 6 8 10 Selenium in Bivalves ( μ g/g dry wt.) 0 50 100 150 200 250 300Selenium in Scoter Liver (μg/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 20Selenium in Sturgeon Flesh (μg/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 40Selenium in Sturgeon Liver (μg/g dry wt.) 

# Bivalves vs. Sturgeon Liver

Potamocorbula

Figure 28. Relation between bivalve selenium concentrations and selenium c oncentrations in sturgeon liver. Data from California Department of Fish and Game Selenium Verification Study (White et al., 1987; 1988; 1989; Urquhart and Regalado , 1991).

## TABLESTable 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 defo rmities/deaths at Kesterson Resv. 1984 USFWS and USGS * Studies show envi ronmental 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 Wa nger 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 WaterResources 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 μ g/L daily concentration maximum limitTable 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 μ g Se/L standard for BayDelta because salt water objective of 71 μ g/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 InteragencyEcological 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 Franci sco 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 Dr ainage 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 2Table 4.Conversion factors for selenium and salt or Total Dissolved Solids (TDS).Selenium (Se)Salt or Total Dissolved Solids (TDS)1 ppb Se =1μg Se/L1 ppm TDS = 1 mg salt/L1 gallon = 3.785 Liters1 gallon = 3.785 Liters1 acre-foot = 325,900 gallons = 1,233,532 Liters1 acre-foot = 325,900 gallons = 1,233,532 Liters1,233,532μgrams Se/acre-foot at 1 ppb Se1.23 grams Se/ acre-foot at 1 ppb Se1,234 grams salt/acre-foot at 1 ppm salt454 grams = 1 lb454 grams = 1 lb0.00272 lbs Se/acre-foot at 1 ppb Se2.72 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 ton1 ppm salt = 0.00136 tons salt/acre-footVolume1 cubic foot per second (cfs) = 1.98 acre-feet/dayTABLE 5.Annual acre-feet or million acre-feet (MAF) and selenium loads from the upstream drainage source (Drainage Problem Area or Grassland Bypass ChannelProject site B) and downstream sites for Mud and Salt Sloughs, and the San Joaquin River at Crows Landing (state compliance point for SJR) and at Vernalis.WateryearUpstream 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 SeMud and Salt Sloughsacre-feet ppb Se lbs SeSan Joaquin River at Crows Landing(USEPA 5 ppb Se standard exceeded> 50% of the year in 1987, 1988,1989, 1990, 1991 and 1994; drainageprohibition of 8,000 lbs/year enactedin 1996)MAF ppb Se lbs SeSan Joaquin River at VernalisMAF ppb lbs Se198667,006529,524284,3168.66,6432.671.611,3055.221.014,601198774,9025410,959233,84312.07,6410.664.98,8571.811.88,502198865,3275710,097230,45413.08,1320.556.29,3301.172.78,427198954,186598,718211,39314.18,0990.446.37,4731.063.08,741199041,662657,393194,65614.67,7190.405.66,1250.923.07,472199129,290745,858102,16214.03,8990.294.53,5480.662.03,611199224,533765,08385,42812.62,9190.303.73,0640.701.93,558199341,197798,856167,95515.06,8710.893.58,3791.701.98,905199438,670808,468183,54616.07,9800.564.87,2701.222.37,760199557,5747611,875263,76914.910,6943.501.614,2916.301.017,238199652,9787010,034267,344139,6971.443.010,6863.951.111,431199737,48362.57,097notavailable30Mud onlynotavailable4.182.98,667-9,0546.770.611,190199845,85866.9*9,118notavailable27Mud onlynotavailable5.131.613,445-15,5018.5--15,810Dailyrange0.4 to 286(1986-1995)15 to 134(1997 and1998)0.5 to 59(1986-1995)3 to 104(1997 and1998)956 to73,458acre-feet(1997-1998)0.4 to 17(1986 –1995)0.1-8.2(1997 and1998)0.4 to 9.6(1986 –1995)0.1-8.2(1997 and1998)DATA SOURCES: 1-Drainage Problem Area) California Central Valley Regional Water QualityControl Board, 1996b;c; 1998d; e; f; g; h; 2000b; c (note: The regionalboard in 1996 recompiled data from 1985 through 1995; therefore earlierversions of the regional board’s data may be quoted insome examples); 2-Grassland BypassChannel Project monthly reports (see website,http://www.mp.usbr.gov/; selectprojects, then selectGBP) and annual reports (USBR et al., 1997, 1998, 1999).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, i rrigation 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

2000Apply 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 90,576 271,728 543,456TABLE 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., meas ured 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 Progr am (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 concentr ations; 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 Tot o, 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 μ g 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 – 1.9Table 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 pr oposed 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 μ g Se/L 816 299 60 1.0 μ g Se/L 8,160 2,990 598 2.0 μ g Se/L 16,320 5,980 1,197 5.0 μ g Se/L 40,800 14,960 2,992 50 μ g Se/L -------- -------- 29,920 150 μ g Se/L -------- -------- 89,760 300 μ g Se/L -------- -------- 179,520Table 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 perm itting 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 , 2 0 3

- 2 , 5 9 5 3

. 3

- 7

. 1 4 4 0 1

. 2 Tosco Corporation at Avon 1 8 0

- 4 8 2 0

. 4 9

- 1

. 3 1 1 8 0

. 3 2 Tosco Corporation at Rodeo (formerly Unocal) 1 , 0 4 5

- 1 , 9 3 8 2

. 9

- 5

. 3 9 8 0

. 2 7 Valero Refining Company (formerly Exxon Corporation) 3 2 1

- 7 5 5 0

. 8 8

- 2

. 1 1 3 2 0

. 3 6 Chevron Corporation 3 5 4

- 1 , 6 8 7 0

. 9 7

- 4

. 6 3 2 7 0

. 9 0 T O T A L 3 , 1 0 3

- 7 , 4 5 7 8

. 5

- 2 0

. 4 1 , 1 1 5 3

. 0 5 1986-1992 data: CSFRW Q CB, 1992 and 1993 1999 data: CSFRW Q CB, personal com m unication, Johnson Lam , 9/19/00Table 11 . Partitioning between dissolved Se and particulate or sedim e nt Se in ecosystem s for which reliable analytical data is available.

E c o s y s t e m T S e diss μ

g/L TSe Sed μ

g/g TSe Sed / Tse diss (Kd) Reference

Kesterson Reservoir (terminal pond) 14 55 4 X 10 3 Presser and Piper, 1998

Belew s Lak e ~11 ~15 1.3 X 10 3 L e m l y , 1 9 8 5 Benton Lak e Pool 1 Channel 4 10 2.5 X 10 3 Zhang and Moore, 1996

Benton Lak e Pool 2 10.4 3.5 0.34 X 10 3 Zhang and Moore, 1996

Benton Lak e Pool 5 0.74 0.35 0.5 X 10 3 Zhang and Moore, 1996

Constructed Wetland <5 - 30 2.1 - 6.7 0.3 X 10 3 Hansen et al., 1998
SLD (means) 62.5 55 0.9 X 10 3 T h i s r e p o r t Delaw a re: Tidal Freshw ater 0.17 - 0.35 0.6 - 1.5 4 X 10 3 Reidel and Sanders, 1998

Diatoms 1.1X10 5 Reinfelder and Fisher, 1991 Dinoflagellate 4.0 X 10 3 Reinfelder and Fisher, 1991 Great Marsh, Delaw a re 0.01 - 0.06 0.3 - 0.7 3 X 10 3
– 1 X 10 4 Velinsky & Cutter, 1991
Bay-Delta SPM (suspended particulate matter) 1986/1995/1996 0.1 - 0.4 1 - 8 1 – 4 X 10 4 Cutter et al., in preparation

Bay-Delta sediment 0.1 - 0.3 0.2 - 0.5 1 - 5 X 10 3 Johns et al., 1988Table 12.Seleniumconcentrations in fish (μg/g dry weight) fromthe Bay-Delta (NorthBay including Suisun, San Pablo, Grizzly andHonker Bays) and Humboldt Bay (SeleniumVerification Study, White et al., 1987; 1988; 1989; Urquhart and Regalado, 1991).flesh (μg Se/g, dry weight)liver (μg Se/g, dry weight)whole-body (μg Se/g, dw)Location/Dateaveragestddev.naveragestddev.naveragestddev.nNorth Bay (January-June, 1986)whitesturgeon7.83.1109.22.910English sole3.00.24starryflounder4.61.079.22.27longfinsmelt1.50.48Pacific staghorn sculpin2.50.286.71.08Pacificherring3.00.74speckledsanddab1.80.032northernanchovy2.10.084yellowfingoby2.40.27North Bay (March-May, 1987)white sturgeon103.713North Bay (December, 1987 and January, 1988)white sturgeon7.24.414North Bay (February, 1989 to March, 1990)whitesturgeon151162302142yellowfingoby2.0NA14.3NA13.1NA1Humboldt Bay (February and June, 1986)English sole1.80.2237.8NA1starryflounder0.913.61longfinsmelt1.20.082Pacific staghorn sculpin1.60.1343.90.463Pacific herring1.60.0824.51speckledsanddab1.60.34n = number of samples; NA = not applicableTABLE 13

. Exam ples of thresholds for Se effects (health, reproductive, teratogenesis, or survival) in fish based on concentrations of Se in food; the exam ple of m a ssive poisoning at Kesterson Reservoir, California also applies to aquatic birds. Selenium concentrati ons in the m o st abundant benthic prey (food) organism in the Bay-Delta are given for com p arison.

Concentration in food ( μ g Se/g, dry weight) Approach Response Observed Reference(s)

0.1 - 0.5 μ g/g Lab Nutritionally sufficient range. Additional nutritional benefits often observed up to 1 μ g/g. Diets containing < 0.1 μ g/g often associated with deficiency sy ndrom e. cited in Lem l y , 1998a (Hodson and Hilton, 1983)

3 - 8 μ g/g Lab, field, and sy nthesis Reproductive im pairm e nt (sim ilar threshold for birds, Skorupa and Ohlendorf, 1992; Skorupa, 1998b; see also Table 15). e.g., Engberg et al., 1998; Skorupa, 1998a; b; Lem l y , 1998a; b; Ham ilton et al., 1996; 2000b 2 - 5 μ g/g Belews Lake, North Carolina (1996) Teratogenesis in fry of four recovering fish species Lem l y , 1993b; 1997b

5 μ g/g Lab Winter stress sy ndrom e (includes m o rtality ) in juvenile bluegill Lem l y , 1993b

9 - 13 μ g/g Lab, field, and sy nthesis Reduced growth and/or m o rtality in rainbow trout and bluegill Cited in Ham ilton et al., 2000a (Goettl and Davies, 1978; Hilton et al., 1980; Cleveland et al., 1993); Skorupa, 1998b 5 - 10 μ g/g in prey (fish)

18 μ g/g in prey (fish) Lab Freshwater

Brackish

water Growth and survival affected in chinook salm on (swim

- up) larvae (SLD diet)

Growth reduced of chinook salm on fingerlings (SLD diet) Ham ilton et al., 1990

30 - 35 μ g/g Sy nthesis Com p lete reproductive failure in adult sensitive species (e.g., bluegill) Cited in Skorupa, 1998b (Coy le et al., 1993; Woock et al., 1987) 20 - 80 μ g/g Belews Lake, North Carolina (1973-1984) Massive poisoning of fish com m unity : 16 of 20 species disappear; two species rendered sterile, but persisted as aging adults; one occasionally re-colonized as adults; and one unaffected. Deform ities in survivors. Som e recovery after Se rem oval. Cum b ie and VanHorn, 1978; Lem l y , 1985; 1997b; 1998a

>100 μ g/g Kesterson Reservoir, California Massive poisoning of fish and birds, including deform ities 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 μ g/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 pressTABLE 14 . Exam ples of thresholds for Se effects (health, reproductive, teratogenesis, or survival) in fish based on Se concentrations in tissues of fish. Seleni um concentrations in tissue of white sturgeon from the Bay-Delta are given for com p arison.

Effect/Threshold Location Concentration in Tissue ( μ g Se/g, dry weight) Reference(s)
Deform ities/tissue Field •
•
• 10 - 20 μ g/g in whole hom ogenate; 6 - 12 μ g/g in m u scle (fillets) 20 - 40 μ g/g in viscera. Lem l y , 1998a

Percent deform ed larvae, fry , juveniles, or adults (e.g., centrarchids)/ whole-body Field •

•

•

•

•

• 5 - 10 μ g/g whole-body = onset of deform ities (<6%) in larvae, fry, juveniles, and adults. 11 - 20 μ g/g whole-body = <11% deform ities in juveniles and adults 25 - 35 μ g/g whole body = rapid rise in rate of deform ities in larvae of som e species (35-65%) 40 - 50 μ g/g - rapid rise in rate of deform ities = 20 - 30% in juveniles and adults. 30 - 40 μ g/g whole body = 80% deform ities in larval fish 70 - 90 μ g/g whole body = 70% deform ities in juveniles and adults Lem l y , 1997a

Growth and survival of salm on (larval; fingerling)/whole-body Lab (SLD diet) and sy nthesis • 4 - 6 μ g/g whole-body Ham ilton et al., 1990; also cited in 2000a Survival of razorbacksucker larval fish/wholebody Field • 4 - 14 μ g/g whole body Ham ilton, et al., 1996

Thresholds

• • whole body (sensitive species) Sy nthesis 4 - 6 μ g/g Skorupa, 1998b

Thresholds

•
•
•
•
• •
•
•
•
• whole body , skeletal m u scle, liver ovary and egg larvae and fry Sy nthesis 5 - 7 μ g/g 6 - 8 μ g/g 15 - 20 μ g/g 5 - 10 μ g/g (6 - 17 μ g/g, terata) 8 - 12 μ g/g (5 - 12 μ g/g, terata) Lem l y , 1998b

Thresholds

•

• •
• whole body
ovary Sy nthesis 6 (coldwater) - 9 (warm w ater) μ g Se/g 17 μ g Se/g Deforest et al., 1999

Thresholds

• • whole body Sy nthesis 4 - 12 Engberg et al., 1998 Selenium concentrations in w h ite sturgeon tissue ( μ g Se/g, dry weight) from the Bay-Delta White sturgeon 1989-1990 (Suisun, San Pablo, Grizzly, and Honker Bays) Field • 30 μ g Se/g in liver (average, n=42) (range 6 – 80 μ g/g)

• 15 μ g Se/g in flesh (average, n=62) (range 2 - 50 μ g/g) Selenium Verification Study (Urquhart and Regalado, 1991)

White sturgeon San Pablo Bay Field • ovaries 3 - 29 μ g Se/g

• plasma 5 - 9 μ g Se/g

• egg yolk components 3 - 90 μ g Se/g Kroll and Doroshov, 1991Table 15 . Exam ples of thresholds for Se effects (health, repr oductive, 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 com p arison

. Selenium in tissue ( μ

g/g, dry weight) Embryo Deformity Threshold Hatchability Threshold Reference(s)

Egg 13 – 24 (m ean egg) (field, western and northern plains, U.S.) Skorupa and Ohlendorf, 1991

Egg 12 – 15 (lab, mallard and chicken) H e i n z , 1 9 9 6

E g g 1 0 (Kesterson Reservoir, California) Skorupa and Ohlendorf, 1991; Skorupa, 1998a; b E g g 6 (m e a n ) (Salton Sea, California) Skorupa, 1998a; b
Egg 4 – 10 (Tulare Basin, California) Skorupa, 1998a; b
Egg (taxa s p ecific) duck, 15-20 stilt, 18-25 avocet, 38-60 - 6 – 7

- Skorupa, 1998a; c; pers. com m .., 2000
Egg (impaired reproduction*) >6 to > 9* Engberg et al., 1998; Skorupa, 1998a; b; Lem l y , 1998b Liver 14 – 19 Heinz et al., 1989; Heinz, 1996 Liver 23 – 32 (terata) Lem l y , 1 9 9 8 b Liver** >30** Skorupa, 1998b Diet 4 - 8 Heinz et al., 1989; Heinz, 1996 Diet 6 - 9 Ohlendorf, 1989 Diet 3 - 8 Lem l y , 1998b Se concentration range in bird (d ucks, coots, grebes, stilts) tissue ( μ

g Se/g, dry weight) From Kesterson Reservoir, California (1983-1984) Egg 2-180 Ohlendorf et al., 1986a; b; Skorupa, 1998a L i v e r 3

- 3 6 0 Presser and Ohlendorf, 1987 Se concentration (average/range) in bird tissue ( μ

g Se/g, dry weight) from the Bay-Delta (1986-1990) Liver surf sc ote r (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 sc ote r (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 ( r

ange onl y) (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 ( r

ange onl y) ( 1988) 46/26-87 (White et al., 1987; 1988; 1989)

**Presented as reproductive im pairm e nt and j uvenile and adult toxicity . Also at Ouray National Wildlife Refuge, Utah, a range of 40 to 50 μ g Se/g in bird liver was associated with adult m o rtality (Skorupa, 1998b). Review of experim e ntally induced selenosis in m a llards proposed a diagnostic Se liver criterion of 66 μ g Se/g (Albers et al., 1996).Table 16. Selenium loads em ployed in forecasts of Se im pacts. Loads were calculated for a six-m onth season. Annual loads would be two tim es higher if Se discharge is continuous (i.e., at a constant rate). Agricultural inputs fall into three groups depending on m a nagem e nt 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
( μ g Se/L or parts per billion) ( cfs cubic feet per second) ( MAF m illion acre-f eet) FLOW : Year/season WET YEAR/HIGH FLOW (lbs Se discharged in six

m onths) FLOW : Year/season WET YEAR/LOW FLOW (lbs Se discharged in six m onths) FLOW : Year/season CRITICALLY DRY/LOW FLOW (lbs Se discharged in six m onths) Agri cul t ural Drai nage via San Joaquin River (targeted load) via SLD 50 μ g/L, 150 cfs (0.05 MAF/season) via SLD 62.5 μ g/L, 300 cfs (0.11 MAF/season) via SLD 150 μ g/L, 300 cfs (0.11 MAF/season) via SLD 300 μ g/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 (m axim um 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/seasonTable 17 . Com p arison of Se hazard in the Bay-Delta and othe r environm ents. Values are Se concentrations in μ g Se/g dry wt. Hazard ratings for each set of concentrations are stated within each cell (as defined by Lem l y, 1995 and 1996b). The individual scores and total score are com p ared to listed evaluation criteria to determ ine a hazard rating (high, m oderate, low, m i nim a l, or none identified) (Lem ly, 1995). For the BayDelta, bird egg concentrations are converted from bird liver. Data sources are Lem l y , 1995; 1996a; b; 1997a; b; c for western U.S. sites and this report a nd *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 Minim a l 2 - 4 Minim a l 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 Minim a l 15 Moderate
Anim as River, Colorado and New Mexico 1 - 20 High 0.1 - 2.3 Low 1.8 - 2.9 Minim a l 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 Minim a l 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

- 1 0 5

- 1 2 9

- 1 1 Moderate 3

- 5 3

- 4 4

- 5 1 0

- 2 0 1 2

- 2 0 1 2

- 1 5 High > 5 > 4 > 5 > 2 0 > 2 0 1 6

- 2 5Table 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.

Concentration at Concentration Volumes Contribution Load Load Concentration Volume Volume Carquinez Strait FW Endmember Sum Sum lbs Se billion ug ug Se/L billion L MAF at 17.5 psu ug Se/L billion liters billion ug ug Se/L Prior to Refinery Cleanup Scenarios (No SLD extension) Wet Year (1997 data), High Flow Season (six months, December through May) 1,850 838 0.04 20961 17 Sac R. 8,160 3699 1 3699 3 SJR 0 0 0 SLD 2,040 925 150 6.165 0.005 Refineries 0.11 0.22 24,666 5,462
Wet Year (1997 data), Low Flow Season (six months, June-November) 250 113 0.04 2835.9 2.3 Sac R. 272 123 1 123.3 0.1 SJR 0 0 0 0 SLD 2,040 925 150 6.165 0.005 Refineries 0.20 0.39 2,965 1,161
Critically Dry Year (1994 data), Low Flow Season (six months, June-November) 176 80 0.04 1997.46 1.62 Sac R. 272 123 1 123.3 0.1 SJR 0 0 0 SLD 2,040 925 150 6.165 0.005 Refineries 0.27 0.53 2,127 1,128Table 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.

Concentration at Concentration Volumes Contribution Load Load Concentration Volume Volume Carquinez Strait FW Endmember Sum Sum lbs Se billion ug ug Se/L billion L MAF at 17.5 psu ug Se/L billion liters billion ug 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). 1,850 838 0.04 20961 17 Sac R. 5,440 2466 1 2466 2 SJR 6,800 3083 50 61.65 0.05 SLD 680 308 50 6.165 0.005 Refineries 0.14 0.28 23,495 6,695
b) SLD at 300 cfs and 62.5 ppb Se (18,700 lbs SLD load in six months). 1,850 838 0.04 20961 17 Sac R. 5,440 2466 1 2466 2 SJR 18,700 8477 62.5 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 0.26 0.51 23,569 12,090
c) SLD at 300 cfs and 150 ppb Se (44,880 lbs SLD load in six months).
1,850 838 0.04 20961 17 Sac R. 5,440 2466 1 2466 2 SJR 44,880 20345 150 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 0.51 1.02 23,569 23,957
d) SLD at 300 cfs and 300 ppb Se (89,760 lbs SLD load in six months). 1,850 838 0.04 20961 17 Sac R. 5,440 2466 1 2466 2 SJR 89,760 40689 300 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 0.94 1.88 23,569 44,302

Targeted SJR load of 7,180 lbs Se annually; 3,590 lbs Se in six months 1,850 838 0.04 20961 17 Sac R. 3,590 1628 1.2 1356.3 1.1 SJR 0 0 0 0 0 SLD 680 308 50 6.165 0.005 Refineries 0.06 0.12 22,323 2,774Table 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.

Concentration at Concentration Volumes Contribution Load Load Concentration Volume Volume Carquinez Strait FW Endmember Sum Sum lbs Se billion ug ug Se/L billion L MAF at 17.5 psu ug Se/L billion liters billion ug

a) SLD at 150 cfs and 50 ppb Se (6,800 lbs SLD load in six months). 250 113 0.04 2835.9 2.3 Sac R. 3 1 1 1.233 0.001 SJR 6,800 3083 50 61.65 0.05 SLD 680 308 50 6.165 0.005 Refineries 0.60 1.21 2,905 3,505
b) SLD at 300 cfs and 62.5 ppb Se (18,700 lbs SLD load in six months).

250 113 0.04 2835.9 2.3 Sac R. 5 2 2 1.233 0.001 SJR 18,700 8477 62.5 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 1.49 2.99 2,979 8,901
c) SLD at 300 cfs and 150 ppb Se (44,880 lbs SLD load in six months).

250 113 0.04 2835.9 2.3 Sac R. 5 2 2 1.233 0.001 SJR 44,880 20345 150 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 3.49 6.97 2,979 20,769
d) SLD at 300 cfs and 300 ppb Se (89,760 lbs SLD load in six months). 250 113 0.04 2835.9 2.3 Sac R. 5 2 2 1.233 0.001 SJR 89,760 40689 300 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 6.90 13.80 2,979 41,113
Targeted SJR load at 6,800 lbs Se annually; 3,400 lbs Se in six months; no SLD.

250 113 0.04 2835.9 2.3 Sac R. 3,400 1541 2.5 616.5 0.5 SJR 0 0 0 0 0 SLD 680 308 50 6.165 0.005 Refineries 0.28 0.57 3,459 1,963Table 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.

Concentration at Concentration Volumes Contribution Load Load Concentration Volume Volume Carquinez Strait FW Endmember Sum Sum lbs Se billion ug ug Se/L billion L MAF at 17.5 psu ug Se/L billion liters billion ug 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). 141 64 0.04 1602.9 1.3 Sac R. 3 1 2 0.6165 0.0005 SJR 6,800 3083 50 61.65 0.05 SLD 680 308 50 6.165 0.005 Refineries 1.03 2.07 1,671 3,456
b) SLD at 300 cfs and 62.5 ppb Se (18,700 lbs SLD load in six months). 141 64 0.04 1602.9 1.3 Sac R. 3 1 2 0.6165 0.0005 SJR 18,700 8477 62.5 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 2.54 5.07 1,745 8,850
c) SLD at 300 cfs and 150 ppb Se (44,880 lbs SLD load in six months).

141 64 0.04 1602.9 1.3 Sac R. 5 2 2 1.233 0.001 SJR 44,880 20345 150 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 5.93 11.87 1,746 20,719
d) SLD at 300 cfs and 300 ppb Se (89,760 lbs SLD load in six months). 141 64 0.04 1602.9 1.3 Sac R. 3 1 2 0.6165 0.0005 SJR 89,760 40689 300 135.63 0.11 SLD 680 308 50 6.165 0.005 Refineries 11.76 23.53 1,745 41,063

Targeted SJR load of 6,800 lbs Se annually; 3,400 lbs Se in six months. 141 64 0.04 1602.9 1.3 Sac R. 3,400 1541 2.5 616.5 0.5 SJR 0 0 0 0 0 SLD 680 308 50 6.165 0.005 Refineries 0.43 0.86 2,226 1,914Table 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%.

Concentration at Concentration Volumes Contribution Load Load Concentration Volume Volume Carquinez Strait FW Endmember Sum Sum lbs Se billion ug ug Se/L billion L MAF at 20 psu ug Se/L billion liters billion ug 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) 1,850 838 0.04 20961 17 Sac R. 3,060 1387 0.5 2774.25 2.25 SJR 0 0 0 SLD 680 308 50 6.165 0.005 Refineries 0.05 0.11 23,741 2,534 5,590 2534 50.54 23741.42 19.255 Total
Wet Year (1997 data), Low Flow Season, conveys 25% of SJR inflow (six months, June-November) 250 113 0.04 2835.9 2.3 Sac R. 1,020 462 0.5 924.75 0.75 SJR 0 0 0 0 SLD 680 308 50 6.165 0.005 Refineries 0.12 0.23 3,767 884 1,950 884 50.54 3766.815 3.055 Total
Dry Year (1994 data), High Flow Season, conveys 75% of SJR inflow (six months, December-May) 544 247 0.04 6165 5 Sac R. 1,115 506 0.5 1011.06 0.82 SJR 0 0 0 SLD 680 308 50 6.165 0.005 Refineries 0.07 0.15 7,182 1,060 2,339 1060 50.54 7182.225 5.825 Total
Dry Year (1994 data), Low Flow Season, conveys 25% of SJR inflow (six months, June-November) 174 79 0.04 1972.8 1.6 Sac R. 381 173 0.5 345.24 0.28 SJR 0 0 0 SLD 680 308 50 6.165 0.005 Refineries 0.12 0.24 2,324 560 1235 560 50.54 2324.205 1.885 TotalTable 23 . Sum m a ry of forecasts of Se concentrations in a com posite freshwater endm ember entering the BayDelta under different conditions. Load is expressed in lbs per six m onths. SLD loads are for the SLD only; targeted load and “restoration” scenario is for the SJR only. C F is a com posite concentration in all sources of freshwater at the head of the estuary (i.e. near the discharge point of a proposed SLD extension); C E is a

com posite concentration at 17.5 practical-salinity units (p su), usually near Carquinez Strait during the low flow

season. Forecast

Year/Season Prior to refinery cleanup SLD: Half capacity, 50 μ g/L SLD: Full capacity, 62.5 μ g/L SLD: Full capacity, 150 μ g/L SLD: Full capacity, 300 μ g/L Targeted Load SJR “Restorati on” in SJR 0.5 μ g Se/L
Wet/High Load (lbs/6 mo) 6 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 8 9 , 7 6 0 3 , 5 9 0 3 , 0 6 0

Conc. F ( μ g/L) 0

. 2 2 0

. 2 8 0

. 5 1 1

. 0 2 1

. 8 8 0

. 1 2 0

. 1 1

Conc. E ( μ g/L) 0

. 1 1 0

. 1 4 0

. 2 6 0

. 5 1 0

. 9 4 0

. 0 6 0

. 0 5

Wet/Low Load (lbs/6 mo) 6 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 8 9 , 7 6 0 3 , 4 0 0 1 , 0 2 0

Conc. F ( μ g/L) 0

. 3 9 1

. 2 1 2

. 9 9 6

. 9 7 1 3

. 8 0

. 5 7 0

. 2 3

Conc. E

( μ g/L) 0

. 2 0 0

. 6 0 1

. 4 9 3

. 4 9 6

. 9 0

. 2 8 0

. 1 2
Dry/Low Load (lbs/6 mo) 6 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 8 9 , 7 6 0 3 , 4 0 0 3 8 1

Conc. F

( μ g/L) 0

. 5 3 2

. 0 7 5

. 0 7 1 1

. 9 2 3

. 5 0

. 8 6 0

. 2 4

Conc. E ( μ g/L) 0

. 2 7 1

. 0 3 2

. 5 4 5

. 9 3 1 1

. 8 0

. 4 3 0

. 1 2

Criteria 2 to 5 μ g Se/LTable 24 . Sum m a ry of forecasts of Se concentrations in particulate m a terial under different conditions. Load is expressed in lbs Se/six m onths. 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 10 4 , typical of suspended sedim e nt; C2 is the concentration forecast at a Kd of 3X10 3 , typical of shallow-water bed sedim e nt; C3 is the low reactivity concentration forecast at a Kd of 10 3 . 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 μ g Se/L SLD: Full capacity,

62.5 μ g

Se/L SLD: Full capacity, 150 μ g Se/L SLD: Full capacity, 300 μ g Se/L Targeted Load SJR “Restoration” in SJR 0.5 μ g Se/L
Wet/High Load (lbs/6 months) 6 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 8 9 , 7 6 0 3 , 5 0 0 3 , 0 6 0
C1 ( μ g Se/g) 2

. 2 2

. 8 5

. 1 1 0

. 2 1 8

. 8 1

. 2 1

. 1
C2 ( μ g Se/g) 0

. 6 6 0

. 8 4 1

. 5 3 3

. 0 6 5

. 6 0

. 3 6 0

. 3 3
C3 ( μ g Se/g) 0

. 2 2 0

. 2 8 0

. 5 1 1

. 0 2 1

. 8 8 0

. 1 2 0

. 1 1
Wet/Low Load (lbs/6 months) 6 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 8 9 , 7 6 0 3 , 4 0 0 1 , 0 2 0
C1 ( μ g Se/g) 3

. 9 1 2

. 1 2 9

. 9 6 9

. 7 1 3 8 5

. 7 2

. 3
C2 ( μ g Se/g) 1

. 2 3

. 6 3 8

. 9 7 2 0

. 9 4 1

. 4 1

. 7 1 0

. 6 9
C3 ( μ g Se/g) 0

. 3 9 1

. 2 1 2

. 9 9 6

. 9 7 1 3

. 8 0

. 5 7 0

. 2 3 Dry/Low Load (lbs/6 months) 6 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 8 9 , 7 6 0 3 , 4 0 0 3 8 1
C1 ( μ g Se/g) 5

. 3 2 0

. 7 5 0

. 7 1 1 8

. 7 2 3 5 8

. 6 2

. 4
C2 ( μ g Se/g) 1

. 6 6

. 2 1 1 5

. 2 3 5

. 6 7 0

. 6 2

. 5 8 0

. 7 2
C3 ( μ g Se/g) 0

. 5 3 2

. 0 7 5

. 0 7 1 1

. 9 2 3

. 5 0

. 8 6 0

. 2 4
Guidelines 1.5 to 4 μ g Se/gTable 25 . Forecast of particulate Se concentrations at the head of the Bay-Delta estuary:

• in years with different clim ate regim e s;
• in different seasons; and

• for alternative speciation and biogeochem i cal behavior patterns. The scenarios considered are:

• a SLD extension discharge of 18,700 lbs per six m onths (full capacity, 62.5 μ g Se/L); and

• a SJR discharge of a targeted load of 3,590 lbs per six m onths for a wet year (1.2 μ g Se/L) and 3,400 lbs per six m onths for a dry year (2.5 μ g Se/L). Forecasts are com p ared to conditions prior to refinery cleanup. Forecast Com posite Freshwater Endm em ber Se ( μ g/L) Particulate Se ( μ g/g) low reactivity Kd: 10 3 ( C3 ) Particulate Se ( μ g/g) shallow sedim e nt Kd: 3 X 10 3 ( C2 ) Particulate Se ( μ g/g) biotransform ed suspended m a tter

Kd: 10 4 ( 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) W e t 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 – 4.0Table 26. Laboratory-derived physiological constants fo r Se bioaccum u lation by several species of bivalve and com posite values for a generic bivalve (data from Luom a et al., 1992; Reinfelder et al., 1997). S p e c i e s F e e d i n g r a t e (grams food/grams tissue/day) Assimilation Efficiency

(AE % ) Rate Constant of Loss k e (d -1 ) AE/ k e

O y s t e r 70 ± 6 Clam (Macom a balthica) 80 ±7 0.03 ± 0.001 2 4

. 6
Clam (Mercenaria m e rcenaria) 92 ± 2 0.01 ± 0.004 9 2

. 0
Mussel (Mytilus edulis) 74 ± 8 0.02 ± 0.007 3 7

. 0
Generic bivalve (from diatom) 0.2 79 0

. 0 2 3 9
Sorbed Se 0.2 40 0.02 2 0 Elemental Se 0.2 23 0.02 10Table 27. Selenium concentrations in a generic bivalve when exposed to different concentrations of particulate organo-Se or particulate elem ental Se (constants from Luom a et al., 1992 and Reinfelder et al., 1997). Exposure to

different concentrations of: Particulate Concentration ( μ g Se/g) Absorption Efficiency (speciation) Rate Constant of Loss (d -1 ) Tissue Concentration at Steady State

( μ g Se/g) Reference

particulate organo-Se Luom a et al., 1992; Reinfelder et al., 1997 0

. 5 0

. 8 0

. 0 2 4.0 1

. 0 0

. 8 0

. 0 2 8.0 1

. 5 0

. 8 0

. 0 2 12.0 2

. 0 0

. 8 0

. 0 2 16.0 3

. 0 0

. 8 0.02 2 4

. 0 particulate elemental Se Luom a et al., 1992; Reinfelder et al., 1997 0

. 5 0

. 2 0

. 0 2 1

. 0 1

. 0 0

. 2 0

. 0 2 2

. 0 2

. 0 0

. 2 0

. 0 2 4

. 0 3

. 0 0

. 2 0

. 0 2 6

. 0 4

. 0 0

. 2 0

. 0 2 8

. 0 5

. 0 0

. 2 0

. 0 2 1 0

. 0 8

. 0 0

. 2 0

. 0 2 1 6

. 0 Particulate concentrations of Se range from 0.3 to 3 μ g Se/g dw in brackish Bay-Delta and 0.3 to 8 μ g Se/g dw at the head of the estuary (Cutter, 1989 and Cutter et al., in preparation).Table 28 . Sum m a ry of forecasts of Se concentrations in a generic bivalve under different conditions. Load is expressed in lbs per six m onths. 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 10 4 , typical of suspended sedim e nt; C2 is the concentration forecast at a Kd of 3 X 10 3 , typical of shallow-water bed sedim e nt; C3 is the low reactivity concentration forecast at a Kd of 10 3 . Four assim ilation efficiencies have been assum e d 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 μ g/L SLD: Full capacity, 62.5 μ g/L SLD: Full capacity, 150 μ g/L Targeted Load in

SJR Particulate bi val ve Particulate bivalve Particulate bivalve Particulate bivalve Particulate bivalve Wet/High Load (lbs/6months) 6 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 3 , 5 0 0
C1-AE4 ( μ g/g) 2.2 22 2.8 19 5.1 34 10 68 1.2 8.0 C1-AE3 ( μ g/g) 2.2 17 2.8 15 5.1 27 10 54 1.2 6.3 C2-AE2 ( μ g/g) 0.66 4.5 0.84 3.9 1.5 7.0 3.1 14 0.36 1.7 C3-AE1 ( μ g/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 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 3 , 5 0 0
C1-AE4 ( μ g/g) 3.9 39 12 81 30 199 70 465 5.7 38 C1-AE3 ( μ g/g) 3.9 31 12 64 30 157 70 366 5.7 30 C2-AE2 ( μ g/g) 1.2 8.0 3.6 17 9.0 41 21 96 1.7 7.8 C3-AE1 ( μ g/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 , 8 0 0 1 8 , 7 0 0 4 4 , 8 8 0 3 , 5 0 0
C1-AE4 ( μ g/g) 5.3 53 21 138 51 338 119 793 8.6 57 C1-AE3 ( μ g/g) 5.3 42 21 109 51 266 119 625 8.6 45 C2-AE2 ( μ g/g) 1.6 11 6.2 28 15 70 36 163 2.6 12 C3-AE1 ( μ g/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 μ g Se/gTable 29. Forecast of Se concentrations bioaccum u lated by a generic bivalve at the head of the Bay-Delta estuary:

• in years with different clim ate regim e s;
• in different seasons; and

• for alternative speciation and biogeochem i cal behavior patterns. The scenarios considered are:

• a SLD extension discharge of 18,700 lbs per six m onths (full capacity, 62.5 μ g Se/L); and

• a SJR discharge of a targeted load of 3,590 lbs per six m onths for a wet year (1.2 μ g Se/L) and 3,400 lbs per six m onths for a dry year (2.5 μ g Se/L). Forecasts are com p ared to conditions prior to refinery cleanup. Forecast Composite Freshw ater Endmember

Se ( μ g/L) Low reactivity: Kd: 10 3 (C3/AE1) Particulate Se [Bioaccum. Se] ( μ g/g) Shallow sediment: Kd: 3 X 10 3

(C2/AE2) Particulate Se [Bioaccum. Se] ( μ g/g) Suspended matter: Kd: 10 4 (C1/AE3) Particulate Se [Bioaccum. Se] ( μ g/g) S L D Wet Year High Flow Season 0.5 0.5 1.5 1.5 7 5.1 27 Wet year Low Flow Season 3.0 3.0 9 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 0.57 1.7 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 0.39 1.7 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 (w ater
a n d p a r t i c u l a t e food) 2 – 5 1.5-4.0 10-40 1.5-4.0 10 - 40 1.5-4.0 10 – 40Table 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 -10.98 Constant North Bay Regression Output: Avg. ppm Se Bivalves 9.07 Std Err of Y Est Avg. ppm Se Bivalves -41.57 Constant Liver avg. ppm Se 0.77 R Squared Flesh avg. ppm Se 51.07 Std Err of Y Est 92.8 4.8 8 No. of Observations 12.5 4.8 0.74 R Squared 92.8 2.77 6 Degrees of Freedom 12.5 2.77 8 No. of Observations 15.5 2.2 4.0 2.2 6 Degrees of Freedom 137.0 5.13 7.12 X Coefficient(s) 21.3 5.13 12.5 2.01 1.57 Std Err of Coef. 3.0 2.01 36.06 X Coefficient(s) 228.0 5.73 37.8 5.73 8.83 Std Err of Coef. 263.8 6.87 51.8 6.87 174.3 7.90 35.8 7.90

Scaup Scaup Regression Output: North Bay Regression Output: North Bay -2.80 Constant Avg. ppm Se Bivalves -8.14 Constant Avg. ppm Se Bivalves 5.19 Std Err of Y Est Flesh avg. ppm Se 13.19 Std Err of Y Est Liver avg. ppm Se 0.59 R Squared 7.1 4.8 0.64 R Squared 25.8 4.8 6 No. of Observations 7.1 2.77 6 No. of Observations 25.8 2.77 4 Degrees of Freedom 3.9 2.2 4 Degrees of Freedom 9.7 2.2 12.0 5.13 29.1 5.13 3.42 X Coefficient(s) 6.57 2.01 9.63 X Coefficient(s) 13.57 2.01 1.42 Std Err of Coef. 23.93 5.73 3.61 Std Err of Coef. 65.12 5.73

Regression Output: WHITE STURGEON WHITE STURGEON -7.15 Constant North Bay Regression Output: North Bay 9.49 Std Err of Y Est Avg. ppm Se Bivalves 1.04 Constant Avg. ppm Se Bivalves 0.62 R Squared Liver avg. ppm Se 2.38 Std Err of Y Est Flesh avg. ppm Se 4 No. of Observations 9.20 4.8 0.66 R Squared 7.81 4.8 2 Degrees of Freedom 9.20 2.77 6 No. of Observations 7.81 2.77 14.19 6.87 4 Degrees of Freedom 9.84 5.13 4.33 X Coefficient(s) 35.50 7.90 7.47 5.73 2.41 Std Err of Coef. 1.68 X Coefficient(s) 12.38 6.87 0.60 Std Err of Coef. 16.81 7.90

Replaced Corbicula from 1990 '88, '89 & '90 scoter data matched to with Potamocorbula Potamocorbula, (replace Corbicula) Regression Output: WHITE STURGEON Regression Output: Scoter -3.50 Constant Avg. ppm Se Bivalves Constant Avg. ppm Se Bivalves 4.63 Std Err of Y Est Liver avg. ppm Se Std Err of Y Est Liver avg. ppm Se 0.91 R Squared 9.20 4.80 R Squared 92.8 4.80 4.00 No. of Observations 9.20 2.77 No. of Observations 92.8 2.77 2.00 Degrees of Freedom 14.19 6.87 Degrees of Freedom 15.5 2.20 35.5 11.63 137.0 5.13 3.15 X Coefficient(s) 0.91 R Squared 19.28 X Coefficient(s) 12.5 2.01 0.70 Std Err of Coef. 3.21 Std Err of Coef. 228.0 11.63 263.8 11.63 174.3 11.63 0.86 R SquaredTable 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.

WHITE STURGEON Scaup Scoter North Bay

North Bay North Bay Avg. ppm Se

Avg. ppm Se Avg. ppm Se Bivalves Liver Flesh Liver Flesh Liver Flesh avg. ppm Se Date 9.20 7.81 25.8 7.1 92.8 12.5 4.8* 1986 9.7 3.9 15.5 4.0 2.2** 1986-Humboldt 9.84 29.1 12.0 137.0 21.3 5.13* 1987 13.57 6.57 12.5 3.0 2.0*** 1988-Humboldt 7.47 65.12 23.93 228.0 37.8 5.73* 1988 14.19 12.38 263.8 51.8 6.9* 1989 35.50 16.81 174.3 35.8 7.9* 1990 35.50 16.81 174.3 35.8 11.6**** 1995-1996Table 32. Forecasts of Se concentrations in bivalves and resulting Se concentrations in livers of surf scoter, greater and lesser scaup, and white sturge on under two Se discharge conditions: 1) the SLD scenario is for 18,700 lbs per six m onths (37,400 lbs per year) and 2) the SJR scenario is for a targeted load of 3,500 lbs per six m onths (7,000 lbs per year) (SJR conditions defined earlier). All forecasts are for six m onths of discharge during the low flow season of a critically dry year. Forecast concentrations are com p ared to average Se concentrations in these organism s ( 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 ( μ g Se/g dry w t) Selenium Concentration in Liver ( μ g Se/g dw ) Scoter Scaup Sturgeon SLD

1. Low Reactivity ( C 3 / A E 1 )

2. Shallow Sediment ( C 2 / A E 2 )
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 ( C 3 / A E 1 )

2. Shallow Sediment ( C 2 / A E 2 )
3. Suspended Sediment ( C 1 / A E 3 ) 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 ( μ g Se/g dw ) C o r b i c u l a fluminea = 8

Potamocorbula amurensis =12 164 64 30

Threshold for Effects ( μ g Se/g dw ) 10 - 40 20 - 50 20 - 50 20 - 50Table 33 . Relation of Se loads, com posite freshwater endm em ber Se concentrations, particulate Se concentrations, Se bioaccum u lation by bivalves, Se bi oaccum u lation by two predators (sturgeon and scaup) and Se guidelines or concentrations at whic h 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 m i xing; and the low flow season of a dry year. Conditions prior to refinery cleanup are given for com p arison. 

### Forecast Dry year/ low flow
season ( lbs Se/six

m onths ) Composite freshw ater endmember ( μ g Se/L) Particulate ( μ g Se/g dw ) Kd = 3 X 10 3 

### (C2) Bioaccumlation, generic bivalve ( μ g Se/g dw )

AE2 (0.55) White Sturgeon Liver ( μ g Se/g dw ) Greater and Lesser Scaup Liver ( μ g Se/g dw )

SLD 6,800 2

. 1 6

. 2 2 8 8 7 2 6 1 18,700 5

. 1 1 5 7 0 2 2 1 6 6 4 44,880 1 2 3 6 1 6 3 5 1 9 1 5 5 7 SJR (targeted load) 3,500 0

. 8 6 2

. 6 1 1

. 8 3 5 1 0 5 Prior to refinery cleanup 0

. 5 3 1

. 6 1 1 3 0 6 5 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

E n vi si oned Di scharges and Sal t L o a d s 3 Planning

....................................................................................................................... ......................... 3 Specific Estim ates

............................................................................................................. ................... 5 Current Managem e nt

............................................................................................................. ............... 7
Geol ogi c Inventory and Reservoi r of Sel e ni um i n the San Joaqui n Val l e y 8 Selenium Geologic Invent ory and Mass Balance

................................................................................. 8 Prediction of Long-Term Selenium Reservoirs

.................................................................................... 9

Estima tes Ba sed o n Alluv i a l Fill—So ils Scena r io 9
E s t i m a t e B a s e d o n P a n o c h e C r e e k R u n o f f

— R u n o f f S c e n a r i o 10 Characteristics and Tim i ng of Selenium ’s Release as Drainage: Source W a ters

.............................. 12 Mobility of Selenium : Source Flow, Concentration, and Load

......................................................... 12
Control and Tim i ng

............................................................................................................. ............... 13



### FIGURES
A1. Map of San Luis Unit of the Central Valley Project (USBR, 1981). A2

. Schem a tic of Ultim ate W a terflow Cond itions of the San Luis Unit (USBR, 1978). A3

. Envisioned salt discharges and drainage volum e 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 perm ission, SJV Drainage Im plem entation Program , 1998). A6. Schem a tic 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 assum e d to be approxim a tely 42,500 lbs per year, loading to the Bay-Delta would take place, at a m i nim u m , for 63 to 304 years at the lower range of projections. Data com p ile d from Presser et al., 1990; Presser and Piper, 1998; and this report. A7. Schem a tic of relation of rate of selenium oxidation and oxygen flux. A8. Schem a tic 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 W Y 1986 through W Y 1998a and 1998b. Lower bar represents 6600 lbs. selenium . Upper bar represents 8,000 lbs selenium

.

Appendix A 1A10. CIMIS (California Irrigation Managem e nt In form ation System ) station #124 (Panoche, Fresno County) precipitation for W Y 1986 through 1998 (CDW R, 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 W Y 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 ultim ate or m a xim u m 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 stor m s of W Y 1998 for Panoche Creek. Storm runoff for W Y 1998 was m easured 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. Sam p ling was done during the storm s of W Y 1998 on a lim ited basis (Kratzer et al., in press). Extrapolations have been m a de here using the integrated area under the hydrograph for W Y 1998. Loads m easured for W Y 1998 m a y represent m a xim u m infrequent loading via Panoche Creek rather that being repres entative of annual historic loading (see text for

m o re details). The forecast Se loads for W Y 1998 form the basis of one of the forecasts of the Se reservoir in the western San Joaquin Valley (see Table A4, one large m a gnitude storm per 10, 50 or 100 years). Flow data with asterisks are approxim a ted from gage height m easurem ents
m a king load values generated from these flows also approxim a te. Loads for W Y 1997 are given for com p arison. Storm runoff from Panoche Creek for W Y 1997 was m easured at the San Luis Drain inflow by Grassland Area Farm ers (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 developm ent 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 m a nagem e nt cost (USBR, 1978; Ogden, 1988). The SLU includes agricultural lands that total over 700,000 acres in the W e stlands, Panoche, Broadview, Pacheco, and San Luis W a ter Districts of the Grassland and W e stlands subar eas (USBR, 1981). Lim iting factors were soil, topography, and drainage. Lands were considered flaw ed because of the presence of alkali (i.e., salt), hardpan (i.e., im peded 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 com p rised of Class 4 lands (i.e., lands known to have a reduced paym ent capacity for irrigation/drainage im provem e nts based on agricultural return). These were m a inly in areas directly affected by erosion from the Coast Ranges to the west (USBR, 1978). A larger segm ent of Class 3 lands (i.e., lands known to require difficult and costly m a nagem e nt) were identified adjacent to the valley trough. Through tim e, agriculture has expanded increasingly into Class 4 lands. This expansion into Class 4 lands was controversial since these lands were considered to require the m o st capital for drainage rem oval and have the least ability to pay for drainage im provem e nts. Recent plans again include further expansion
of the place of use for CVP water supplies by W W D (CH2MHILL, 1997).
Historic estim ates of drainage needs (i.e., estim ates of envisioned rates of flow or volum e of drainage in acre-feet to lower the water table) provide an interesting context for m odern estim ates. Although the am ounts of drainage for conveyance out of the SJV have increased since planning began in 1955, the design capacity of the m a in com ponent of a drainage facility has rem a ined relatively unchanged through tim e [i.e., 300 cubic feet per second (cfs)]. However, estim ates 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 exam ples of the m a ny sets of values for drainage volum e and drained acreage that exist throughout the planning history for a drain, but our re view is by no m eans exhaustive. For exam ple,
references are m a inly docum entation by or for federal agencies and joint federal and state efforts (e.g.,
Appendix A 3Hydroscience, 1977; USBR, 1978; SJV Interagency Drainage Program , 1979a; CH2M Hill, 1985; SJV Drainage Program , 1990a; USBR, 1992; SJV Drainage Im plem entation Program , 1998). A parallel set of reports that docum ent early state planning effo rts are not as extensively cited (e.g., CDW R , 1965a; b; 1969; 1974; 1978; CSW RCB, 1979). Many docum ents contain sim ilar estim ates (or reference the

sam e data) based on generalized data for future conditions. For exam ple, studies in 1979 and 1990 both state concern over 400,000 acres of affected farm land 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 engineer ing and net revenue disposal benefit of different drainage conveyances (e.g., USBR, 1955; 1962; CD W R , 1965a; SJV Interagency Drainage Program , 1979b; Brown and Caldwell, 1986), m a inly address m a nagem e nt aspects, not source loads estim ates. Com p arison of the am ount of volum e discharged per subareas is useful as a m easure of hydrologic balance and hence, the volum e of drainage expected. For exam ple, in a 1988 analysis (CH2M HILL, 1988), the Northern and Grassland subareas were considered in hydrologic equilibrium which im plies
little f u ture change in the extent of lands that need drainage. A distinction was m a de in the analysis
between m a naging the accum u lated hydrologic im balance (area of drainage affected land) and

m a naging the annual im balance (rate of water table rise). Short-term objectives would work toward hydrologic balance by stem m i ng the rate of deterioration while reclaim i ng existing problem lands would require releasing from storage a large accu m u lation of water, salt, and Se. Achieving hydrologic balance also would not achieve salt balance. Salts would continue to accum u late in the soils and aquifers of the SJV.
Besides estim ates of f

l ow and volum e, historical docum entation gave estim ates of water quality (i.e., m illigram s 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 m i d-1980’s (Presser and Ohlendorf, 1987). The am ounts of salt projected for discharge from the SJV, as a whole, help identify the m a gnitude of the salt build-up. Difference in the

am ounts of salt discharged per subarea help identify differences due to geology and hydrology in the affected areas. The affect of salinity on receiving wa ters is not considered here, only the m a gnitude of source salinity loads. Both the levels of salt and nitrate (7,604 tons of nitrate [NO 3 + NO 2 (N)] during the worst case year of 2020) were considered problem a tic in historical water-quality studies of the SLD (USBR, 1978; SJV Interagency Drainage Program , 1979a; b). Salt would aggravate problem s of salinity intrusion into the Delta thereby interf ering with benef i cial uses of Delta waters and nitrates
4would disturb the balance of nutrient levels in the estuarine system thereby causing eutrophication and high turbidity levels. Lim ited data on toxicity and concentrations of other constituents of concern (e.g., nitrate, phosphate, pesticides, dissolved oxygen, boron, arsenic, heavy m e tals) present in agricultural drainage are listed in historical reports (CDW R, 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 estim ates 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 m iles. Estim ates of the quantity of the SLU drainage discharge were calculated through the year 2080 (i.e., approxim a tely 100 years into the future) and of quality through the year 2030 (Table A1). Maxim u m quantities of drainage were not anticipated for “at least another 100 years” in the original plan. But revised estim ates showed the
“ultim ate” (i.e., m a xim u m ) quantity of drainage w ould be available by 2030 (Table A1). A hydrologic
schem a tic 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 subs urface drainage pipes (Figure A2). The
historic num erical m odel sim u lations were based on salinity m easurem ents. The m odel 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 m i nerals in the drainage water were expected to decrease”. The m odel also predicted salt concentration (m g/L total dissolved solids, TDS) w ould 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 m a xim u m of 1.5 m illion tons salt/year after 40 years of discharge, as the volum e of drainage water discharged increased (USBR, 1978). In 1979, a final report was prepared by th e SJV Interagency Drainage Program recom m e nding

com p letion of a valley-wide drain (i.e., encom p a ssing five areas, North, Delta-Mendota, San Luis, Tulare Lake, and Kern County) which would discharg e into the Bay-Delta at Chipps Island. The report also included a first stage environm ental im pact re port (SJV Interagency Drainage Program , 1979a, b).
Estim ates 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 m illion acres. Estim ated tons of salt requiring disposal ranged from 3.1 m illion to 3.9 m illion tons of salt/year for a valley-wide drain. Appendix A 5In 1983, the USBR estim ated drainage quantity and quality (i.e., concentration of salt, seven m a jor
elem ents, and twelve m i nor elem ents, but Se data wa s absent) for expected discharge to the SLD from the SLU during the period 1995 to 2095 (USBR, 1983) (F igure A3). W a ter-quality projections were based on concentration averages in the SLD for the period Septem ber 1982 to January 1983 (USBR, 1983), before the discovery of deform ities at Kester son NW R. Estim ates of drainage volum e ranged
from 84,525 acre-feet in 1995 to 274,270 acre-feet in 2095 for the com b ined discharge from the San Luis Service Area (equivalent to W W D ; 48,885 to 192,105 acre-feet) and the Delta-Mendota Service Area (encom passing Grassland subarea and other nor thern water districts; 35,660 to 82,158 acre-feet). A steady rise in discharge was predicted from 1995 to approxim a tely 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 m illion 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 determ ined the annual groundwater and salt

accum u lation. Results of these studies showed volum es of water and tons of salt recharged or discharged by specific processes (e.g., evapotranspira tion), sources (e.g., canal im ports), or reservoirs (e.g., confined aquifer). The annual salt accum u lation determ ined for the sem i -confined aquifer in
1988 for all five subareas was 3.3 m illion tons of salt/year. The annual accum u lation per subarea ranged from 1,000 tons salt/year to 1.5 m illion t ons/year, due to differing hydrology, geology, and drainage options (see later discussion). An analysis for the W e stlands subarea showed 44% of the salt
was f r om dissolution of salts internal to the SJV, 49% im ported from outside sources including irrigation water and 7% from other sources such as seepage. The predicted conditions in the W e stlands subarea showed the largest proportion of internal salt to im ported salt for the five subareas. W e stlands
subarea is the m o st im pacted by Coast Range sources of Se because of its location on the Panoche alluvial fan (Presser et al., 1990; Presser, 1994b). For the W e stlands subarea, im portation of higher quality water would have a dim i nished ef f

ect com p ared to other subareas because of this large
reservoir of salt. The Northern and Grassland subareas show high proportions of im ported salt to internal salt and relatively low salt accum u lations because of the availability of the SJR for salt discharge. A 1989 analysis for the SJV Drainage Program estim ated that salt is accum u lating at a rate of approxim a tely 100,000 tons salt/year in the Grassl and subarea (SJV Drainage Program , 1989). On a recent detailed basis, calculations for the lower SJR basin, that includes the Grassland subarea and
6recycling 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 m ean salt inflow of 917,000 tons/year) (Grober, 1996).
Re-evaluation in 1998 of salt im portation data (neglecting salt reservoir calculations as done in 1988) showed an excess of salt inflow over outflow in all subareas (SJV Drainage Im plem entation Program , 1998) (Figure A5; one railroad car is equivalent to 100 tons salt). The total annual im ported
salt was 1.5 m illion tons/year. This value does not include the calculated 620,000 tons salt/year discharged out of the valley through the SJR (SJV Drainage Im plem entation Program , 1998). No data were given for internal salt or the status of subarea salt reservoirs. The input of 1.5 m illion tons salt/year calculated as part of the 1997-re-evaluation, is the value quoted in 1978 by the San Luis Task Force that re viewed the m a nagem e nt, organization, and operation
of the SLU to determ ine the extent to which the SLU conform s to the purpose and intent of Public Law 86-488. The task force noted that planning docum ents had looked 40 years into the future (1950 to 1990): At about the 1990 level of agricultural developm ent in the San Joaquin River Basin, slightly m o re than
1.5 m illion tons of new salt will be added annually to the valley from applied irrigation water (Page 161).

Current Management The current im plem ented agricultural wastew ater m a nagem e nt plans for the five SJV Drainage Program subareas are:

• The Northern (26,000 drained acres) and Grassl and (51,000 drained acres) subareas discharge agricultural drainage to the SJR. A state perm it 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 (CCVRW QCB, 1998a). The SLD has been renam e d the Grassland Bypass Channel for this project
for re-use of a 28-m ile section of the drain.

• W e stlands subarea (5,000 drained acres, relieving salinization in 42,000 acres) has a "no discharge" policy, that is, storage of drainage in the unde rlying groundwater aquifer and use of agricultural water supplies and the aquifer for dilution. Som e consider this a recycling program (SJV Drainage Program , 1989) although it has tem poral storage, disp lacem ent, and distribution com ponents to it.

Appendix A 7Degradation of groundwater aquifers is expected to occur. Ground water with dissolved solids of greater than 2,500 m g /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 evapor ation ponds. Discovery of bird deform ities in 1987 through 1989 caused the state to call for closure of som e ponds and operation of the rem a ining ponds under perm its (CSW RCB, 1996a). State perm its have regulated evaporation pond discharges since 1993 with various areas of m itigation wetlands required (CCVRW QCB, 1993, 1997, and 1998c). Many evaporation ponds have closed or are in the process of closure; rem a ining ponds have been m odified to lessen bird-use. Docum e ntation in 1999 (SJV Drainage
Im plem entation Program , 1999d) showed the num ber of individual basins and pond operators decreasing by approxim a tely 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 sedim e nt has been accum u lating on the alluvial fans of the SJV
for 1.0 to 1.2 m illion years, originating from Coast Range sources of m a rine sedim e ntary rocks (Bull, 1964; Deverel and Gallanthine, 1989; Gilliom et al., 1989; Andrei Sarna-W o jcicki, U.S. Geological Survey, Menlo Park, CA, personal com m unication, 7/23/ 98). Figure A6 visually illustrates som e 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 invent ory com ponents). A sum m a ry of Se concentration
and load data that are the basis of the conceptual m odel of Se sources, transport, and m obility is given in Figure A6. The SJV has a net negative annual water budget (evaporation exceeds precipitation). Prior to developm ent of the water m a nagem e nt system , a perm anent shallow groundwater table only occurred in groundwater discharge zones near the SJV trough. The present shallow ground water and attendant subsurface drainage flows are m a inly the result of water m a nagem e nt including m a ssive irrigation.
Micro-m a nagem e nt seem ingly has enabled agricultura l production to continue at a high rate without
excessive abandonm ent of lands.

8An estim ate of the tim e necessary to discharge the accum u lated Se from the aquifers and alluvial fans of the SJV can provide som e perspective on th e size of the geologic and hydrologic reservoirs of
Se. Estim ates of the geologic and hydrologic reservoirs of Se within the alluvial fans and in the valley also provide perspective on the am ount of Se potentially available for discharge via a drainage conveyance. Such estim ates are necessary to understand the m i nim u m bounds on how m u ch Se would be discharged over the course of tim e 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 prelim inary
calculation of the reservoir of Se within the alluvial f a ns of the SJV; that is, the Se potentially available for discharge via a drainage conveyance over the long-term . To determ ine the tim e necessary to discharge the accum u lated Se from the alluvial fans of the SJV, two m e thodologies for estim ating 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 am ount 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 m i crogram s Se per gram or parts per m illion (ppm ). Across the conterm i nous 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 (Tidba ll 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 (m axim um ungridded value 4.5 ppm ). The geom etric m ean for the Panoche Creek alluvial fan is 0.68 ppm Se (1985, 721 sites, 1.6 kilom e ter interval, 66-72 inch depth). Tidball et al. (1986; 1989) also found a geom etric m ean of 0.14 ppm for the SJV western slope (1983, 297 sites,
10 kilom e ter intervals, 0-12 inch depth). The Se concentration in soils was extrapolated to estim ate the am ount of Se in the soil reservoir of the Panoche Creek alluvial fan. An average c oncentration of 0.68 ppm Se was em ployed along with
several estim ates of affected acreage, soil densities, and soil depths. Selenium deposition under the Appendix A 9various conditions ranges from 2.7 to 356 m illion pounds (lbs) Se (Table A2). If a rem oval 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
estim ate does not factor in the loading that would occur over the course of that tim e due to further weathering and runoff from the Coast Ranges, nor the am ount of Se in the groundwater reservoir.



### Estimate Based on Panoche C reek Runoff—Runoff Scenario

No com p lete sets of data (i.e., flow, Se concentration in water and sedim e nt, and am ounts of
sedim e nt) exist for Panoche Creek prior to 1997. Reconnaissance in 1987 to 1988 (Presser et al., 1990)
showed dissolved Se concentrations of 44 to 57 μ g/L in runoff sam p les. Suspended sedim e nt Se concentrations were relatively low (1.2 to 2.9 ppm Se), but the volum e of sedim e nt relatively high (10% or 91,500 m g /L). Estim ation of runoff transported in the SLD in water year (W Y) 1995 (a water year begins on October 1 st ), when extrem e 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 (CCVRW QCB, 1996a; b; Presser and Piper, 1998). This am ount 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 m a jor storm of W Y
1997 was estim ated at 137 lbs Se based on m onitoring downstream channels (USBR et al., 1998; Table B8). This am ount represents 1.9% of the annual load discharged to the SJR in W Y 1997. In 1998, 487
lbs was estim ated 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 approxim a tions of anecdotal events and only shoul d be used to assess the order-of-m a gnitude for runoff loads during an extrem ely wet year in W Y 1995 (total precipitation greater than 11.5 inches)
and a short duration series of storm s (total precipitation of 0.6 inches) in W Y 1997.

10 The rate of sedim e nt and Se loading has been under study at Panoche Creek only since Septem ber 1997 (U.S. Geological Survey, 1999; Kratzer et al., in press). The recently installed gaging station provides flow data and hydrographs for W Y 1998 stor m s . Storm s of W Y 1998 were the result of an El
Nino year of precipitation and therefore represent an extrem ely wet year (see below, occurrence interval of large m a gnitude storm s ). Sedim e nt and water sam p les were taken during flood events to
determ ine 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 m easured inrunoff discharged from Panoche Creek for two storm s was 5,995 lbs Se (Table A3). Estim ation of two intervening storm s shows a total of 2,050 lbs. The to tal of the these forecast runoff loads of Se for W Y 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 sedim e nt is relatively low (1-2 ppm Se) (Presser et al., 1990; T. Presser, unpublished data), the large volum e of m a terial leads to a high load in the particulate

m a terial as com p ared to the dissolved load. Calculations cannot be m a de at this tim e to estim ate the load of Se discharged from the watershed to receiving waters to com p are to input loads because of the lack of adequate downstream m onitoring stations. So influx and efflux cannot be directly com p ared. However, 8,045 lbs Se/year source influx m easured in the extrem ely wet year of 1998 is com p arable to
the state lim itation on discharge from the SJV via the SJR, that is, an efflux of 8,000 lbs Se/year (CCVRW QCB, 1996c). In general though, under average rainfall am ounts, the annual load from these
natural sources is calculated to be a sm all 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 m a gnitude storm occurs, are the influx am ounts significant

com p ared to efflux am ounts currently regulated. The Se discharge data for Panoche Creek for W Y 1998 were extrapolated to give estim ates of the

am ount of Se deposition that has occurred over a tim e period of either 0.5 m illion years or 1.1 m illion years to give a range of accum u lation. Deposition over these two tim e periods was calculated for one large m a gnitude storm in 10 years, one large m a gnitude storm in 50 years, or one large m a gnitude

storm in 100 years. Table A4 shows am ounts of total Se, dissolved Se, and suspended Se deposited under those conditions. The range of dissolved Se deposition over 0.5 m illion years is 13 to 86 m illion
lbs Se and over the course of 1.1 m illion years, 28 to 188 m illion lbs Se. The range of suspended Se deposition over the course of 0.5 m illion years is 67 to 449 m illion lbs Se and over the course of 1.1

m illion years, 147 to 989 m illion lbs Se. The range of total Se deposition over the course of 0.5

m illion years is 80 to 535 m illion lbs Se and over the course of 1.1 m illion years, 175 to 1,177 m illion
lbs Se. If the rem oval 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 estim ates do not factor in the loading that would occur over

Appendix A 11the course of that tim e due to further weathering and runoff from the Coast Ranges. The estim ate does

attem p t 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 m obility, are determ ined by a

com b ination 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 m obility from source geologic form ations of the Coast Ranges and the adj acent 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 m obile in aqueous system s, 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 m a y approach a constant value and Se rem a ins in its highest oxidation state (i.e., +6,
SeO 4 = ) (Figure A7). Source agricultural drainage waters are selenate-dom inated, a fact of m a jor significance in determ ining the m obility of Se in surface water and groundwater system s and, hence,
the extent and im pact of Se in drainage wate r discharges (e.g., subsurface drainage) from those system s. 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 f r om data collected (USBR et al., 1999) during frequent sam p ling of dr ainage source water (i.e., current agricultural discharges to the SJR in W Y 1997 and 1998 from the Gr assland 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 extrem ely wet years (i.e., the m a xim u m 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 indicati on of the m a gnitude of the Se reservoir and the conditions under which displacem ent of variable-quality shallow ground water m a y occur. Selenium load in source water also increases as a result of increased water flux (Figure A8). The com b ined effect of increasing concentration and increasing flow as water flux increases assures an increase in Se load discharged as m o re irrigation water is applied or m o re precipitation falls.

12Control and Timing The highest annual loads from agricultural drainage in the SJV (Figures A9) are discharged in years
of norm a l or above average precipitation (CCVRW Q CB, 1996b; c; 1998d; e; f; g; h; 2000b; c; CDW R , 1986-1998) (Figure A10) (also see later discussion). Regulatory load targets also are highest during February, March, April, and May, reflecting agri cultural practices (Figure A11) (USBR, 1995;
CCVRW QCB, 1996c; 1998a). It is possible that dilution afforded during wetter years by the increased
volum e of water in rivers could decrease salt and Se concentrations at com p liance points in the SJR, or especially in the Bay-Delta, seaward from the inflows of the Sacram ento 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 predom inantly Se-laden water. An out-of-valley agricultural drainage discharge to the Bay-Delta also m a y be subjected to these natural or seasonal effects (see later discussions on m odeled discharge to the SJR). The effect could be larger loads to receiving waters during wet seasons than

m i ght otherwise be expected through m a nagem e nt. Control of release of agricultural discharge to take advantage of the high-volum e river flows was suggested in 1955, when the SLD was planned and throughout m a ny of the later planning reports (e.g., SJV Interagency Drainage Program , 1979a; b). Recently, the SW RCB Draft Environm ental Im pact Report (DEIR) for Im plem entation of the 1995 Bay-Delta W a ter Quality Control Plan concluded that scheduling the release of subsurface agricultural drainage from the western SJV is crucial to m eeting the Bay-Delta water-quality standards including salinity (CSW RCB, 1997). Further docum entation in the DEIR of future drainage system s conceptualizes the tem porary control of drainage discharges stored in the soil profile using a system of valves, weirs, and sum p s. A sim ilar m a nagem e nt technique using “DOSIR” valves is in practice in the Grassla nd subarea to enable storage of subsurface drainage [Grassland Area Farm ers (GAF), 1997; USBR et al., 1999]. Grassland area farm ers in discussions with regulators have pointed out the effect of this type of storage technique by calculating the am ount of Se they have not discharged to the SJR on an annual basis (e.g., W Y 1997, 3,680 lbs Se not discharged

com p ared to 7,097 lbs Se discharged) (USBR et al., 1999). These types of drainage m a nagem e nt activities em phasizes the im portance of the consideration of the reservoir of Se and of docum enting the Se inventory as opposed to focusing on short-term av erages of discharges representing annual leaching to sustain a year-to-year farm ing effort. Appendix A 13

# 0

50000 100000 150000 200000 250000 300000Drainage (acre-feet)



# 0 0.5 1 1.5 2Salt (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).

### F i g u r e A 5

. S u r f a c e w a t e r s a l t i n f l o w / o u t f l o w ( r a i l r o a d c a r s p e r d a y ) f r o m t h e w e s t e rn S a n J o a q u i n V a l l e y ( p r i n t e d w i t h p e r m i s s i o n , S J V D r a i n a g e I m p l e m e n t a t i n P r o g r a m , 1 9 9 8 )

.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

ppmSan Joaquin River



# San Francisco Bay/DeltaCOAST RANGES

Panoche FormationSIERRA 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 rese rvoir of selenium within the western San Joaquin Valley If the discharge rate from the valley is assumed at approximatel y 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 (se e Tables A2 and A4). Data compiled from Presser et al., 1990; P resser and Piper, 1998; and this report. Scenarios:Selenium Concentration



## Water Flux 

# Load Concentration

El Nino summer fall

Figure A8. Schematic of selenium load and selenium concentration as a function of water flux.Selenium LoadRate 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 20000Selenium (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 18Precipitation (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 1200Selenium, (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 A1Historical (USBR, 1978) prediction of drainage from San Luis Unit (San Luis ServiceArea and the Delta-Mendota Service Area). The ultimate or maximum condition is drainage of 300,000 acres.SJV Interagency DrainageProgram 1975 estimatedacre-feet/yearUSBR 1977 estimatedacre-feet/yearUSBRmodeled*tons salt/year198020,0003,10043,7101985-8,700159,210199047,00019,000317,300200064,00033,100521,400201071,000107,4001,385,460202078,000152,3001,538,230203088,000154,1001,094,110204098,0002050107,0002060114,0002070122,0002080129,000Ultimate150,000* Model predictions verified by sampling andanalyses of drainage waters (USBR, 1978)TABLE A2Forecast selenium reservoir in San Joaquin Valley based on soils of the Panoche Fan.Panoche CreekAlluvial FanSoils ScenarioAcreageDepthMeters*Densitygrams/cm2*SoilSe**(ppm)ReservoirMillion lbs Se(M lbs Se)ksts(17,400 lbs Se =1 kst)Assumed removal rate42,785 lbs Se/year*(*seeTable 5orgeneralized314,000 AF@50 ppb)Years ofloading toBay/DeltaProblem acreage(SJVDP, 1990a)444,0002(6.6 feet)2.00.6810.862142,785 lbs/year(0.043 M lbs/year)252444,00021.460.687.744242,785 lbs/year(0.043 M lbs/year)180444,00015(50 feet)1.460.68593,39142,785 lbs/year(0.043 M lbs/year)1,379444,00091(300 feet)1.460.6835620,46042,785 lbs/year(0.043 M lbs/year)8,321Panoche FanAcreage*160,00021.460.682.715542,785 lbs/year(0.043 M lbs/year)63160,000151.460.6820.311,66742,785 lbs/year(0.043 M lbs/year)474160,000911.460.681237,06942,785 lbs/year(0.043 M lbs/year)2,875*Bull, 1964** Tidball et al., 1986; 1989TABLE 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 av ailable. 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 ma y represent maximum infrequent loading via Panoche Creek rather that being representative of annual historic loading (see text for mo re 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 137TABLE A4Forecast selenium reservoir inSan Joaquin Valley based on storm runoff from Panoche Creek (seeTable 3Afor data used for extrapolation).Panoche Creek Alluvial Fan Depositionand Recharge Scenariomillion lbs SeTOTAL(dissolved plussuspended)million lbs SeDISSOLVED(dissolved16% of total)million lbs SeSUSPENDED(suspended84% of total)ksts(17,400 lbs Se= 1 kst)(range)AssumedRemoval RateM lbs Se/ year(see Table 5,42,785lbs/year)Years ofloading toBay-Delta(range basedon total Se)Minimum yearsof loading toBay-Delta(based ondissolved Se)0.5 million years1 large magnitude storm year/10 yearsTOTAL345-53555-86290-4493,161-30,7470.0438,064-12,5041,2850.5 million years1 large magnitude storm year/50 yearsTOTAL140-38722-62118-3251,264-22,2410.0433,272-9,0455140.5 million years1 large magnitude storm year/100 yearsTOTAL80-18813-3067-158747-10,8040.0431,870-4,3943041.1 million years1 large magnitude storm year/10 yearsTOTAL759-1,177121-188638-9896,954-67,6440.04317,740-27,5102,8281.1 million years1 large magnitude storm year/50 yearsTOTAL240-49938-80201-4202,184-28,6780.0435,609-11,6638881.1 million years1 large magnitude storm year/100 yearsTOTAL175-41528-66147-3481,609-23,8500.0434,090-9,700654

## APPENDIX B

San Joaquin Valley Agricultural Drainage Projections

## APPENDIX B San Joaquin Valley Agricultural Drainage Projections

CONTENTS
Projected L oad i n gs from H i stor i c Data and E v i d ent i ary T e st i m o n y 4



### Westlands Water District and Subarea

....................................................................................... 4 Projections from Historic Data

................................................................................................. ........ 4 Projections from Evidentiary Testim ony

......................................................................................... .5 Grassland Subarea (W Y 1986-1996)

............................................................................................... .... 6

Projections from Historic Data

................................................................................................. ........ 6 Grassland Bypass Channel Project (Reuse of the San Luis Drain, W Y 1997 to present)

................ 8
W e stlands Subarea in Com b ination with Grassland Subarea

............................................................ 10 Projections from San Joaquin Valley Dr a i n a g e P r o g r a m M a n a g e m e n t O p t i o n s 11
P r o j e c t i o n s f r o m C u r r e n t l y A v a i l a b l e D a t a 12
E s ti mates of Capaci ty of Drai nage Conv eyance (i .e., proposed SL D extensi o n ) 15
T o tal fl ux from Agri cul t ural Drai nage Di scharge (l bs Se/ d a y ) 15



### FIGURES

B1a. Annual selenium load projections (lbs) at 50 ( μ g Se/L) for drainage discharges from the Northern, Grassland, W e stlands, Tulare, and Kern subareas. B1b. Annual selenium load projections (lbs) at 150 ( μ g Se/L) for drainage discharges from the Northern, Grassland, W e stlands, Tulare, and Kern subareas. B1c. Annual selenium load projections (lbs) at 300 ( μ g Se/L) for drainage discharges from the Northern Grassland, W e stlands, Tulare, and Kern subareas. B2a. Projected drainage volum e and annual selenium loads for variable selenium concentrations (50,150,300 μ g/L) for the Northern subarea. B2b. Projected drainage volum e and annual selenium loads for variable selenium concentrations (50,150,300 μ g/L) for the Grassland subarea. B2c. Projected drainage volum e and annual selenium loads for variable selenium concentrations (50,150,300 μ g/L) for the W e stlands subarea. B2d. Projected drainage volum e and annual selenium loads for variable selenium concentrations (50,150,300 μ g/L) for the Tulare subarea. B2e. Projected drainage volum e and annual selenium loads for variable selenium concentrations (50,150,300 μ g/L) for the Kern subarea.

Appendix B 1 B3a. Projected drainage volum e and annual selenium loads for select m i nim u m and m a xim u m selenium concentrations for the Northern subarea.B3b. Projected drainage volum e and annual selenium loads for select m i nim u m and m a xim u m selenium concentrations for the Grassland subarea. B3c. Projected drainage volum e and annual selenium loads for select m i nim u m and m a xim u m selenium concentrations for the W e stlands subarea. B3d. Projected drainage volum e and annual selenium loads for select m i nim u m and m a xim u m selenium concentrations for the Tulare subarea. B3e. Projected drainage volum e and annual selenium loads for select m i nim u m and m a xim u m selenium concentrations for the Kern subarea. B4a. Projected m i nim u m annual selenium loads (lbs perday) for the Northern, Grassland, W e stlands, Tulare, and Kern subareas. B4b. Projected m a xim u m annual selenium loads (lbs perday) for the Northern, Grassland, W e stlands, Tulare, and Kern subareas.



### TABLES
B1. W e stlands W a ter 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 μ g/L for W W D drainage and 62.5 μ g/L for Grassland Area drainage 1) if drainage to the San Luis Drain is to resum e by W e stlands W a ter District; and 2) if drainage to the San Luis Drain is to resum e by W e stlands W a ter District and drainage by the Grassland Area Farm ers 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 volum es and selenium concentrations for Zones A, B, and C. B4. Annual acre-feet, selenium concentrations, and selenium loads from the Grassland Area Farm ers 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 m easured at the San Joaquin River near Patterson/Crows Landing. B7. Annual acre-feet, selenium concentrations, and selenium loads m easured at the San Joaquin River near Vernalis.
B8. San Luis Drain Re-use Project/G rassland Bypass Channel Project (1997-2001) B9. San Luis Drain Re-use Project/Grassland Bypass Channel Project W Y 1997 Average Monthly Drainage Volum e s and Selenium Concentrations, Annual Discharge, and Load Targets B10. San Luis Drain Re-use Project/Grassland Bypass Channel Project W Y 1998 Average Monthly Drainage Volum e s 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 im plem entation of the recom m e nded SJVDP Managem e nt Plan (1990). The without future (i.e., no im plem entation of a m a nagem e nt plan) includes abandonm ent of lands due to salinization. B13. The SJVDP 1990, 2000, and 2040 volum es of drai nage with no drainage im provem e nt (0.75 acre-feet/acre) or m i nim a l im provem e nt ( 0.55 acre-feet/acre). The conditions without im plem entation of SJVDP m a nagem e nt plan is designated by the SJVDP as the without future alternative and includes abandonm ent of lands due to salinization. An additional calculation is
2m a de for W e stlands based on upslope contributions to the tile drained acreage from non-tile drained acreage (SW RCB, 1985). B14. Calculated volum e of drainage using a draina ge im provem e nt factor of 0.40 acre feet per acre per year. The alternative with im plem entation of the SJVDP m a nagem e nt plan is designated by the SJVDP as the with future alternative. An additional calculation is m a de for W e stlands based

on upslope contributions to the tile drained acreage from non-tile drained acreage (SW RCB, 1985). B15a. Projections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Program problem water volum es ( without future alternative, 0.60 to 0.75 acrefeet/acre/year) and a 50- μ g/L Se concentration in drainage discharge. B15b. Projections of annual selenium loading pe r subarea for year 2000 using San Joaquin Valley Drainage Program problem water volum es ( without future alternative, 0.60 to 0.75 acrefeet/acre/year) and a 150- μ g/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 volum es ( without future alternative, 0.60 to 0.75 acrefeet/acre/year) and a 300- μ g/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 μ g/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 μ g/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 μ g/L. B17. Our projections of annual selenium loading for subareas for year 2000 using Se concentrations of 50 ppb, 150 ppb, and 300 μ g/L and SJVDP volum es of problem water without future alternative , of drainage volum es in the without future alternative, of drainage volum es in the with future alternative, and with targeted future alternative. B18. Sum m a ry of projections of annual selenium loads by SJVDP subareas for year 2000 (for details concerning drainage volum es and acreage used in calculations see Tables 13, 16a, b, c). Scenarios 1, 2, 3: assigned selenium concentrations of 50, 150, 300 μ g/L Se and SJVDP estim ates of drainage volum e. 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 generali zed projected annual selenium discharge from the western San Joaquin Valley to a San Luis Dr ain extension to the San Francisco Bay-Delta. A selenium concentration of 50 μ g/L Se was hypothesized to be attainable with treatm e nt; a concentration of 150 μ g/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. Appendix B 3

## APPENDIX B San Joaquin Valley Agricultural Drainage Projections

Projected Loadings from Historic Data and Evidentiary Testimony Envisioned drainage volum es were presented in earlier discussions concerning the sustainability of discharge from the SJV and the conditions of wate r-quality in ground- water aquifers (Appendix A). Presented here are projections for the W e stlands, Grasslands, Tulare, Kern, and Northern subareas
based on lim ited available m easurem ents of drainage discharge and planning estim ates.



### Westlands Water District and Subarea

Projections from Historic Data
W e stlands subarea projections are based on lim ited historic m easurem ents of drainage discharge
from W W D into the SLD from 1981 until closure of the SLD in 1986 and planning estim ates used in hearing testim ony by W W D . Using a historical range of 330 to 430 μ g 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 am ounts are higher than those estim ated in the USBR Kesterson Program 1986 Environm ental Im pact Statem ent (EIS) as having occurred over the 57-m onth period of SLD operation (January 1981-Septem ber 1985, average of 4,776 lbs Se/year) (USBR, 1986). A recent

com p ilation from W W D indicates a discharge of 38,450 acre-feet from January 1981 through May 1986 (W W D , 1998). The estim ate of the total am ount of Se discharged to Kesterson Reservoir from 1981-1985 was 22,660 lbs (USBR, 1986). The estim ated input of Se includes 17,400 lbs that were distributed in the water, biota, and sedim e nt of Kesterson Reservoir and 5,280 lbs of Se contained in 95,271 cubic yards of bed sedim e nt still residing in the SLD. Selenium transferred from the seleniferous agricultural drainage water-colum n to the sedim e nt contributed to the Se load rem a ining in
the bed sedim e nt. The 17,400-lbs am ount is hereafter referred to as one kesterson (kst). This am ount represents a unit of m easure of potential cum u lative hazard to wildlife based on load directly released

4into an ecosystem (Presser and Piper, 1998). It will be used later for com p arison to provide a historical perspective.

Projections from Evidentiary Testimony Evidence presented in 1996 referred to estim ates prepared in 1965 for planned discharges from
W W D , before em phasis was placed on efficient on-farm water m a nagem e nt in the 1980’s (W W D , 1996). Table B1 shows the planned discharge in 1980 in com p arison to the Se loading estim ated to
have occurred from 1981 to 1985. The 1980’s plans were expressed as volum es of drainage or acreage to be drained. If the 330-430 μ g Se/L concentration range is used in conjunction with
estim ates of 38,000 acre-feet of annual drainage di scharge, then plans were for discharge of 34,109- 44,445 lbs Se/year from 76,000 acres in W W D (W W D , 1996). Using these estim ates, the am ount of drainage generated per acre is 0.50 acre-foot/acre. Calculated am ounts 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-m ile segm ent of the SLD in 1986, W W D 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 pl anning process as a justification for the out-of-valley
drain. Trade-offs were to be am ong lands kept in production, water export from the Bay-Delta, ground-water quality, and SJR degradation (USBR, 1978). The SJV Drainage Program in 1990
estim ated the rem a ining life of the sem i -confined aquifer beneath the W e stlands subarea (576,000 acres) at a m ean of 110 years (aquifer water-quality greater than 2,500 ppm TDS at a thickness of from 150 to 220 feet at current pum ping rates). Minim u m life rem a ining in som e areas of the western SJV was as low as 25 years. Several evidentiary proceedings concerning the disposition of drainage from W W D and the SLU have resulted in judgm ents and testim ony concerning the quantity of drainage (Table B2) ( WWD , 1996). Annual drainage discharge from the SLU of the CVP was estim ated as part of the Barcellos decision (1986) to be an am ount 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 μ g Se/L, the am ount of annual loading from the SLD would range from 8,160-81,600 lbs Se/year (Table B2).

Appendix B 5Estim ates presented in testim ony in 1996 of drainage from W W D include 42,000 acres in the
northeastern corner of W W D , where subsurface drains have been installed but are not connected to the
SLD. The evidence stated that an additional 29.5 m iles of SLD will be constructed to reach this area if drainage is to be provided for all areas of W W D needing drainage. Data for the annual volum e of drainage (1,900-2,300 acre-feet) to be discharged upon initial reconnection to the SLD from W W D is not well justified, but is presented for com p arison to those estim ates given by W W D in 1980 (i.e., 7,000 acre-feet/year). The evidence presented shows a total problem acreage of 200,000 acres for
W W D , with 60,000 acre-feet of drainage generated annually (W W D , 1996). This estim ate represents a 0.3 acre-feet/acre rate of generation of drainage. Using assigned Se concentrations of 50, 150, and 300

μ g Se/L, projected Se loads of 8,160 to 48,960 lbs Se/year were calculated for W W D, with an initial hook-up contributing 258 to 1,877 lbs Se (Table B2).

Grassland Subarea (WY 1986-1996)

P r o j e c t i o n s f r o m H i s t o r i c D a t a Although provision of a drainage outlet was initially focused on W W D, parts of the Grassland subarea are within the SLU for which drainage is re quired (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 approxim a tely 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 m a inly 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 dr ainage of poor enough quality to im pair state beneficial uses of receiving waters and therefore is the focus for drainage analysis. The water and drainage districts of the Grassland subarea con tinue to consolidate into regional groups based on varying needs and legal ram i fications, adding to th e already com p lex historical alignm ents (USBR, 1992; Environm ental Defense Fund, 1994). The Se discharge to the SJR from the state- designated Grassland Drainage Area has been

m onitored since 1986 and is continuing currently ( CCVRW QCB, 1996b; c; 1998 d; e; f; g; h; 2000b;c;
6Henderson et al., 1995; USBR et al., 1998; 1999). Di scharge occurred in the sam e configuration through the period 1986 to 1996 (drains to Grassland wetlands to SJR). Tables B4-B7 give sum m a ries of the data for Se loads on a water-year basis from 1986 to 1998. An annual 8000-lb Se prohibition (CCVRW QCB, 1996c and 1998a) has been im posed 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 W Y 1997 and 1998 Se loads m easured further downstream in the SJR at Crows Landing is applicable to the state 8,000-lb prohibition lim itation for Se discharge to the SJR effective October 1, 1996 (CCVRW QCB, 1998b). The Se load for the SJR at Crows Landing was 8,667 lbs Se in W Y 1997 (CCVRW QCB, 1998h) and 15,501 lbs Se in W Y 1998 (USBR et al., 1999).
Selenium is persistently discharged from the Grassland area to the SJR, but Se load values are dependent on the m onitoring site location within the Grassland area (Tables B4-B7). The upstream drainage source discharge represents m a naged com ponents of flow and load. Annual data are not
available for individual farm -field sum p s 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, approxim a tely 50 m iles downstream from the farm agricultural discharge sum p s), and the SJR at Vernalis (VERN, approxim a tely 130 m iles downstream
from the agricultural discharge). Data for W Y 1986 to W Y 1998 generally can be related to physical variables that affect drainage conditions (e.g., A ppendix A, Figure A10, annual rainfall m easured at station #124, com p iled from CDW R database). Noted clim atic changes during this tim e 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 W Y 1986 to 1988 reported an annual average of 10,850 lbs Se per year (Environm ental Defense Fund, 1994). The range of annual loads for W Y 1986 to 1998 for the

m a naged source discharge is from 5,083 to 11,875 lbs Se/year (Table B4). For the sam e tim e period, the range of annual loads for the state com p liance 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
W Y 1986 to W Y 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) st ate control plans for agricultural drainage issued in 1985 and 2) joint federal-state agricultural drainage m a nagem e nt 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 enactm e nt in 1996. For W Y 1986 through W Y 1998, the cum u lative Se load discharged to the SJR Appendix B 7at Crows Landing/Patterson is 114,879 lbs Se (Table B6). This equates to 6.6 kestersons (ksts) as a

m easure of potential cum u lative hazard based on load (see later discussion) (Presser and Piper, 1998). Of course, all sources, reservoirs, and discharg es of Se are not known for the SJR system

. As described earlier, regulatory efforts through enactm e nt 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 we tland contam ination (i.e., drains to SLD to Mud Slough to SJR). Table B3 shows estim ates by the SJ V Drainage Program of potential drainage from the zones of the Grassland subarea. They assum e d concentrations of 2 μ g 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 estim ated at either 10,700 acre-feet containing a Se concentration of 150 μ g Se/L or 21,000 acrefeet containing a Se concentration of 75 μ g 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

m easured 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 μ g Se/L from approxim a tely 90,000 acres yielded 7,097 lbs Se in W Y 1997, Table B8) and those m easured 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 W a shington, D.C., as part of
testim ony on continuing agricultural drainage issues (U.S. House of Representatives, 1993). Although,
environm ental concerns were voiced, the interim

- use project was seen as a way to relieve the pressure of a long-standing problem agricultural drainage pr oblem in the SJV (U.S. House of Representatives, 1993). On Septem ber 23, 1996 a cooperative project am ong agricultural, governm e nt, and
environm ental parties was initiated by the USBR (1995), which reopened the SLD on an interimfiveyear basis. The drain transports drainage to the SJR and thereby rem oves it from wetland channels.
Nam e d the Grassland Bypass Channel Project (GBCP), the project focuses on the use of a 28-m ile portion of the SLD to provide drainage for approxi m a tely 97,400 acres in the Grassland subarea. The Grassland Bypass Channel Project is a regional ef f

o rt to im prove water quality by regulating Se loads.The goals include: 1) m easuring and eventually reducing drainage loads through a regional program ; 2) protecting riparian wildlife habitat by assuring the we tlands of an adequate clean-water supply; and 3)

exam ining possible adverse effects that m a y result from the routing of drainage through the SLD and Mud Slough to the SJR. The GBCP contains com m itm ents to m eet and further define environm ental concerns for wetlands and the SJR. A regional draina ge agency that includes local water and drainage districts has been created and assigned responsibility for pollution. A federal/state interagency

com m ittee m onitors flow, water-quality, sedim e nt qua lity, 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 m a nagem e nt 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 com m itm ent that the input loads to the SJR “will not worsen” over historical loads (USBR, 1995). Appendix A (Figure A11)
shows the m onthly load targets adopted for the firs t two years of Grassland Bypass Channel Project.
Com p liance loads are m easured at the discharge of the SLD into Mud Slough rather than at the SJR at Crows Landing, as previously regulated by the state (CCVRW QCB, 1996c). In Septem ber 1998, a waste discharge perm it was issued for the GBCP by the state (CCVRW QCB, 1998a), which contained the negotiated load targets. Tables B8, B9, and B10 show the annual and m onthly 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. Al so shown is the state’s prohibition of drainage discharge lim itation for the SJR, which lim its Se discharge to the SJR and tributaries to 8,000 lbs/year. If the annual target am ount is exceeded by 20%, consideration would be given to shutting down the
SLD and term inating the GBCP (USBR, 1995). The co m p arison of targets with m easured loads shows that in neither year did the project m eet 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 m o re consistently concentrated than were the historic discharges to the wetlands channels system . The wastewater in the SLD is not diluted by wetlands fl ows, and loss of Se to sedim e nt and biota, as occurred during transit through wetland channels (i.e., “in-transit loss”), m a y be reduced (USBR, 1995; Presser and Piper, 1998). Recent adoption by the state of a water-quality objective of less than 2 μ g Se/L for the Grassland wetland channels as prom ulgated by USEPA (USEPA, 1992; CCVRW QCB, 1996c; 1998a), has essentially rem oved these channels as alternative flow paths for drainage water,

Appendix B 9however. This regulation will m a ke it dif f i cult to re-use the wetland channels, f o r exam ple, as alternative channels during flood runoff or in the event that W W D once again uses the SLD. Tables B9 and B10 give the detailed m onthl y data for the GBCP including volum es and Se targets, loads, and concentrations (USBR et al., 1998 and 1999). The annual load of 7,104 for W Y 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 Farm ers for
exceedances of the m onthly 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 W Y 1997 was 62.5 μ g Se/L and the
total volum e was 37,483 acre-feet. The annual load for the second year of the GBCP, W Y 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 norm a l rainfall in 1998 (note, 1998 was an El Nino year). The W Y -1998 upper watershed load was estim ated at 487 lbs Se,
with 350 lbs docum ented in overflow to wetland channels. The average Se concentration in the discharge for W Y 1998 was 67 μ g Se/L and the total volum e 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 com b ined discharge for the SLU and Delta-Mendota Services Areas which includes the Grassland subarea. Taking the worst-case scenario for the year 2020, the am ount of drainage from the SLU Serv ice Area is 135,240 acre-feet and fromthe DeltaMendota Service Area is 65,783 acre-feet. Usi ng assigned concentrations of 50, 150, and 300 μ g Se/L
with these am ounts of drainage, the range of Se di scharged 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 (W W D , 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 W W D discharges (although, under current agreem ents, the GBCP would term inate if W W D is given perm ission 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 m easured average concentration (62.5 μ g Se/L) for Grassland discharge for W Y 1997 is 105,100-6,800 lbs Se/year (Table B2). Thus, the range for a total annual load from W W D and the Grassland Area discharged under this scenario to the SLD is 13,518-15,273 lbs Se/year, if W W D drainage contains a concentration of 50 μ g Se/L. The loads increase to 30,355 to 32,218 lbs Se/year if
W W D drainage contains a concentration of 150 μ g Se/L, and 55,610 to 57,637 lbs Se/year if W W D drainage contains a concentration of 300 μ g Se/L.



### Projections from San Joaquin Valley Dr ainage Program Management Options The data for acreage and drainage volum es 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 im plem entation of the SJV Drainage Program m a nagem e nt plan, 0.60 to 0.75 acre-feet/acre generated drainage, nam e ly, without future and 2) with im plem entation of the SJV Drainage Program m a nagem e nt plan, 0.40 acre-feet/acre generated drainage, nam e ly, 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, exem plifying the lowest, although probably not realistic, irrigation water return. Like earlier plans, the SJV Drainage Program did not cal culate concentrations of Se in drainage water, or Se loads directly, but rather focused on estim ati ng the volum e of drainage and the affected acreage for subareas. Assigning Se concentrations of 50, 150 and 300 μ g Se/L to these volum es, gives the general m a gnitude of expected Se discharge or loading. Table B18 gives the details of specific loadings from each of the five subareas based on the
estim ates given by the SJV Drainage Program fo r year 2000 and assigned concentrations of 50, 150,
and 300 μ g Se/L. This sum m a ry 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 μ g 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 μ g Se/L; 2,774 to 10,608 lbs Se/year for an assigned concentration of 150 μ g Se/L; and 5,549 to 21,216 lbs Se/year for an assigned concentration of 300 μ g Se/L. Appendix B 11• 

### 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 μ g Se/L; 8,813 to 35,088 lbs Se/year for an assigned concentration of
150 μ g Se/L; and 17,626 to 70,176 lbs Se/year for an assigned concentration of 300 μ g Se/L.

• 

### Westlands subarea. W W D (i.e, encom p assing the W e stlands 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 W e stland subarea is 1,877 to 11,016 lbs Se/year for an assigned concentration of 50 μ g Se/L; 5,630 to 33,048 lbs Se/year for an assigned concentration of 150 μ g Se/L; and 11,261 to 66,096 lbs Se/year for an assigned concentration of 300 μ g 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 μ g Se/L; 7,834 to 30,600 lbs Se/year for an assigned concentration of
150 μ g Se/L; and 15,667 to 61,200 lbs Se/year for an assigned concentration of 300 μ g 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 μ g Se/L; 3,264 to 18,768 lbs Se/year for an assigned concentration of
150 μ g Se/L; and 6,528 to 37,536 lbs Se/year for an assigned concentration of 300 μ g Se/L.



### P r o j e c t i o n s f r o m C u r r e n t l y A v a i l a b l e D a t a 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 com p ilation of currently available data on problem acreage, drainage volum e, and Se concentration. These data have becom e available since the SJV Drainage Program was com p leted in 1990. Depe nding on the type of data available from each subarea, projections were m a de concerning concentration and load. Because of the lim ited data and broad range of m a nagem e nt alternatives across the subareas, m a xim u m and m i nim u m Se concentrations are given to bracket possible load scenarios given a specific volum e of drainage for each subarea. The projected concentration range is 5 to 10 μ g Se/L for the Northern subarea, 68 to 152

μ g Se/L for Grassland subarea, 49 to 150 μ g Se/L for W e stlands subarea (note, no current data, only
testim ony on acreage is available), 1.7 to 9.8 μ g Se/L for Tulare subarea, and 175 to 254 μ g Se/L for

12Kern subarea. Although site-specific in nature, these projections address only the present discharge to

m a nage the annual im balance and not general am ounts 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 μ g Se/L for the Northern subarea. The Northern subarea m i nim u m projection is based on a nom inal 5 μ g Se/L Se concentration applied to adhere to the USEPA

prom ulgated Se standard for the SJR. Because m a nagem e nt options were not recom m e nded for the Northern subarea, the assum e d drainage volum e is that estim ated by the SJV Drainage Program for year 2000 without im plem entation of the m a nagem e nt 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 m a xim u m concentration of 10 μ g Se/L is applied to the sam e drainage volum e.

• 

### Grassland subarea

. Discharge from the Grassland subarea is to the SJR. The projected concentration range is 68 to 152 μ g Se/L for the Grassland subarea. The Grassland subarea projection is based on the Grassland Bypass Channe l Project m easured volum e of discharge in W Y 1997 (Tables B9 and B10). The projected Grassland subarea m i nim u m load is 6,960 lbs Se/year. The projected Grassland m a xim u m load is 15,500 lbs Se/year, a load sim ilar to that m easured for the SJR at Crows Landing in an extrem ely wet year (i.e., W Y 1998). The m a xim u m load attem p ts to represent a load that includes upstream SJR loads of Se and recycled Se loads fromthe DeltaMendota Canal

.

• 

### Westlands subarea . W e stlands subarea (or W W D ) currently recycles its drainage and therefore no discharge data is available. The projected concentration range is 49 to 150 μ g Se/L f o r the
W e stlands subarea (note, no current data, only testim ony on acreage is available). The W W D
subarea m i nim u m acre-feet discharge and load are for conditions presented as evidence for W W D (60,000 acre-feet at 49 μ g Se/L Se, W W D , 1996) (Tables B1 and B2). The m a xim u m load is based
on a Se concentration of 150 μ g Se/L (163 μ g Se/L m e dian and USBR conservative estim ate of “at
least 150 μ g Se/L”) applied to 60,000 acre-feet. The projected range of annual Se loads for W W D 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 m easurem ents for volum e and Se concentration from 1993 Appendix B 13to1997 (personal com m unication 1/98, Anthony Tot o, CCVRW QCB). A com p ilation of available
data from discharges in the Tulare subarea is given in Tables B19 and B20. Concentration and
volum e data for 1988, 1989, 1994, and 1996 are shown for com p arison, although sets of data are not available in order to calculate load. An average volum e is used in the projections in conjunction with the m i nim u m and m a xim u m 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 μ g Se/L. The range of projected annual loads for the Tulare subarea is 91 lbs to 519 lbs Se/year, with the

m a jority of the discharge to the Tulare Lake Drainage District ponds. A m a in point of these
calculations is to com p are the m a gnitude of loading from subareas even in view of lim ited data. The projected annual Se load from this area is sm all relative to that projected from W W D and Grassland subareas, largely because the projected Se concentrations are low in m a naged drainage
from the Tulare subarea.

• 

### Kern subarea. Kern subarea currently discharges to privately owned evaporation ponds. A

com p ilation of available data from discharges in the Kern subarea is given in Table B21. Kern subarea projections are based on m easurem ents for volum e and Se concentration from 1993 to1997 (personal com m unication 1/98, Anthony Toto, CCVRW QCB). An average volum e is used in the projections in conjunction with the m i nim u m and m a xim u m Se loads. From the sparse data available, the projected concentration range is 175 to 254 μ g 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 m a in point of
these calculations is to com p are the m a gnitude of loading from subareas even in view of lim ited data. The projected annual Se load from this area is sm all relative to that from W W D and Grassland subareas, largely because the projected volum es of drainage are low from the Kern
subarea.
A com p ilation of our projections based on curren tly available data is given in Table 7. Sets of graphs in Figures B2 and B3 com p are generalized projections from SJVDP volum es (Table B18) with those based on currently available data (Table 7). The ranges of drainage volum e and annual Se loads are presented graphically for each assigned concentration, i.e., 50, 150, and 300 μ g Se/L for each subarea (Figures B2a through e). The ranges of pr ojected drainage volum es and annual Se loads are presented graphically for the m i nim u m and m a xim u m concentrations derived from current data (Figures B3a through e). In general, this graphical technique enables a prediction or projection of an

14annual Se load for any assigned concentration or cu rrent condition given a specific drainage volum e. Again, the ranges are due to varying estim ates of predicted problem water and subsurface drainage
under different m a nagem e nt alternatives. The com p arisons 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 lo ad that are indicative of the geology, hydrology, and
chosen m a nagem e nt options for each subarea.



### Estimates of Capacity of Drainage Co n v e y a n c e ( i

. e . , p r o p o s e d S L D e x t e n s i o n )

As a f i nal check of the m a gnitude of the load projections, the various design capacities of the SLD
or a SLD extension are com b ined with assigned Se concentrations to calculate load (Table B22). The
concentration is held constant to sim u late a constant discharge from a constructed conveyance system as opposed to a seasonally im pacted 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; CSW RCB, 1999a), which is equivalent to 216,810 acre-feet/year. At a concentration of 50 μ g Se/L, the annual Se load is 29,486 lbs Se. Using an assigned concentration of 150 μ g Se/L, the annual load to the BayDelta is 88,458 lbs Se. For a 300 μ g Se/L discharge, the annual load is 176,917 lbs Se. Other
historical estim ates of annual discharge for th e SLD (e.g. 144,200 acre-feet/year in early planning; 150,000 estim ated during 1975-1977 for 50-100 years of drainage; and 84,525 to 279,270 acre-feet
estim ated in 1983 for the period 1995-2095) also can be used to estim ate loads by applying assigned concentrations to discharge capacity. An estim ate 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 (M ontgom ery-W a tson, 1993). All of these estim ates show a need for a drain of greater than 200,000 acre-feet/year.



### T o t a l f l u x f r o m A g r i c u l t u r a l D r a i n a g e D i s c h a r g e ( l b s S e / d a y ) It is also useful to present projected Se loading from the western SJV to the Bay-Delta in term s of rate of discharge (lbs Se/year and lbs/day) and in term s of cum u lative load expressed in kestersons (ksts) (Presser and Piper, 1998). The kst unit is the cum u lative total of 17,400 lbs Se, which when released directly into Kesterson Reservoir caused ecot oxicity and visible ecological dam a ge. It is used
here as a m easure of potential ecological dam a ge base d on Se load. Table B23a shows that a projected
Appendix B 15Se discharge from the western SJV to a SLD exte nsion to the Bay-Delta based on generalized SJV Drainage Program data (i.e., 314,000 acre-feet of probl em water with an assigned concentration of 50

μ g Se/L, or 144,000-163,000 acre-feet of subsurface drai nage with an assigned concentration of 150 μ g 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. Ta bles 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 m i nim u m and m a xim u m 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; W e stlands, 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 assum e d conditions. The W e stlands and Grassland subareas discharge the largest proportion of the daily annual load (Figures B4a and B4b). The range of com b ined loads from the Grasslands and W e stlands subareas is 0.86 to 2.29 ksts/year.
For com p arison, the current prohibition lim itation for the Grassland subarea to the SJR is 8,000 lbs/year or 0.46 ksts/year.

16Figure B1a

Figure B1b

Figure B1c 0 2000 4000 6000 8000 10000 12000lbs 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 70000lbs 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 35000lbs Se/year

0 20000 40000 60000 80000 Acre-feet/year Annual Se load projections, 150 ppb

Northern Kern Tulare Westlands Grassland

150 ppb lineFigure B2a

Figure B2c Figure B2b

Figure B2e Figure B2d 0 2500 5000Selenium (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 40000Selenium (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 60000Selenium (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 60000Selenium (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 1250Selenium (lbs)

0 10000 20000 30000 40000 Acre-feet Northern Subarea

26,000 acre-feet

700 lbs

350 lbs 10 ppb

5 ppbFigure B3a

Figure B3c Figure B3b

Figure B3e Figure B3d 0 500 1000 1500 2000Selenium (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 30000Selenium (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 2000Selenium (lbs)

0 10000 20000 30000 40000 50000 60000 Acre-feet Tulare Subarea

19,493 acre-feet
9.8 ppb

1.7 ppb 91 lbs 519 lbs 0 5000 10000 15000 20000 25000 30000Selenium (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 2000Selenium (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 B3bFigure 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 ) Northern (1.9 ) Tulare (1.4 ) Kern (4.3 )

Westlands (67 ) 

### Projected Annual Selenium - maximum

lbs per day

Total = 117 lbs Se / dayTable B1Westlands Water District Historical Selenium LoadingUse of San Luis Drain by Westlands WaterDistrict to discharge selenium to KestersonReservoirWWD planneddrainage acreage/total acreageProblemacreagewith on-farmdrainsProblem acrefeetppb Selbs Se/time intervalCalculatedacre-feet/acrelbs Se/acre-footSan Luis Drain discharge (measurement average1983-1984) (CSWRCB, 1985; WWD, 1998)38,450(total dischargefor 65 months;January 1981 toMay 1986)330-430Estimated Westlands Water District annualdischarge to San Luis Drain from January, 1981-September, 1985 (Se concentrations from use ofdrain in 1983-1984) (CSWRCB, 1985)5,0007,000(*42,000)330-4306,283-8,187/year0.17-1.4 acrefeet/acre0.898-1.17 lbs/AFProjected Westlands WaterDistrict discharge toSan Luis Drain by 1980 (based on 1965management plans and Se concentrations fromuse of drain in 1983-1984) (WWD, 1996)300,000/600,000(approximately566,500 irrigatedacres)76,00038,000/year330-43034,109-44,445 /year0.50 acre-feet/acre0.898-1.17 lbs/AF1986 Environmental Impact Statement (EIS)estimated San Luis Drain discharge (USBR,1986):Total (January, 1981- September, 1985)Annual (total averaged over 57 months )22,6604,776/year1986 EIS estimated San Luis Drain discharge toKesterson Reservoir (1981-1985) (USBR, 1986)17,400***(1 kesterson, kst)1986 EIS estimated San Luis Drain bed sedimentaccumulation (95,271 cubic yards) (USBR, 1986)5,280*WWD contends that the drainage from 5,000subsurface-drained acres actually representsdrainage from 42,000 acres because of upslope contributions drained to thisdownslope area (CSWRCB, 1985); ** The 17,400-lb amount is referred toas one kesterson (kst). The use of this unit provides perspective on the quantity of Se that wasa hazard to wildlife when released directly to the wetland at Kesterson Reservoir (Presser and Piper, 1998).TABLE B2Projections of annual selenium loading in the San Luis Drainusing evidentiary evidence and selenium concentrations of 50, 150, and 300 ppb forWWD drainage and 62.5 ppb for Grassland Area drainage if drainage to the San Luis Drain is to resume by Westlands Water District and 2) if drainage to the SanLuis Drain is to resume by Westlands Water District and drainageby the Grassland Area Farmers to the San Luis Drain is to continue.Westlands Subarea orSan Luis UnitProblemacre-feet*CalculatedAcre-feet/acreProjectedppb SeProjectedlbs Se/yearProjectedppb SeProjectedlbs Se/yearProjectedppb SeProjectedlbs Se/yearBarcellos Judgment*not < 60,000not > 100,000508,160-13,60015024,480-40,80030048,960-81,600DEIS PlanningAlternatives*24,0000.23503,2641509,79230019,584Initial hook-up of 7,600**acreage of on-farm drains1,900-2,30050258-313150775-9383001,550-1,877Drainage of 200,000 acresof problem acreage**60,0000.30508,160(0.041lbs Se/acreor 0.136 lbs Seacre-foot)15024,480(0.122 lbs Se/acreor 0.408 lbs Seacre-foot)30048,960(0.245 lbs Se/acreor 0.816 lbs Seacre-foot)Additional drainage from**Grassland Area Farmers30,000-40,00062.5***5,100- 6,80062.5***5,100- 6,80062.5***5,100-6,800Total for Westlandsand Grassland (range)90,000-100,00013,518-15,27330,355-32,21855,610-57,637Evidence presented by Westlands Water District, 1*) Draft Environmental Impact Statement, December 20, 1991, San Luis Drainage Program, Central ValleyProject, California, in partial answer to the Barcellos Judgment of December 30, 1986 (USBR, 1992) and 2**)Statement Concerning Current Estimates of theWestlands Water District Drainage Problem, submitted on the behalf of Westlands Water District, by William R. Johnston, April 4, 1996 (WWD, 1996); ***measured in water year (WY) 1997.TABLE B3Grassland Subarea discharge to the San Joaquin River for year 2000 and year 2040 using San Joaquin Valley DrainageProgram drainage volumes and selenium concentrations for Zones A, B, and C (SJVDP, 1989; 1990a).Grassland SubareaSJVDP 2000drainedacreage*SJVDP 2000problem wateracre-feet**SJVDP 2000discharge toSan JoaquinRiver(acre-feet)**Projectedppb Se**lbs Se/acrefootProjectedlbs Se/yearSJVDP 2040discharge toSan JoaquinRiver(acre-feet)**Projectedppb Se**Projectedlbs Se/yearlbs Se/acrefootZone A72,00054,00010,7001500.4084,36621,000754,2840.204Zone B14,00010,6007,00020.00543817,6002960.0054Zone C30,00022,00022,00020.005412063,50023450.0054Total116,00086,60039,7004,524102,1004,725* Preliminary Planning Alternatives, SJVDP, 1989, page 4-23 (assumption, drained acres will morethan double by year 2000); **SJVDP data from Table 29and page 139.Table B4Annual acre-feet, selenium concentrations, and selenium loads from the GrasslandArea Farmers Drainage Problem Area.Water-yearacre-feet/yearppb Se (total)lbs Se/yearlbs Se/acre-foot198667,00652.39,5240.142198774,90253.810,9590.146198865,32756.810,0970.154198954,18659.28,7180.161199041,66265.27,3930.177199129,29073.55,8580.200199224,53376.25,0830.207199341,19779.08,8560.215199438,67080.58,4680.219199557,57475.811,8750.206199652,9787010,0340.1891997*37,48362.57,0970.1861998*9,118TOTAL113,080average 8,698 lbs/yearDATA: 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 BypassChannel ProjectTable B5Annual acre-feet, selenium concentrations,and selenium loads from Mud and Salt Sloughs.Water-yearacre-feet/yearppbSe(total)lbs Se/yearMud Sloughconcentration rangeSalt Sloughconcentration range1986284,3168.66,6432.3-221.4-221987233,84312.07,6411.7-265.2-261988230,45413.08,1321.4-181.6-271989211,39314.18,0990.7-5.02.7-331990194,65614.67,7190.6-8.14.2-361991102,16214.03,8990.7-380.9-30199285,42812.62,9190.8-480.6-271993167,95515.06,8711.0-5.00.5-421994183,54616.07,9800.5-221.2-441995263,76914.910,6940.7-4.20.8-381996267,344139,697----1997288,253107,7225.0-800.5-3.41998Not availableTotal88,016average 7,335 lbs/yearDATA: DATA: CCVRWQCB, 1996b; c; 1998d; e; f; g; h; 2000,b; c; USBR et al., 1998, 1999.Table B6Annual acre-feet, selenium concentrations, and selenium loads measured at the San Joaquin River near Patterson/Crows Landing.Water-year (WY)million acre-feet/yearppb Se (total)lbsSe/yearconcentration range19862.671.611,305<1-419870.664.98,8573.6-1219880.556.29,3300.8-1219890.446.37,4733.4-1719900.405.66,1251.6-1319910.294.53,5480.9-1119920.303.73,0640.7-1119930.893.58,3790.4-8.019940.564.87,270<0.4-1319953.501.614,2910.6-1219961.44310,686--19974.18 (range 986 to 73,458 daily) (3.73 USGS fromGBCP data)18,667 (9,054 USGS from GBCP data)0.1-1019985.13 (range 956-47,916 daily) (GBCP data)15,501 (GBCP data)0.4 to 4.1Total114,496average 8,807 lbs/yearDATA: DATA: CCVRWQCB, 1996b; c; 1998d; e; f; g; h; 2000,b; c; USBR et al., 1998, 1999.Table B7Annual acre-feet, selenium concentrations, and selenium loads measured at the SanJoaquin River near Vernalis.Water-yearmillion acre-feet/yearppb Se (total)lbs Se/yearconcentration range19865.221.014,601<0.1-1.4 (17?)19871.811.88,5020.6-3.219881.172.78,4270.8-4.019891.063.08,7411.7-6.819900.923.07,4720.8-9.619910.662.03,6110.5-4.819920.701.93,5580.4-4.419931.701.98,905<0.4-6.119941.222.37,7600.4-6.319956.301.017,2380.5-3.519963.951.111,43119976.770.611,19019988.515,810Total127,246average 9,788 lbs/yearDATA: DATA: CCVRWQCB, 1996b; c; 1998d; e; f; g; h; 2000,b; c; USBR et al., 1998, 1999.Table B8San 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 tothe San Joaquin RiverproblemacreageMeasuredproblem acrefeet or dischargeMeasuredppb Selbs Se/yearCalculatedlbs/acre orlbs/acre-feetCalculatedacre-feet/acreCCVRWQCB prohibition limitation of Se discharge tothe San Joaquin River or tributaries from tile or opendrainage systems (effective October 1, 1996;CVRWQCB, 1996a; d)8,000WY 1997-2001 San Luis Drain /Grassland BypassChannel Project negotiatedannual load target fordischarge through the San Luis Drain to the SanJoaquin River (USBR, 1995)93,4005,661-6,6600.06-0.07/acreWY 1997 San Luis Drain /Grassland Bypass ChannelProject measured load **** discharged through thedrain to the San Joaquin River (USBR et al., 1998)97,40037,48362.56,9600.073/acre0.189/AF0.38January 26, 1997 estimated load from Coast Rangerunoff discharged through the drain (Grassland AreaFarmers, 1997)137WY 1998 San Luis Drain /Grassland Bypass ChannelProject measured load discharged through the drain tothe San Joaquin River (USBR et al., 1999)97,40045,85866.99,1180.094/acre0.199/AF0.47February, 1998 estimated load from Coast Range runoffdischarged through the drain (Grassland Area Farmers,1997)487Table B9San Luis Drain Re-use Project/Grassland Bypass Channel Project WY 1997 Average Monthly Drainage Volumes and SeleniumConcentrations, Annual Discharge, and Load Targets (USBR et al., 1998).WY 1997Measured acre-feet (AF)MeasuredSe (ppb) (total)CalculatedSe (lbs)NegotiatedSe (lbs target)Incentivefee ($)Sept. 23-30,1996[55 (est.)] *see Sept, 1997October1,27460.8 (58.6)2023480November1,56658.32523480December1,94351.52853890January, 19973,69659.5599**5332,800February4,16676.6878**866700March4,86784.211191066700April4,446105.512807992,800May4,20875.78496662,800June3,45164.3611599700July3,27148.14285990August3,15340.63485330Sept, 1-30, 19971,44225.31093500Total (monthly)37,4836,9607,096 (monthly)10,500Total (yearly)37,48362.5 (average)6,9606,660 (yearly)50,000WY 1997 storm discharge (lowerwatershed, Agatha Canal)137**Total (project plus storm discharge)7,097$60,500* not counted in total; ** 89 lbs Se in January and 48 lbs Se inFebruary discharged to wetland sloughs (Agatha Canal) during SLD overflow eventsdue to storms in January and February, 1998.Table B10San Luis Drain Re-use Project/Grassland Bypass Channel Project WY 1998 Average Monthly Drainage Volumes and SeleniumConcentrations, Annual Discharge, and Load Targets (USBR et al., 1999)WY 1998Measured acre-feet (AF)MeasuredSe (ppb) (total)CalculatedSe (lbs)NegotiatedSe (lbs target)Incentivefees ($)October, 19971,75351.92483480November1,55548.92073480December1,40348.71783890January, 19981,41985.03355330February6,98052.5965*8664,200**March7,09483.3160010664,200**April5,517105.41554 (1560)7994,200**May4,881104.513716664,200**June3,62982.18075994,200**July4,56449.76155991200August3,87647.55005330September3,18743.13883502,200Total (monthly)45,8587,096(monthly)Total (yearly)45,85866.9 (average)8,7686,660 (yearly)150,000**WY 1998 storm discharge (lowerwatershed, Agatha Canal))350*Total (project plus storm discharge)9,118174,400(3,400 paid)*350 lbs Se discharged to wetland sloughs (Agatha Canal) during SLDoverflow events due to storms in February, 1998; fees waived because ofabove average rainfall for WY 1998.Table B11Acreage used for planning purposes in1985-1990 by the SJVDP (SJVDP, 1989, Table 1-1)SubareaSJVDPAcreageSJVDPirrigable*acreageSJVDPirrigated*acreageSJVDPdrainedacreageNorthern236,000165,000157,00026,000Grassland*707,000345,000311,000**51,000Westlands770,000640,000576,0005,000Tulare883,000562,000506,000**42,000Kern1,210,000762,000686,00011,000Total3,806,0002,474,0002,235,000135,000* A factor of 90 to 95% was used to calculate irrigated acres from irrigableacres (SJVDP, 1990a, Table 11; ** SJVDP, 1990a, Table 11, Grasslandsubarea 329,000 acres; Tulare subarea 551,000 acres.Table B12The SJVDP 1990 and year 2000 irrigated acreage, abandoned acreage, problem acreage and cost for problem water reduction basedon implementation of therecommended SJVDP Management Plan (1990a). The “without future”(i.e., no implementation of a management plan) includes abandonment of lands due tosalinization.SubareaSJVDP1990irrigatedacreage**SJVDP2000irrigatedacreage**withoutfutureSJVDP2000abandonedacreage**withoutfutureSJVDP 2000problemacreage***withoutfutureSJVDPproblem watergenerationacre-feet/acre SJVDP 2000problemacre-feet** ***SJVDP 2040problemacre-feet*****SJVDPannualizedcost/acrefor problemwaterreduction******SJVDP annualizedcost formanagement planimplementation******Northern157,000152,000034,0000.70-0.7526,00038,000---Grassland*329,000325,0000116,0000,70-0.7586,000155,000$107$12,412,000Westlands576,000551,00028,000108,0000.6081,000153,000$136$14,688,000Tulare551,000517,00038,000125,0000.70-0.7575,000209,000$104$13,000,000Kern686,000665,00018,00061,0000.7146,000111,000$137$ 8,357,000Total2,299,0002,210,00084,000444,000314,000666,000$48,457,000* Grassland subarea total acreage is 707,000 with 329,000 irrigatedacres (90% of irrigable lands) and the Grassland Area/Drainage Problem Area within the subarea isapproximately 100,000 acres; ** SJVDP Table 11; *** SJVDP Table 9;   SJVDP page 76;** *** SJVDP Table 10; ****** 50 year planning period and based onyear 2000 problem acreage SJVDP pages 5, 143, 148, 153, and 156 (approximately $42, 000,000, page 5); cost/acre includes the cost of fish and wildlife components.Table B13The SJVDP 1990, 2000, and 2040 volumes of drainage with no drainage improvement (0.75 acre-feet/acre/year) or minimalimprovement (0.55 acre-feet/acre/year) (SJVDP, 1990a). The conditions without implementation of SJVDP management plan is designated by the SJVDPas the“without future”alternative and includes abandonment of lands due to salinization. An additional calculation ismade for Westlands based on“upslope” contributions tothe tile drained acreage from non-tiledrained acreage (CSWRCB, 1985).SubareaSJVDP 1990tile-drainedacres *factorAF/acre/yearSJVDP 1990drainagevolumes (acrefeet)**SJVDP 2000tile-drainedacreswithoutfuture*factorAF/acre/yearSJVDP 2000drainagevolumes (acrefeet) withoutfuture**SJVDP 2040tile-drainedacreswithoutfuture*factorAF/acre/yearSJVDP 2040drainagevolumes (acrefeet withoutfuture **Northern24,0000.7518,00034,000--***26,00051,0000.7538,000 Grassland50,0000.7538,00085,000--54,000152,0000.5584,000** **Westlands5,0000.754,00050,000--28,00049,0000.5527,000Westlands42,000*****0.7531,500*****----Tulare43,0000.6032,00086,000--47,00094,0000.5552,000Kern11,0000.758,00014,000--8,00040,0000.5522,000Total133,000100,000269,000--163,000386,000223,000* SJVDP Table 11; ** SJVDP Table13; *** no factor given by SJVDP, Table 13;   In SJVDP Table 13 the values are 37,000 and 105,000 acre-feet.** *** not included in totalTable B14Calculated volume of drainage using a drainage improvement factor of 0.40 acre-feet/acre/year (SJVDP, 1990a). The alternativewithImplementation of the SJVDP management plan is designated by the SJVDP as the“with future”alternative. An additional calculation is made forWestlands based on “upslope”contributions to the tile drained acreagefrom non-tile drained acreage (CSWRCB, 1985).SubareaSJVDP 1990tile-drainedacres**factorAF/acre/year***Calculated1990 drainagevolumes(acre-feet)with futureSJVDP2000tile-drainedacreswithfuture**factorAF/acre/year***Calculated2000 drainagevolumes(acre-feet)with futureSJVDP2040tile-drainedacreswithfuture**factorAF/acre/year***Calculated2040 drainagevolumes(acre-feet)with futureNorthern*24,0000.409,60034,0000.4013,60044,0000.4017,600Grassland50,0000.4020,000108,0000.4043,200192,0000.4076,800Westlands5,0000.402,00069,0000.4027,600140,0000.4056,000Westlands42,000****0.4016,800****Tulare43,0000.4017,20096,0000.4038,400277,0000.40110,800Kern11,0000.404,40053,0000.4021,200106,0000.4042,400Total133,00053,200360,000144,000759,000303,600* No management plan recommended for Northern subarea; **SJVDP Table 27; *** factor applied from SJVDP Table 26; **** not included in total.Table B15aProjections of annual selenium loading per subareafor year 2000 using San Joaquin Valley Drainage Programproblem watervolumes(“without future”alternative, 0.60 to 0.75 acre-feet/acre/year; SJVDP, 1990a)and a 50-ppb Se concentration in drainage discharge.SubareaSJVDP 2000problem acreage*SJVDPproblem watergenerationacre-feet/acre/year**SJVDP 2000problem acre-feet***Projectedppb SeProjectedlbs Se/yearCalculatedlbs Se/acreCalculatedlbs Se/acre-footNorthern34,0000.70-0.7526,000503,5360.10.136Grassland116,0000,70-0.7586,0005011,6960.10.136Westlands108,0000.70- 0.7581,0005011,0160.10.136Tulare125,0000.6075,0005010,2000.080.136Kern61,0000.70-0.7546,000506,2560.10.136Total444,0000.71314,0005042,7040.0960.136* SJVDP Table 9; ** SJVDP page 76 and *** SJVDP Table 10Table B15bProjections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Programproblem watervolumes(“without future”alternative, 0.60 to 0.75 acre-feet/acre/year; SJVDP, 1990a) and a 150-ppb Se concentration in drainage discharge.SubareaSJVDP 2000problem acreage*SJVDPproblem watergenerationacre-feet/acre/year**SJVDP 2000problem acre-feet***Projectedppb SeProjectedlbs Se/yearCalculatedlbs Se/acreCalculatedlbs Se/acre-footNorthern34,0000.70-0.7526,00015010,6080.310.408Grassland116,0000,70-0.7586,00015035,0880.310.408Westlands108,0000.70- 0.7581,00015033,0480.310.408Tulare125,0000.6075,00015030,6000.240.408Kern61,0000.70-0.7546,00015018,7680.310.408Total444,0000.71314,000150128,1120.290.408* SJVDP Table 9; ** SJVDP page 76 and *** SJVDP Table 10Table B15cProjections of annual selenium loading per subarea for year 2000 using San Joaquin Valley Drainage Programproblem watervolumes(“without future”alternative, 0.60 to 0.75 acre-feet/acre/year; SJVDP, 1990a) and a 300-ppb Se concentration in drainage discharge.SubareaSJVDP 2000problem acreage*SJVDPproblem watergenerationacre-feet/acre/year**SJVDP 2000problem acre-feet***Projectedppb SeProjectedlbs Se/yearCalculatedlbs Se/acreCalculatedlbs Se/acre-footNorthern34,0000.70-0.7526,00030021,2160.310.816Grassland116,0000,70-0.7586,00030070,1760.310.816Westlands108,0000.70- 0.7581,00030066,0960.310.816Tulare125,0000.6075,00030061,2000.240.816Kern61,0000.70-0.7546,00030037,5360.310.816Total444,0000.71314,000300256,2240.290.816* SJVDP Table 9; ** SJVDP page 76 and *** SJVDP Table 10Table B16aProjections of annual selenium loading per subareafor year 2000 using San Joaquin Valley Drainage Programsubsurfacedrainage volumes(“without future”alternative, 0.60 to 0.75 acre-feet/acre/year; SJVDP,1990a) and Se concentrations of 50, 150, and 300 ppb.SubareaSJVDP 2000drained acreagewithout future*SJVDP 2000subsurface drainagevolume (acre-feet)without future**Projectedppb SeProjectedlbs Se/yearProjectedppb SeProjectedlbs Se/yearProjectedppb SeProjectedlbs Se/yearNorthern34,00026,000503,53615010,60830021,216Grassland85,00054,000507,34415022,03230044,064Westlands50,00028,000503,80815011,42430022,848Tulare86,00047,000506,39215019,17630038,352Kern14,0008,000501,0881503,2643006,528Total269,000163,0005022,16815066,504300133,008* SJVDP Table 11; ** SJVDP Table 13.Table B16bProjections of annual selenium loading per subareafor year 2000 using San Joaquin Valley Drainage Programsubsurfacedrainage volumes(“with future”alternative, 0.40 acre-feet/acre/year; SJVDP, 1990a)and Se concentrations of 50, 150, and 300 ppb.SubareaSJVDP 2000drained acreagewith future*SJVDP 2000subsurface drainagevolume (acre-feet)with future**Projectedppb SeProjectedlbs Se/yearProjectedppb SeProjectedlbs Se/yearProjectedppb SeProjectedlbs Se/yearNorthern34,00013,600501,8501505,54930011,098Grassland108,00043,200505,87515017,62530035,251Westlands69,00027,600503,75415011,26130022,522Tulare96,00038,400505,22215015,66730031,334Kern53,00021,200502,8831508,65030017,299Total360,000144,0005019,58415058,752300117,504* SJVDP Table 11; ** SJVDP Table 13.Table B16cProjections of annual selenium loading per subareafor year 2000 using San Joaquin Valley Drainage Programsubsurfacedrainage volumes, our“with targeted future”alternative (0.20 acre-feet/acre/year; SJVDP, 1990a),and Se concentrations of 50, 150, and 300 ppb.SubareaSJVDP 2000drained acreagewith future*SJVDP 2000subsurface drainagevolume (acre-feet)with targeted future**Projectedppb SeProjectedlbs Se/yearProjectedppb SeProjectedlbs Se/yearProjectedppb SeProjectedlbs Se/yearNorthern34,0006,800509251502,7743005,549Grassland108,00021,600502,9381508,81330017,626Westlands69,00013,800501,8771505,63030011,261Tulare96,00019,200502,6111507,83430015,667Kern53,00010,600501,4421504,3253008,650Total360,00072,000509,79315029,37630058,753* SJVDP Table 11; ** applied factor of 0.20 acre-feet/acreTable B17Our projections of annual selenium loading for subareas for year 2000 using Se concentrations of 50 ppb, 150 ppb, and 300 ppband SJVDP volumes ofproblemwater “ without future”alternative, ofdrainage volumesin the“without future”alternative and in the“with future”alternative (SJVDP, 1990a). In the “with targetedfuture”alternative, we applied a factorof 0.2 acre-feet/acre/year.Subarea1990subsurfacedrainageacre-feet/yearppbSelbs Se/yearprojected2000problemwateracre-feet/year*ppbSelbs Se/yearprojected2000drainageacre-feet/yearwithoutfuture**ppbSelbs Se/yearprojected2000drainageacre-feet/yearwithfuture***ppbSelbs Se/yearprojected2000drainageacre-feet/yearwith targetedfuture***ppbSelbs Se/yearNorthern*18,000502,44826,000503,53626,000503,53613,600501,8506,80050925Grassland38,000505,16886,0005011,69654,000507,34443,200505,87521,600502,938Westlands4,0005054481,0005011,01628,000503,80827,600503,75413,800501,877Tulare32,000504,35275,0005010,20047,000506,39238,400505,22219,200502,611Kern8,000501,08846,000506,2568,000501,08821,200502,88310,600501,442Total100,00013,600314,00042,704163,00022,168144,00019,58472,0009,793Subarea1990subsurfacedrainageacre-feet/yearppbSelbs Se/yearprojected2000problemwateracre-feet/year*ppbSelbs Se/yearprojected2000drainageacre-feet/yearwithoutfuture**ppbSelbs Se/yearprojected2000drainageacre-feet/yearwithfuture***ppbSelbs Se/yearprojected2000drainageacre-feet/yearwith targetedfuture***ppbSelbs Se/yearNorthern*18,0001507,34426,00015010,60826,00015010,60813,6001505,5496,8001502,774Grassland38,00015015,50486,00015035,08854,00015022,03243,20015017,62521,6001508,813Westlands4,0001501,63281,00015033,04828,00015011,42427,60015011,26013,8001505,630Tulare32,00015013,05675,00015030,60047,00015019,17638,40015015,66719,2001507,834Kern8,0001503,26446,00015018,7688,0001503,26421,2001508,65010,6001504,325Total100,00040,800314,000128,112163,00066,504144,00058,75172,00029,376Subarea1990subsurfacedrainageacre-feet/yearppbSelbs Se/yearprojected2000problemwateracre-feet/year*ppbSelbs Se/yearprojected2000drainageacre-feet/yearwithoutfuture**ppbSelbs Se/yearprojected2000drainageacre-feet/yearwithfuture***ppbSelbs Se/yearprojected2000drainageacre-feet/yearwith targetedfuture***ppbSelbs Se/yearNorthern*18,00030014,68826,00030021,21626,00030021,21613,60030011,0986,8003005,549Grassland38,00030031,00886,00030070.17654,00030044,06443,20030035,25121,60030017,626Westlands4,0003003,26481,00030066,09628,00030022,84827,60030022,52213,80030011,261Tulare32,00030026,11275,00030061,20047,00030038,35238,40030031,33419,20030015,667Kern8,0003006.52846,00030037,5368,0003006,52821,20030017,29910,6003008,650Total100,00081,600314,000256,224163,000133,008144,000117,50472,00058,753*SJVDP Table 10; ** SJVDP Table 13; *** see calculation this report Table – (SJVDP Table 27 acreage with factor applied from SJVDP Table 26); **** this reportTable 15.Table B18Summary of our projections of annual selenium loads for SJVDP subareas for year 2000. Scenarios 1, 2, 3: assigned selenium concentrationsof 50, 150, 300 ppb Se and SJVDP estimates of drainage volume (SJVDP, 1990a).Subareaacre-feet/yearAssigned concentration50 ppb (0.136 lbs Se/acre-foot)(lbs Se/year)Assigned concentration150 ppb (0.408 lbs Se/acre-foot)(lbs Se/year)Assigned concentration300 ppb (0.817 lbs Se/acre-foot)(lbs Se/year)Northern6,80013,60026,0009251,8503,5362,7745,54910,6085,54911,09821,216Grassland21,60043,20054,00086,0002,9385,8757,34411,6968,81317,62522,03235,08817,62635,25144,06470,176Westlands13,80027,60028,00081,0001,8773,7543,80811,0165,63011,26011,42433,04811,26122,52222,84866,096Tulare19,2008,40047,00075,0002,6115,2226,39210,2007,83415,66719,17630,60015,66731,33438,38261,200Kern8,00010,60021,20046,0001,0881,4422,8836,2563,2644,3258,65018,7686,5288,65017,29937,536Total drainage/year, all subareasRange 69,400 to 314,000 acre-feetTotal lbs Se/yearMinimum lbs, all subareasMinimum lbs without NorthernMaximum lbs, all subareasMaximum lbs, without Northern9,2848,36742,70439,16827,84725,073128,112117,50455,65250,103256,224235,008Table B19Tulare subarea 1988-1989 drainage discharges and selenium concentrations.Discharge to 21 privately owned evaporation basins1988 and 1989*Drainageacre-feet/yearppb Se(measurement or range)lbs Se/year1988 TOTAL/YEARTLDD (Total)northhaciendasouthWestlakeMeyerStoneBritzOthers14,2942.6--301-1.111.6-4.3--9.6-7571989 TOTAL/YEARTLDD (Total)northhaciendasouthWestlakeMeyerStoneBritzOthers13,7052.0---210.4-6.50.82.3-7.4---1.0-62*Discharge data from CCVRWQCB, pers. com., Anthony Toto, 1998; Se concentration data fromWater Quality inEvaporation 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 discha rges 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 sampli ngs for WY 1997, June and September, 1997.Table B21Kern subarea 1988-1997 drainage discharges and selenium concentrations.Kern SubareaDischarge to privately owned evaporation basins 1988, 1989, 1993-1997*Drainageacre-feet/yearppb Selbs Se/year1988 TOTAL/YEARLost Hills Water DistrictRainbow RanchLost Hills Ranch2,452142---2.49471989 TOTAL/YEARLost Hills Water DistrictRainbow RanchLoast Hills Ranch3,83183-6712122.1865-6,9921993 TOTAL/YEARLost Hills Water DistrictRainbow Ranch2,4671,8546132201901,42611093171994 TOTAL/YEARLost Hills Water DistrictRainbow Ranch2,3181,7395792084051,5869486381995 TOTAL/YEARLost Hills Water DistrictRainbow Ranch2,2371,5496882402131,41010113991996 TOTAL/YEARLost Hills Water DistrictRainbow Ranch2,3651,5018642381851,4079724351997 TOTAL/YEARLost Hills Water DistrictRainbow Ranch2,0721,6204521951871,089859230* Data from CCVRWQCB, pers. com. Anthony Toto, 1998, except for selenium concentrations for 1988 and 1989 which arefromWaterQuality in Evaporation Basins Used for the Disposal of Agricultural Subsurface Drainage Water in the SanJoaquin Valley, California, 1988 and 1989 (CCVRWQCB, 1990).Table B22Planned capacity of the San Luis Drain or Valley-Wide Drain. Loading scenarios useassigned selenium concentrationsof 50 ppb, 150, ppb, and 300 ppb.San Luis Drain Design Capacity@ 50 ppblbs Se/year@ 150 ppblbs Se/year@ 300 ppblbs Se/year300 cfs or 216,810 acre-feet/year (USBR, 1955)planned capacity Bakersfield to Mendota section29,48688,458176,917450 cfs or 325,215 acre-feet/year (USBR, 1955)planned capacity Kesterson Reservoir to Bay/Deltasection44,229132,688265,375144,200 acre-feet/year (USBR, 1950’s, initiallyneeded)19,61158,834117,667after 50 years 154,100 acre-feet/year, maximum(range 3,100 to 154,100 acre-feet/year (USBR,1978)20,95862,873125,746after 25 years 201,025 acre-feet/year (range 84,525to 279,270 acre-feet/year (USBR, 1983)27,33982,018164,036Barcellos Judgment 60,000 to 100,000 acrefeet/year (USBR,1992)8,160-13,60024,480-40,80048,960-81,600Westland Water District 60,000 acre-feet/year8,16024,48048,960375,000 acre-feet/year (400,000-500,000 acrefeet/year needed capacity) (San Francisco OceanOut-fall, Montgomery Watson, 1993)51,000153,000306,000Table B23aSan Joaquin Valley Drainage Program generalized projected annual selenium discharge from the western San Joaquin Valley to a proposed San Luis Drainextension to the Bay/Delta. A selenium concentration of 50 ppb Sewas hypothesized to be attainable with treatment; a concentration of 150 ppb Se is assigned tosubsurface drainage.San Joaquin Valleyacre-feet (all subareas)lbs Se/ yearkestersons*/year(ksts/year)lbs Se/daySe ConcentrationppbSe Concentrationlbs Se/acre-foot314,000 (problem waterat 50 ppb Se)42,7042.45117500.136144,000-163,000(subsurface drainage at150 ppb Se)58,752-66,5043.4-3.8161-1821500.408Table 23bProjected low-range annual selenium discharges from the westernSan Joaquin Valley to a San Luis Drain extension to the San Francisco Bay/DeltaSan Joaquin ValleySubarealbs Se/ yearkestersons*/year(ksts/year)lbs Se/daySe ConcentrationppbSe Concentrationlbs Se/acre-footNorthern3500.020.9550.0135Grassland6,9600.4019680.186Westlands8,0000.4622490.133Tulare910.0050.251.70.0047Kern1,0890.0623.01750.475TOTAL16,4900.9545.2Table 23cProjected high-range annual selenium discharges from the western San Joaquin Valley to a San Luis Drain extension to the San Francisco Bay/DeltaSan Joaquin ValleySubarealbs Se/ yearkestersons*/year(ksts/year)lbs Se/daySe ConcentrationppbSe Concentrationlbs Se/acre-footNorthern7000.041.9100.027Grassland15,5000.89421520.414Westlands24,4801.4671500.408Tulare5190.031.49.80.0266Kern1,5860.094.32540.692TOTAL42,7852.46117*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

M o d e l s o f D i s c h a r g e t o t h e S a n J o a q u i n R i v e r 2 Models that Target Load Reduction

.............................................................................................. ....... 3
Models that Maxim i ze the Allowed Selenium L o a d b y T a r g e t i n g C o n c e n t r a t i o n

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6



## FIGURES

C1. Num b er of selenium water quality exceedance m onths (U.S. EPA criteria) for the San Joaquin River at Crows Landing during W Y 1986 through W Y 1997. C2. Com p arison of wet, dry, and critically dry years (TMDL m odel) for 5 μ g/L, 4-day average, 1 out of 3 year exceedance inputs. C3. Com p arison of TMDL and TMML m odel projections during a wet year for 5 μ g/L, 4-day average, 1 out of 3 year exceedance inputs. C4. Com p arison of TMDL and TMML m odel projections during a dry year for 5 μ g/L, 4-day average, 1 out of 3 year exceedance inputs. C5. Com p arison of TMDL m odel projections at Crow s Landing during critically dry years for a) 5 μ g/L, 4-day average, 1 out of 3 year exceedance inputs, b) 5 μ g/L, m onthly average, 1 out of 3 year exceedance inputs, and c) 5 μ g/L, 4-day average, 1 out of 5 m onth exceedance inputs. C6. Com p arison of TMDL m odel projections at Cr ows Landing during dry and below norm a l years for a) 5 μ g/L, 4-day average, 1 out of 3 year exceedance inputs, b) 5 μ g/L, m onthly average, 1 out of 3 year exceedance inputs, and c) 5 μ g/L, 4-day average, 1 out of 5 m onth exceedance inputs. C7. Com p arison of TMDL m odel projections at Cr ows Landing during above norm a l and wet years for a) 5 μ g/L, 4-day average, 1 out of 3 year exceedance inputs, b) 5 μ g/L, m onthly average, 1 out of 3 year exceedance inputs, and c) 5 μ g/L, 4-day average, 1 out of 5 m onth exceedance inputs. C8. TMML m odel projection at Crows Landing for 8 μ g/L and 1 out of 3 year exceedance inputs. C9. Com p arison of TMML m odel projections dur ing a dry year at Crows Landing for a) 5 μ g/L and 4-day average inputs, and b) 5 μ g/L and m onthly m ean inputs. C10. Com p arison of TMML m odel projections duri ng a wet year at Crows Landing for a) 5 μ g/L,

m onthly average, and 1 out 3 years exceedance inputs, and b) 5 μ g/L, 4-day average, and 1 out of 3 year exceedance inputs. C11. Monthly selenium loads for a dynam i c real tim e m odel during a wet year using a 5 μ g/L input.



## TABLES
Appendix C 1C1. Modeled Selenium Load Allocation and Discharg e to the San Joaquin River from the Grassland Drainage Problem Area. C2. Modeled (TMDL, Total Maxim u m Daily Load m odel) Annual Selenium Load Allowance to the San Joaquin River from the Grassland Area.
C3. Modeled (TMML m odel, Total Maxim u m Monthly Load m odel and DRT m odel, Dynam i c RealTim e m odel) 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-m ile reach of the SJR a water-quality limited segment (e.g., CCVRW QCB, 1994a; 1998b) and the Se levels in the bay of concern (CSFBRW QCB, 1992a). Discharge of Se to the SJR has continued based on an agreem ent to im plem ent a regulatory control

program for Se discharges started the year th at Kesterson Reservoir was buried (CSW RCB, 1985 and 1987). Figure C1 shows the num ber of m onths per year that the USEPA 5 μ g Se/L Se standard was
violated at the state com p liance point for the SJ R as a receiving water (i.e., SJR at Crows Landing)
from 1986 to 1997. The num ber of violations is based on a m ean m onthly average of a varying num ber of collected grab sam p les (CCVRW QCB, 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 (CSW RCB, 1999c). Besides the USEPA prom ulgated Se standard for the protection of aquatic life, an annual prohibition lim itation of 8,000 lbs Se exists as part of the state San Joaquin and Sacram ento River Basin Plan since 1996 and waste discharge requirement for Se discharge to the SJR since 1998. Violations of this prohibition recently have o ccurred at the SJR at Crows Landing from W Y 1995 through W Y 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 W a ter Act as am ended in 1987 [section 303 (d)(l)(c)] requires that water-quality
standards be converted into Total Maxim u m Daily Loads (TMDLs) in the water-quality im paired water bodies like the lower reach of the SJR. The TMDL approach allows a state to im plem ent water-quality
control m easures where beneficial uses are known to be im paired, but the resource is not beingregulated because of lack of adequate data. In the case of Se, both the existing record and developed

m odels for the SJR have im portant lim itations (Presser and Piper, 1998). The existing record of waterquality conditions in the SJR is inadequate to ascertain if progress is being m a de towards either
lim iting loading of Se, m eeting the water-quality objectives, or protecting the SJR (W estcot, et al., 1996; Presser and Piper, 1998). The m odels are conservative-elem ent dilution m odels that have not considered the potential for Se to accum u late in sedim e nt or bioaccum u late in biota (Environm ental Defense Fund, 1994; Karkoski, 1996). The assim ilative capacity for the SJR in existing m odels is defined only by flow (i.e., dilution capacity). In one derivation of the TMDL m odel, acknowledgem e nt is m a de of the shortcom ings of the approach by stating that, if in the future load lim its are derived based on the capacity of the ecosystem to safely absorb pollutants, the m e thodology to derive the load allowances would change, but the im plem entation issues for the agricultural dischargers would rem a in
the sam e (Environm ental Defense Fund, 1994). Im plem entation issues m a y include an econom ic justification of continued im pairm e nt of the SJR’s beneficial uses required by anti-degradation policies (Code of Federal Regulations 40:131.12; Clean W a ter Act Section 303(d) as am ended, 1987). Hydrologic-econom ic m odels for the SJV and inform ation regarding the cost/benefit of agriculture in the SJV have been developed and com p iled at various stages of planning for irrigation and drainage projects (e.g., SJV Interagency Drainage Progr am , 1979a; b; CDW R , 1982; Horner, 1986; W illey, 1990; Dinar and Zilberm a n, 1991; Environm en tal Defense Fund, 1994; CCVRW QCB, 1996c). Monthly Se concentrations greater than 5 μ g/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 m i ght be discharged to the SJR with the goal of m eeting a federal 5 μ g Se/L concentration standard and a state 8 μ g Se/L concentration objective. USEPA rejected the 8 μ g Se/L objective for the SJR in 1992 and prom ulgated a 5 μ g Se/L
standard for the SJR and a 2 μ g Se/L standard for associated wetland channels (i.e., wildlife refuge supply channels) (USEPA, 1992). A TMDL m odel was developed by the Environm ental Defense
Fund and an alternative m odel nam e d the Total Maxim u m Monthly Load (TMML) m odel was developed in conjunction with the state (CCV RW QCB, 1994b; Environm ental Defense Fund, 1994).
The Environm ental Defense Fund m odel was a test case for agricultural non-point source pollution

Appendix C 3control that applies point source control regulation m e thodology. The m odel focuses on pollution

sources, a program of load reductions, and econom ic incentives which include tradable discharge

perm its and tiered water pricing (Environm ental Defense Fund, 1994). The m odified version of the
TMDL m odel for the SJR was adopted as part of a waste discharge permit for the Grassland subarea in 1998 (CCVRW QCB, 1998a).
The choice of a com p liance site for the m odels and the waste discharge perm it has critical
im plications f o r the perception of water quality in the SJR. Little f r esh water f l ows into the SJR upstream of Crows Landing due to regulation of the SJ R by Friant Dam

. Most of the SJR is diverted south through the Friant-Kern Canal, leaving agricultura l drainage as the m a jority of the flow in the SJR heading north in the 22 m iles of river above confluence with the Merced River. A com p liance site upstream of the Merced River would be the m o st pr ecautionary. It would closely reflect the quality of the drainage water and be indicative of conditions in the upstream 22 m iles. Com p liance 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 m o re indicative of downstream water quality. The current

com p liance point is the SJR downstream the Merced River at Crows Landing. It represents the 130-

m ile reach of the lower SJR that is listed as im paired. The state perm it for discharge to the SJR allows for a twelve-year com p liance schedule. Full com p liance for the SJR above and below the Merced River to a Se water-quality objective of 5 μ g/L (4-day average) is scheduled for October 2010. Variables considered in deriving a Se load allocation from the TMDL-type m odels are:

• water-year type,

• water-quality objective,

• averaging period,

• exceedance frequency, and

• flow derivation. Table C1 and Figures C2, C3 and C4 give a sum m a ry of volum e of discharge and loads to com p are

exam ple load allocations from the TMDL and the TMML m odels for different types of water years. Figure C2 shows the TMDL m odel loads for all water-year types (norm a l/wet, dry/below norm a l, and critically dry) for the case of a 5 μ g Se/L standard, 4-day average, and a one-in-three-year violation rate. Figure C3 shows a com p arison of the TMDL and TMML m odel loads for a wet-year allocation
under the sam e conditions as above. Figure C4 shows a com p arison of the TMDL and TMML m odel

4loads for a dry-year allocation under the sam e conditions as above. Tables C2 and C3 and Figures C5 through C10 docum ent in m o re detail the load allocations for the SJR calculated from several different

com b inations of m odel assum p tions using a Se water-quality objective of 8 or 5 μ g/L. These data are

com p iled from docum entation for the TMDL and TMML m odels (CCVRW QCB, 1994b and
Environm ental Defense Fund, 1994). The base case for the SJR TMDL was a single de sign flow of approxim a tely 92,000 acre-feet at 5

μ g Se/L. The m odel allocated a load of 1,248 lbs Se (Table C2) (Environm ental Defense Fund, 1994). The quasi-static type TMDL m odel has three water-year classifications for the SJR (critically dry, dry/below norm a l, and above norm a l/wet; Table C2 and Figures C5, C6, and C7). The TMML m odel,
as subm itted to USEPA f o r approval, derives loads f o r only two types of water years (critically dry/dry/below norm a l and above norm a l/wet; Table C3 and Figures C8, C9, and C10). Figures C5 through C10 also depict the seasonal nature of the m odels, with the greatest loads being discharged
from Decem ber through May. W ithin a specific m odel, 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 m onthly averages, and when allowable fre quencies of violations of once-in-three-years are replaced by a frequency of once-in-five-m onths (Figures C5 through C10). The TMDL m odel 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 norm a l 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 m odel allows loads of 3,165 to 6,547 lbs Se/year and the TMML m odel predicts loads of 3,760 to 5,334 lbs Se/year.
The Clean W a ter Act requires a margin of safety be considered in regulatory load m odels based solely on dilution. The purpose is to take into account any lack of knowledge concerning the relation
of effluent lim itations and water quality (Environm ental Defense Fund, 1994). Tables C1, C2, and C3
also show Se loads used as a nom inal 10% m a rgin of safety to account for the uncertainties in the data
and as estim ated background loads from tributary rivers and wetlands. The m a rgin 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 m odeled TMDL allowances for the dischargers, thereby increasing the m odeled discharge to the SJR at Crows Landing (Tables C1, C 2, and C3), but leaving in doubt protection of the
SJR. Appendix C 5Models that Maximize the Allowed Selenium Load by Targeting Concentration An alternative approach is to define a concentration target in a receiving water and m a nage Se discharges to m a intain that target concentration under different flow conditions. Such a m odel, designed to m a nage loads using dynamic drainage effluent lim its based on the real-time dilution capacity of the SJR, was recently suggested as a drainage m a nagem e nt tool (Karkoski, 1996; CSW RCB, 1999a). In this proposal, Se-load-reduction is deferred to a plan of tem poral storage and tim ed release
of concentrated effluent to m a tch dilution by tributary flows to obtain com p liance to the 5 μ g Se/L objective. The dynam i c real-tim e (DRT) m odel, thus, uses tim ed-release of Se-laden drainage to take

m a xim u m advantage of the dilution capacity of the river at the given water-quality objective (e.g., the
Se concentration in the SJR will be m a intained at 5 μ g Se/L at all tim es). Figure C11 shows an

exam ple from lim ited data of the DRT m odel loads for wet-year conditions using a 5 μ g Se/L objective (Karkoski, 1996). Table C1 com p ares the loadings allowed by the DRT m odel to those allocated by
the TMDL and TMML m odels, for a m i nim u m , m ean, and m a xim u m am ount of allowable loads of Se discharged per m onth in a wet year. Figure C11 shows that an order-of-m a gnitude higher loads occurs
in som e m onths than allowed by the TMDL or TMML m odels (e.g., 400 versus 4000 lbs Se) for som e

m onths. 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 m ean of 7,347 lbs Se/year. A

m o re recent reference to the DRT m odel shows the wet year load to be approxim a tely 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
Im plem entation Program , 1999b). W ith real-tim e dr ainage m a nagem e nt, ponds for flow regulation would be necessary in order to m a xim i ze release of Se loads during variable flow conditions in the river. The holding pond concept is rem i niscent 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 com p leted to the Bay-Delta. As m e ntioned earlier, m o re sophis ticated storage, control, and tim ing are envisioned by m a nagers and state regulators. Nevertheless, the ecological consequences of the ponds them selves
need to be considered. Managing a constant concentration in receiving waters, although in response to a TMDL requirem e nt, is the goal of the dynam i c-effluent-type of m odeling. It is unclear whether this deviation
f r om the load m odel 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 6dilution water to m a xim i ze disposal of Se. Regulation of loads based on dynam i c effluent lim its provides no certainty for the am ount discharged per m onth or year, nor for an assessm ent of the longterm progress toward Se load reduction. The focus of the TMDL and TMML m odels is to reduce or

m i nim i ze Se loads by establishing a load target. W ith real-tim e drainage m a nagem e nt, the focus is shifted to a concentration target that, in essence, m a xim i zes Se loads by adjusting the tim ing of discharges to coincide with dilution capacity. As a result the allowed Se load would increase over those allocated by the TMDL or TMML m odels. The DRT approach is best applied to m a intaining 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.
Som e additional practical considerations add com p lexity to applying the DRT concept. These include the fact that a regulatory authority for the responsibility of im plem enting real time regulation has not been identified. Uncertainty exists about the regulatory control program that would determ ine the target concentration. Different agencies and stakeholders have called for revisions of the Se objective upward from 5 μ g Se/L, upward to 8 μ g Se/L, or downward to 2 μ g Se/L. The choice of a

com p liance point (SJR at Patterson or Crows La nding or SLD at Mud Slough) will have a strong influence on objectives, and therefore, it is also critical to determ ining the allowed load (as described above). Uncertainties about the use of the conveyance channel for the drainage (wetland channels or the SLD) could have im plications for concentrations . Since agricultural drainage is regulated as nonpoint source pollution, a 5 μ g Se/L effluent stream from the discharger has not been required in the past. It is unclear how this would be integrat ed into the regulatory control program . Finally,
refinem e nt of the assim ilative capacity operations plan using real-tim e m a nagem e nt does not include collecting data to assess whether re-def ining the assim ilative capacity of the SJR based on the
bioaccum u lative nature of Se is necessary (GAF, 1998a). Understanding the sources of Se and how Se

m oves through the agricultural discharge system becom e s very im portant in a strategy that m a xim i zes loads to m eet concentration objectives.
A second reason for m odeling the influence of tim ed releases of agricultural discharges to the SJR
has been to m eet the salinity standard for the SJR at Vernalis (CSW RCB, 1994, 1997, and 1999a; EA Engineering, Science, and Technology, 1999). The state m odel predicted that controlled tim ing or
wetland releases or a com b ination of drainage and wetland releases did not obtain com p liance with that standard. Focus then shifted toward taking advantage of additional seasonally available downstream dilution by releasing dilution water from the New Mel ones Reservoir on the Stanislaus River. Control Appendix C 7of drainage release to the SJR also includes im plem entation of a system of storage including recycling facilities, evaporation ponds, and in-field subsurface storage (CSW RCB, 1997). Despite the several opportunities for m a nipulating the m a ssively engineered CVP water supply, the ultim ate alternative for salinity control seem s to depend on m a naging the sam e lands that need drainage and that discharge Se, but the state plan does not include an analysis of Se im pacts.

8

# 0

1 2 3 4 5 6 7 8 9 10 11 12NO. 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 35000SJR @ Crows L., (ac-ft)



# 0 100 200 300 400 500Se, (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, Dr y, Criticall y 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 35000SJR flow @ Crows L., (ac-ft)



# 0 50 100 150 200 250 300 350 400 450Se, (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 30000SJR @ Crows L., (ac-ft)



# 0 100 200 300 400Se, (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 30000SJR@Crows L., (ac-ft)



# 0 50 100 150 200 250 300 350 400Se, (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 40000SJR @ Crows L., (ac-ft)



# 0 100 200 300 400 500 600Se, (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 60000SJR@Crows L., (ac-ft)



# 0 100 200 300 400 500 600 700 800Se, (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 16000SJR flow @ Crows L., (ac-ft)



# 0 50 100 150 200 250 300 350Se, (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 16000SJR flow @ Crows L., (ac-ft)



# 0 50 100 150 200Se, (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 40000SJR flow @ Crows L., (ac-ft)



# 0 100 200 300 400 500Se, 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 - 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 5000Se, (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 C11Table C1Modeled Selenium Load Allocation and Discharge to theSan Joaquin River from the Grassland Drainage Problem AreaModelsIrrigated/drainedacresRange used to model Sedischarge (San JoaquinRiver at Crows Landing)(acre-feet/year)Range ofmodeled Seloadallocation(lbs Se/year)Range ofModeled Sebackground(lbs/Se/year)Range ofmodeled SeMOS (marginof safety)(uncertainty)(lbs Se/year)Range ofmodeled Se dischargeto San Joaquin Riverat Crows Landing (lbsSe/year)Total Maximum Daily Load (TMDL)*(5 ppb Se objective in San JoaquinRiver4-day or monthly averaging period1in 3 year or 1 in 5 month violationfrequency)Critically Dry**Dry/Below Normal**Above Normal/Wet**93,390/49,273104,030-260,859225,995-328,002233,186-481,9341,163-3,0602,504-3,7372,598-5,46391-129257-273250-428140-352305-448317-6561,394-3,5413,066-4,4583,165-6,547Total Maximum Monthly Load(TMML)***(5 ppb Se objective in San JoaquinRiver4-day or monthly averaging period1in 3 year violation frequency)DryWet90,620/44,86091,255-133,210276,772-392,5701,001-1,5143,088-4,451116-114294-362123-179381-5341,240-1,8093,760-5,334Dynamic Real Time (DRT) ****5 ppb Se objective in San JoaquinRiverWet2,605-17,605(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 (CCVRWQCB, 1994b, Table 7);reference to San Joaquin River Index , threshold millionsof 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 C2Modeled (TMDL, Total Maximum Daily Load model) Annual SeleniumLoad Allowance to the San Joaquin River from the Grassland AreaSelenium Performance Goalor Regulation ScenarioIrrigatedacreage/drainedacreage** **Modeledload allocationlbs Se/yearModeledbackgroundlbs Se/yearModeledMOS (Margin ofSafety)(Uncertainty)lbs Se/yearModeled discharge toSan Joaquin River atCrows Landing/Pattersonlbs Se/yearModeled flow (SanJoaquin River atCrows Landing/Patterson)(acre-feet/year)TMDL Model*Single design flow5 ppb Se4-day average1 in 3 yr violation frequency93,390/49,2731,24892,363TMDL Model5 ppb Se4-day average1 in 3 yr violation frequencyCritically DryDry/Below NormalAbove Normal/Wet93,390/49,2731,1632,5042,5981102572501403053171,4153,0693,166104,030225,995233,186TMDL Model5 ppb Semonthly average1 in 3 yr violation frequencyCritically DryDry/Below NormalAbove Normal/Wet93,390/49,2731,6763,0363,3741192652802003664051,9943,6664,061147,029270,000299,049TMDL Model5 ppb Se4-day average1 in 5 month violationfrequencyCritically DryDry/Below NormalAbove Normal/Wet93,390/49,2733,0603,7375,4631292734283524486563,5464,4546,549260,859328,002481,934* Developed by Environmental Defense Fund (EDF, 1994) and CCVRWQCB, 1994b)** Draft submittal of TMML Model for Selenium inthe San Joaquin River to USEPA (CCVRWQCB, 1996a)*** Modeled effluent load datafrom October, 1985 to December, 1988;modeled San Joaquin River flow at Crows Landing and Patterson from WY 1970 to 1991(Notes: Flow record for Crows Landing is from 1970-1972; the remainder of the data used in the model for Crows Landing was reconstructed from flow data collected atSJR at Patterson. Data was also “adjusted” for averaging period because record isincomplete, CCVRWQCB, 1994 b; Karkoski, 1996)  Environmental Defense Fund, 1994, Table II-4 Baseline Datafor Pollution Allocation Subtotal (does not include 10,000 irrigated acres and 5,276 drained acres asnoted 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 Normal3.1-3.8 MAF; and Wet >3.8 MAF (CCVRWQCB,1994b, Table 7)Table C3Modeled (TMML model, Total Maximum Monthly Load model and DRT model, Dynamic Real-Time model) Annual Selenium Load Allowance to the SanJoaquin River from the Grassland AreaSelenium Performance Goal orRegulation ScenarioIrrigatedacreage/drainedacreage****Modeledload allocationlbs Se/yearModeledbackgroundlbs Se/yearModeledMOS (Margin ofSafety)(Uncertainty)lbs/yearModeled discharge toSan Joaquin River atCrows Landing/Pattersonlbs Se/yearModeled flow (SanJoaquin River atCrows Landing/Patterson)acre-feet/yearTMML Model*8 ppb Semonthly mean1 in 3 yr violation frequencycritically dry/dry/below normal90,620/44,8602,4911142902,896133,210TMML Model5 ppb Se4-day average1 in 3 yr violation frequencycritically dry/dry/below normalabove normal/wet90,620/44,8601,0013,0881162941233811,2403,76091,255276,772TMML Model5 ppb Semonthly average1 in 3 yr violation frequencycritically dry/dry/below normalabove normal/wet90,620/44,8601,5144,4511143621795341,8095,334133,210392,570DRT Model**5 ppb Sewetmeanminimummaximum7,3472,60517,605* Draft submittal of TMML Model for Selenium inthe San Joaquin River to USEPA (CCVRWQCB, 1996a);** Karkoski, 1996;*** Modeled effluent load datafrom October, 1985 to December, 1988; model SanJoaquin River flow atCrows Landing and Patterson from WY 1970 to 1991(Note: flow record for Crows Landing is from 1970-1972. The remainder of the data used in the model for Crows Landing was reconstructed from flow data collectedat SJR at Patterson);****CCVRWQCB, 1994b, Table 1.

## APPENDIX D

Variability

## APPENDIX D Variability 

## CONTENTS

Introducti o n 4
T i m e 5 Seasonal and inte r-annual va riability

.......................................................................................... ......... 5 Monthly, Daily and Hourly Measurem ents

......................................................................................... .6
S p a c e 7
P r e d i c t i o n o f S h o r t

- T e r m S e l e n i u m R e s e r v o i r s 9



### FIGURES

D1. Monthly selenium concentration ( μ g Se/L) and volum e (acre-feet) at site B (SLD outflow to Mud Slough) for W Y 1997. D2. Monthly selenium load (lbs) and volum e (acr e-feet) at site B (SLD outflow to Mud Slough) for W Y 1997. D3. Monthly salt concentration (m g/L) and volum e (acre-feet) at site B (SLD outflow to Mud Slough) for W Y 1997. D4

. Monthly salt load (tons) and volum e (acre-feet) at site B (SLD outflow to Mud Slough) for W Y 1997. D5. Monthly selenium concentration ( μ g Se/L) and volum e (acre-feet) at site B (SLD outflow to Mud Slough) for W Y 1998. D6. Monthly selenium load (lbs) and volum e (acre- feet) at site B (SLD outflow to Mud Slough) or W Y 1998. D7. Monthly salt concentration (m g/L) and volum e (acre-feet) at site B (SLD outflow to Mud Slough) for W Y 1998. D8. Monthly salt load (tons) and volum e (acre-feet) at site B (SLD outflow to Mud Slough) for W Y 1998. D9. Continuous flow m onitoring (cfs) at site B for W Y 1997. D10. Continuous selenium concentration m onitoring ( μ g Se/L) at site B for W Y 1997. D11. Continuous specific conductance m onitoring ( μ S/cm ) at site B for W Y 1997. D12. Calculated total dissolved solids (m g/L salt) at site B for W Y 1997. D13. Continuous selenium load m onitoring (lbs) at site B for W Y 1997. D14. Calculated salt (tons/day) at site B for W Y 1997. D15. Continuous flow m onitoring (cfs) at site B for W Y 1998. D16. Continuous selenium concentration m onitoring ( μ g Se/L) at site B for W Y 1998. D17. Continuous specific conductance m onitoring ( μ S/cm ) at site B for W Y 1998. D18. Calculated total dissolved solids (m g/L salt) at site B for W Y 1998. D19. Continuous selenium load m onitoring (lbs) at site B for W Y 1998. D20. Calculated salt (tons/day) at site B for W Y 1998.
2D21. San Luis Drain Special Study. Hourly relations between electrical conductance ( μ m hos) and selenium concentrations ( μ g Se/L) during 1 – 24 hour period (6/26/97). D22. Relation between selenium load (lbs) and selenium concentrations ( μ g Se/L) at Crows Landing for W Y 1997. D23. Relation between selenium load (lbs) and selenium concentrations ( μ g Se/L) at Crows Landing for W Y 1998. D24. Relation between salt load (tons) and salt concentration (m g/L) at Crows Landing for W Y 1997. D25. Relation between salt load (tons) and salt concentration (m g/L) at Crows Landing for W Y 1998. D26. Continuous flow m onitoring (cfs) at Crows Landing for W Y 1997. D27. Continuous selenium concentration m onitoring ( μ g Se/L) at Crows Landing for W Y 1997. D28. Continuous specific conductance m onitoring ( μ S/cm ) at Crows Landing for W Y 1997. D29. Calculated total dissolved solids (m g/L salt) at Crows Landing for W Y 1997. D30. Continuous selenium load m onitoring (lbs) at Crows Landing for W Y 1997. D31. Calculated salt (tons/day) at Crows Landing for W Y 1997. D32. Continuous flow m onitoring (cfs) at Crows Landing for W Y 1998. D33. Continuous selenium concentration m onitoring ( μ g Se/L) at Crows Landing for W Y 1998. D34. Continuous specific conductance m onitoring ( μ S/cm ) at Crows Landing for W Y 1998. D35. Calculated total dissolved solids (m g/L salt) at Crows Landing for W Y 1998. D36. Continuous selenium load m onitoring (lbs) at Crows Landing for W Y 1998. D37. Calculated salt load (tons/day) at Crows Landing for W Y 1998. D38. Percent selenium load (norm a lized to the selenium load at Vernalis) for Drainage Problem Area (DPA), Mud Slough + Salt Slough (MS+SS), and Crows La nding-Patterson (CL-PATT) for W Y 1986 through W Y 1997. D39. Percent salt load (norm a lized to the salt load at Vernalis) for Drainage Problem Area (DPA), Mud Slough + Salt Slough (MS+SS), and Crows Landing-Patterson (CL-PATT) for W Y 1986 through W Y 1997. D40. Relation between total water applied (acre-f eet) a nd drainage flow (acre-feet) for the Drainage Problem Area (DPA) for W Y 1986 through W Y 1997. D41. Relation between total water applied (acre-f eet), total dissolved solids (m g/L), and selenium ( μ g Se/L) for the Drainage Problem Area (DPA) for W Y 1986 through W Y 1997. D42. Relation between total water applied (acre-f eet), total dissolved solids loads (tons), and selenium load (lbs) for the Drainage Problem Area (DPA) for W Y 1986 through W Y 1997. D43. Relation between drainage flow (acre-feet), selenium ( μ g Se/L), and total dissolved solids (m g/L) for the Drainage Problem Area (DPA) for W Y 1986 through W Y 1997. D44. Relation between drainage flow (acre-feet), seleni um load (lbs), and total dissolved solids load (tons) for the Drainage Problem Area (DPA) for the W Y 1986 through W Y 1997. D45. Relation between 1) flow and selenium load a nd 2) between flow and selenium concentration at site B (SLD outflow to Mud Slough) for W Y 1997. D46. Relation between 1) flow and selenium load a nd 2) between flow and selenium concentration at site B (SLD outflow to Mud Slough) for W Y 1998. D47. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), and selenium concentration of drainage ( μ g Se/L) at site B for W Y 1997. D48. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), Appendix D 3and selenium load of drainage (lbs) at site B for W Y 1997. D49. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), and selenium concentration of drainage ( μ g Se/L) at site B for W Y 1998. D50. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), and selenium load of drainage (lbs) at site B for W Y 1998. D51. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), and selenium concentration of drainage ( μ g Se/L) for base average W Y 1986 through W Y
1994. D52. Monthly relation between drainage discharge (acr e-feet, irrigation + precipitation (acre-feet), and selenium load of drainage (lbs) for base average W Y 1986 through W Y 1994. D53. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), and salt concentration of drainage (m g Se/L) at site B for W Y 1997. D54. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), and salt load of drainage (tons) at site B for W Y 1997. D55. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), and salt concentration of drainage (m g Se/L) at site B for W Y 1998. D56. Monthly relation between drainage discharge (acr e-feet), irrigation + precipitation (acre-feet), and salt load of drainage (tons) at site B for W Y 1998.



### TABLES
D1. Selenium load (lbs) from the Grassland Dr ainage 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 Probl em Area, Mud and Salt Sloughs, and the San Joaquin River at Patterson/Crows Landing as a per centage of salt load at the San Joaquin River at Vernalis.



## APPENDIX D Variability

Introduction
The above estim ates of loadings contain som e substantial uncertainties that have not been
discussed. The m o st im portant of these are associated with the tim e dependence and the spatial dependence of Se loads or the ways those loads are determ ined. Given here are a series of graphs (Figures D1 through D56) based on available data that docum ent the variability of agricultural drainage Se loads to the SJR and the SLD. Flow and concentration data also have been com p iled and

4graphed as determ inants of load. Because collection of data suitable for m o re detailed projections is essential in the future, suggestions for m onitoring also are given. Discharge data from the Grassland Area (or hist orically the Drainage Problem Area) represent drainage from the source area (i.e., farm land sum p s or agricultural drainage canals). Discharge was

m easured at the SLD outflow to Mud Slough (i.e., site B). Downstream sites from the SLD discharge
are the com b ined 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, approxim a tely 50 m iles
downstream from the farm agricultural discharge sum p s), and the SJR at Vernalis (VERN, approxim a tely 130 m iles downstream from the agricultural discharge).



### Time

Seasonal and inter-annual variability
The salt im balance in the SJV is also a driving f o rce f o r m a nagem e nt activities. Selenium loads

are com p ared to salt loads to elucidate the behavior of a conservative elem ent, represented by salt (i.e.,total dissolved solids or specific conductance as a surrogate for salt concentrations), to that of the nonconservative elem ent, Se. Salt concentrations were calculated from specific conductance by using the equation:

specific conductance X 0.65 = m g /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 volum e of dr ainage (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 m illion (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 com p iled in Table 4.

Appendix D 5Monthly, Daily and Hourly Measurements The Grassland Bypass Channel Project (GBCP) Monitoring Plan provides for m o re frequent

m easurem ents of flow and Se and salt concentrations in the SLD (USBR et. al., 1996). The Grassland Area or Drainage Problem Area discharge was m easur ed at the SLD outflow to Mud Slough (i.e., site B) for W Y 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 W Y 1997 and W Y 1998 in m onthly SLD discharge (averages of daily flow m easurem ents), m onthly Se concentrations (averages of daily m easurem ents),

m onthly salt concentrations [averages of daily specific conductance converted to TDS or salt concentration] , and calculated m onthly Se and salt loads. W ith initiation of the GBCP, drainage

m a nagem e nt is aim e d at m eeting m onthly Se load ta rgets 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.
Maxim u m pre-irrigation occurs in February, m a xim u m irrigation in July, and m a xim u m discharge in February or March. Ranges of m onthly variati on for W Y 1997 are: flow, 1,274 to 4,867 acre-feet; Se
concentration 25 to 105 μ g Se/L; salt concentration 2,175 to 3,255 m g /L, Se load 109 to 1,278 lbs, and salt load 4,325 to 20,091 tons. Ranges of m onthly variation for W Y 1998 are: flow, 1,403 to 7,094 acre-feet; Se concentration 43 to 105 μ g Se/L; salt concentration 2,391 to 3,704 m g /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 W Y 1997 and W Y 1998 in SLD flow (based
on 20-m i nute interval m easurem ents), Se concentrations, TDS or salt concentrations (based on specific
conductance m easurem ents), Se loads, and salt loads (USBR et al., 1998 and 1999). Ranges of daily
variation for W Y 1997 are: flow 21 to 181 acre-feet; Se concentration 15 to 116 μ g Se/L; and salt concentration 1,703 to 3,671 m g /L. Daily loads vary from 1.1 to 54 lbs Se and 66 to 860 tons salt. Ranges of daily variation for W Y 1998 are: flow 20 to 288 acre-feet; Se concentration 20 to 128 μ g Se/L; and salt concentration 4,114 to 2,230 m g /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, CCVRW QCB, personal com m unication, 6/1/98). Ranges of hourly
variations are: Se concentration 47 to 78 μ g Se/L; and conductivity 4,280 to 4,675 μ m hos/cm (equivalent to 2,782 to 3,039 m g /L TDS).

6 Figures D22 and D23 com p are m onthly Se load and concentration data for the SJR at Crows Landing downstream of the SLD discharge for W Y 1997 and 1998 (USBR et al., 1998 and 1999). InW Y 1997 Se concentrations were lower com p ared to those of W Y 1998 because flow in the SJR below
the Merced River in W Y 1998 was sustained at a higher level for a longer period than W Y 1997 due to
increased snowm e lt flowing in the Merced River. The com p eting 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 W Y 1997 and 15,884 lbs for W Y 1998, but only violation of the 5 μ g Se/L objective in
W Y 1997, not in W Y 1998 at the SJR below the Merced River. Figures D24 and D25 com p are salt load and concentration data for the SJR at Crows Landing for W Y 1997 and 1998. Salt load and concentration patterns generally follow those for Se load and concentration in W Y 1997, but the salt concentration pattern deviates from that of Se c oncentration in W Y 1998. Ranges of m onthly variation
for W Y 1997 are: flow 28,761 to 1,212,948 acre-feet; Se concentration, 0.36 to 6.8 μ g Se/L; salt
concentration 109 to 952 m g /L; Se load, 149 to 1,533 lbs; and salt load, 24,563 to 242,735 tons. Ranges of m onthly variation for W Y 1998 are: flow 40,200 to 998,158 acre-feet; Se concentration,
0.69 to 2.6 μ g Se/L; salt concentration 108 to 934 m g /L; Se load, 262 to 3,133 lbs; and salt load, 37,006 to 284,356 tons. Daily m easurem ents also were taken during W Y 1997 and 1998 for the SJR at Crows Landing (USBR et al., 1998 and 1999). Figures D26 through D31 show the W Y -1997 daily variation of flow, Se and salt concentrations, and calculated daily Se and salt loads. Ranges of daily variation for W Y 1997 are: flow 413 to 37,100 cfs or 818 to 73,458 acre-feet; Se concentration 0.1 to 9.7 μ g Se/L; salt concentration 82 to 1,165 m g /L; Se load 1.3 to 183 lbs; and salt load 500 to 15,956 tons. Figures D32 through D37 show the W Y 1998 daily variation of flow, Se and salt concentrations, and calculated daily Se and salt loads. Ranges of daily variation for W Y 1998 are: flow 483 to 24,200 cfs or 956 to 47,916 acre-feet; Se concentration 0.5 to 4.1 μ g Se/L; salt concentration 79 to 1,165 m g /L; Se load 3.4 to 183 lbs; and salt load 809 to 15,482 tons.



### Space
Given in Tables D1 and D2 for W Y 1986 to 1997 are the percentages of the input Se (nonconservative elem ent) and salt (conservative elem ent) loads to the discharged load of Se and salt for the SJR at Vernalis, the entrance to the Bay-Delta (CCVRW QCB, 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 fr om both slough and river sources (i.e., the SJR is the

Appendix D 7only outlet from the SJV). The Merced River inflow to the SJR is approxim a tely 60 m iles above Vernalis, which is the entrance of the SJR to the Bay-Delta. Between the Merced River conf luence and Vernalis, the Tuolum ne and Stanislaus Rivers fl ow into the SJR. Approxim a tely 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, com b ined Mud and Salt Sloughs, and Crows Landing/Patterson norm a lized to the Se load at the SJR at Vernalis. Figure D39 shows the percent of the salt load from the Drainage Problem Area, com b ined Mud and Salt Sloughs, and Crows Landing/Patterson norm a lized 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 m easured as the input to the system (i.e., prim ary drainage canals, Drainage Problem Area) are perpetually different
from those m easured as the outputs from the system (i.e., downstream in wetland sloughs or the SJR).
Downstream Se loads show both decreases (m easured 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 s ource 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

m onitoring site location within the Grassland area (Table 5; Appendix B, Tables B4 to B7; Appendix A, Figures A9 and A10). The upstream discharge re presents m a naged com ponents of flow and load. Data in these graphs for W Y 1986 to W Y 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 W Y 1986 to 1997 for the DPA are: flow, 24,533 to 67,006 acre-feet; Se concentration 52 to 80 μ g 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 μ g Se/L; Se load 2,919 to 10,694 lbs. Com b ining the data for Mud and Salt sloughs dam p ens 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 m illi on acre-feet/year; Se concentration 1 to 6.3 μ g 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 m illion acre-feet/year; Se concentration 0.6 to 3.0 μ g Se/L; and Se load 3,611 to 17,238 lbs/year.

8Except for W Y 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). Com p rehensive m onitoring data are not available to determ ine the Se “loss” (i.e., that am ount of load unaccounted for) after transit through the Grasslands wetlands (estim ated annual m a xim u m 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 m easured at Mud and Salt Sloughs, and in som e cases, over loads m easured furthe st upstream (i.e., Drainage Problem Area). The
increases m a y be due to other sources of Se entering the SJR or errors introduced through lim itations of the data as noted above. During W Y 1986 to W Y 1998, the loads in the SJR at Patterson/Crows range from 3,064 to 15,884 lbs Se with the m a xim u m occurring in W Y 1998 (Appendix B, Table B6).
The Se loads for the SJR at Vernalis from W Y 1986 to W Y 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 W Y 1998 (15,501 lbs and 13,445 lbs) depending on sets of flow data. For W Y 1998 for the SJR at Vernalis, the reported value is 15,810 lbs Se/year which is less than or sim ilar to the value m easured for the SJR at Crows Landing. A state prohibition lim itation for drainage over 8,000 lb s Se from the Grassland Area was enacted in
1996.



### Prediction of Short-Term Selenium Reservoirs
Data from W Y 1986 to 1994 from the Grassland Area (or generically, the drainage source area) are given as an exam ple of a m a naged agricultural drainage discharge system (CCVRW QCB, 1996a;b; 1998d; e; f; g; h; GAF, 1998b). Measurem ents for the drainage problem area are referred to agricultural drainage canals for W Y 1986 to 1996 and site B (SLD discharge into Mud Slough) for W Y 1997 and
W Y 1998. Figures D40 through D44 show, using data from W Y 1986 to 1997, general relations

am ong annualized am ounts 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.

Appendix D 9This series of figures show som e of the variables that affect load generation, but not the fundam e ntal 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 incr ease. 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 m onthly and daily data these annual relations are not valid

. Figures D45 and D46 show
the relation am ong flow, concentration, and load using daily m easurem ents for W Y 1997 and 1998 at the SLD discharge to Mud Slough (site B) (USBR et al., 1998; 1999). In W Y 1997 Se load and
concentration increase with flow. In W Y 1998 however, concentration and load decrease at flows greater than approxim a tely 100 cubic feet per s econd, thus showing som e drainage relief through dilution at the higher flows during storm s 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 discharg e at site B in the SLD on a m onthly basis for the Grassland Area. Figures D47 through D50 ar e W Y -1997 and -1998 sum m a ries using m onthly averages of flow (i.e., discharge), Se load, and Se concentration along with am ounts of applied water (irrigation and precipitation). Figures D51 and D52 show a m onthly average of W Y 1986 through 1994 (the base year average used for generating the GBCP load targets, see Appendix B, Figure B1)
for the sam e param e ters. For com p arison, Figures D53 through D56 are sum m a ries of salt load and salt concentration data for the SLD discharge shown in a sim ilar series of graphs for that of Se discharge in W Y 1997 and 1998. Patterns of loading to the SLD are sim ilar through the series of graphs, showing peak Se loads and concentrations during the m onths of March or April. Maxim u m application of water occurred in June, July, and August. W i nter rainfall peaks can be seen especially in
W Y 1998 during February.

10Figure D2 Figure D1

Figure D4 Figure D3 0 1000 2000 3000 4000 5000 6000 7000Acre-feet

0 200 400 600 800 1000 1200 1400 1600Se, (lbs)

10 11 12 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 7000Acre-feet

0 4000 8000 12000 16000 20000 24000 28000 32000Salt 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 7000Acre-feet

0 20 40 60 80 100 120Se, ppb

10 11 12 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 7000Acre-feet

0 400 800 1200 1600 2000 2400 2800 3200 3600Salt CONC, (mg/L)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH
Acre-ft Salt, mg/L SITE B - Acre - feet vs Salt CONC

WY 1997Figure D6 Figure D5

Figure D8 Figure D7 0 1000 2000 3000 4000 5000 6000 7000Acre-feet

0 200 400 600 800 1000 1200 1400 1600Se, lbs

10 11 12 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 7000Acre-feet

0 20 40 60 80 100 120Se, ppb

10 11 12 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 7000Acre-feet

0 4000 8000 12000 16000 20000 24000 28000 32000Salt 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 7000Acre-feet

0 400 800 1200 1600 2000 2400 2800 3200 3600Salt CONC, (mg/L)

10 11 12 1 2 3 4 5 6 7 8 9

MONTH
Acre-ft Salt, mg/L SITE B - Acre - feet vs SALT CONC

WY 1998Figure D10 Figure D9

Figure D12 Figure D11

Figure D14 Figure D13 0 20 40 60 80 100 120 140 160FLOW (cfs)

10/01/96 12/18/96 03/06/97 05/23/97 08/09/97 DATE SITE B - CONTINUOUS MONITORING - FLOW

10/1/96 to 9/30/97

0 20 40 60 80 100 120 140Se CONCENTRATION, (μg/L)

10/01/96 12/18/96 03/06/97 05/23/97 08/09/97 DATE SITE B-CONTINUOUS MONITORING-Se CONC

10/1/96 to 9/30/97

0 1000 2000 3000 4000 5000 6000 7000SPECIFIC CONDUCTANCE (μS/cm)

10/01/96

12/18/96 03/06/97 05/23/97 08/09/97

DATE SITE B-CONTINUOUS MONITORING-SP COND

10/1/96 to 9/30/97

0 500 1000 1500 2000 2500 3000 3500 4000 4500mg/L salt (calculated)

10/01/96

12/18/96 03/06/97 05/23/97 08/09/97

DATE SITE B - TDS (calculated) 10/1/96 to 9/30/97

0 10 20 30 40 50 60 70Se LOAD (lbs)

10/01/96 12/18/96 03/06/97 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 1200salt (tons/day), calculated

10/01/96

12/18/96 03/06/97 05/23/97 08/09/97

DATE SITE B - SALT (calculated) 10/1/96 to 9/30/97Figure D16 Figure D15

Figure D18 Figure D17

Figure D20 Figure D19 0 20 40 60 80 100 120 140 160FLOW (cfs)

10/01/97 12/18/97 03/06/98 05/23/98 08/09/98 DATE SITE B - CONTINUOUS MONITORING - FLOW

10/1/97 to 9/30/98

0 20 40 60 80 100 120 140Se CONCENTRATION, (μg/L)

10/01/97 12/18/97 03/06/98 05/23/98 08/09/98 DATE SITE B-CONTINUOUS MONITORING-Se CONC

10/1/97 to 9/30/98

0 1000 2000 3000 4000 5000 6000 7000SPECIFIC CONDUCTANCE (μS/cm)

10/01/97

12/18/97 03/06/98 05/23/98 08/09/98

DATE SITE B-CONTINUOUS MONITORING-SP COND

10/1/97 to 9/30/98

0 500 1000 1500 2000 2500 3000 3500 4000 4500mg/L salt (calculated)

10/01/97

12/18/97 03/06/98 05/23/98 08/09/98

DATE SITE B - TDS (calculated) 10/1/97 to 9/30/98

0 10 20 30 40 50 60 70Se LOAD (lbs)

10/01/97 12/18/97 03/06/98 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 1200salt (tons/day), calculated

10/01/97 12/18/97 03/06/98 05/23/98 08/09/98 DATE SITE B - SALT (calculated) 10/1/97 to 9/30/98

# 4200

4300 4400 4500 4600 4700Lab EC (μmhos)



# 45 50 55 60 65 70 75 80Se (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 D21Figure D23 Figure D22

Figure D25 Figure D24 0 400 800 1200 1600 2000 2400 2800 3200Se, lbs

0 1 2 3 4 5 6 7Se, 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 3200Se, lbs

0 1 2 3 4 5 6 7Se, 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 350000Salt (tons)

0 200 400 600 800 1000Salt (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 350000Salt, (tons)

0 200 400 600 800 1000Salt, (mg/L)

10 12 2 4 6 8

MONTH Salt load, tons Salt, mg/L Crows Landing - Salt LOAD vs Salt CONC

WY 1997Figure D27 Figure D26

Figure D29 Figure D28

Figure D31 Figure D30 0 10000 20000 30000 40000FLOW (cfs)

10/01/96

12/18/96 03/06/97 05/23/97 08/09/97 DATE Crows Landing, Cont. Monitoring, FLOW

10/1/96 to 9/30/97

0 2 4 6 8 10Se CONCENTRATION, (μg/L)

10/01/96 12/18/96 03/06/97 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 1800Specific Conductance, μS/cm

10/01/96

12/18/96 03/06/97 05/23/97 08/09/97

DATE Crows Landing, Cont. Monitor., S. Cond

10/1/96 to 9/30/97

0 200 400 600 800 1000 1200mg/L salt, (calculated)

10/01/96 12/18/96 03/06/97 05/23/97 08/09/97 DATE Crows Landing - TDS (calculated) 10/1/96 to 9/30/97

0 2000 4000 6000 8000 10000 12000 14000 16000tons/day salt, (calculated)

10/01/96

12/18/96 03/06/97 05/23/97 08/09/97 DATE Crows Landing - Salt (calculated)

10/1/96 to 9/30/97

0 50 100 150 200Se LOAD (lbs)

10/01/96 12/18/96 03/06/97 05/23/97 08/09/97 DATE Crows Landing, Cont. Monitoring, LOAD

10/1/96 to 9/30/97Figure D33 Figure D32

Figure D35 Figure D34

Figure D37 Figure D36 0 10000 20000 30000 40000FLOW (cfs)

10/01/97

12/18/97 03/06/98 05/23/98 08/09/98 DATE Crows Landing, Cont. Monitoring, FLOW

10/1/97 TO 9/30/98

0 2 4 6 8 10Se CONCENTRATION, (μg/L)

10/01/97 12/18/97 03/06/98 05/23/98 08/09/98 DATE Crows Landing, Cont. Monitoring, Se

10/1/97 to 9/30/98

0 50 100 150 200Se LOAD, (lbs)

10/01/97 12/18/97 03/06/98 05/23/98 08/09/98 DATE Crows Landing, Cont. Monitoring, LOAD

10/1/97 TO 9/30/98 0 200 400 600 800 1000 1200 1400 1600 1800Specific Conductance, μS/cm

10/01/97

12/18/97 03/06/98 05/23/98 08/09/98

DATE Crows Landing, Cont. Monitor., S. Cond

10/1/97 to 9/30/98

0 200 400 600 800 1000 1200mg/L salt, (calculated)

10/01/97

12/18/97 03/06/98 05/23/98 08/09/98 DATE Crows Landing - TDS (calculated)

10/1/97 to 9/30/98

0 2000 4000 6000 8000 10000 12000 14000 16000tons/day salt, (calculated)

10/01/97

12/18/97 03/06/98 05/23/98 08/09/98 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 98a 98b 

# 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 D39Figure D41 Figure D40

Figure D43 Figure D42

Figure D44 0 400 800 1200 1600 2000 2400 2800 3200TDS (mg/L)

0 10 20 30 40 50 60 70 80Se (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 80000FLOW (acre-ft)

180000 220000 260000 300000 340000

TOTAL WATER (acre-ft)

FLOW TOTAL WATER vs FLOW

DPA

0 40000 80000 120000 160000 200000 240000TDS (tons)

0 2000 4000 6000 8000 10000 12000Se (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 3200TDS (mg/L)

0 10 20 30 40 50 60 70 80Se (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 240000TDS (tons)

0 2000 4000 6000 8000 10000 12000Se (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 140Se (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 140Se (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 D46Figure D48 Figure D47

Figure D50 Figure D49

Figure D52 Figure D51 0 10000 20000 30000 40000 50000acre-feet (average)

0 20 40 60 80 100 120ppb Se (average)

10 11 12 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 50000acre-feet (average)

0 200 400 600 800 1000 1200 1400 1600 1800 2000Se lbs (average)

10 12 2 4 6 8

MONTH
DISCHARGE PPT+IRR Se lbs BASE AVERAGE WY 1986-1994 0 10000 20000 30000 40000 50000acre-feet

0 20 40 60 80 100 120ppb Se

10 11 12 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 50000acre-feet

0 200 400 600 800 1000 1200 1400 1600 1800 2000Se, 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 50000acre-feet

0 20 40 60 80 100 120ppb Se

10 11 12 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 50000acre-feet

0 500 1000 1500 2000Se lbs

10 12 2 4 6 8

MONTH
DISCHARGE PPT+IRR Se lbs SITE B-DISCHARGE,PPT+IRR,Se lbs

WY 1998Figure D54 Figure D53

Figure D56 Figure D55 0 10000 20000 30000 40000 50000acre-feet

0 400 800 1200 1600 2000 2400 2800 3200 3600Salt, 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 50000acre-feet

0 5000 10000 15000 20000 25000 30000 35000Salt, 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 50000acre-feet

0 400 800 1200 1600 2000 2400 2800 3200 3600Salt, 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 50000acre-feet

0 5000 10000 15000 20000 25000 30000 35000Salt, tons

10 12 2 4 6 8

MONTH
DISCHARGE PPT+IRR Salt load, tons SITE B-DISCHARGE,PPT+IRR,Salt tons

WY 1998TABLE D1Selenium load (lbs) from the Grassland Drainage Problem Area, Mud and Salt Sloughs,and the San Joaquin River at Patterson/Crows as a percentageof selenium load at the San Joaquin River at Vernalis.Selenium (lbs/year)DPA/ Vernalis (%)Mud andSalt/Vernalis (%)Patterson (Crows)/Vernalis (%)19866546721987126881011988120961101989100938519909910382199116210898199214382861993997792199410910294199569628319968883941997626977TABLE D2Salt 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 (%)198617397819872748791988285486198928547519902556791991274687199224438519932138781994245484199517358719961740681997103274

## APPENDIX E

Sediment Quality and Quantity Tables

## APPENDIX E Sediment Quality and Quantity Tables

TABLES
E1. Quantity of bed sedim e nt and suspended sedim e nt and concentrations and loads of selenium in bed sedim e nt of the San Luis Drain (constructed concrete channel). E2. Concentration of selenium in bed sedim e nt , su spended sedim e nt, and plankton in natural channels

Appendix E 1APPENDIX ESediment Quality and Quantity TablesTABLE E1Quantity ofbed sediment and suspended sediment and concentrationsand loads ofseleniumin bed sediment ofthe San Luis Drain(constructed concrete channel).Sediment in agricultural drainagecanal (constructed concrete channel)tons (dryweight)cubic yards(dry weight)lbs Seppm range/average (dryweight)mg/Lsuspendedsediment(avg. input)mg/Lsuspendedsediment(avg. output)San Luis Drain (1986, USBR)28-mile segment85-mile segment (1984)80,583211,0005,2805 - 190/84San Luis Drain (1984-1993) compilation of fivesurveys (Presser et al., 1996)1.4 - 210/55San Luis Drain (1987) (USBR et al., 1998; 1999;2000)28-mile segment85-mile segment58,094----San Luis Drain 1994 (Presser et al., 1996 ;Presser and Piper, 1998)8/949/943.2 - 110/4311 - 94/44San Luis Drain 1995 (Presser and Piper, 1998)28-mile segment85-mile segment55,788177,9004,500*14,400*San Luis Drain 1997 (USBR et al., 1998; 1999;2000)28-mile segment60,5932.9 - 100/30(whole coreaverageexcept 0.1value)San Luis Drain WY 1997 (USBR et al., 1998)(estimated from suspended solids)465 tonsdeposited/year@1.8gm/cc308 cy@2.6 gm/cc213 cynodataavailable10228* Calculated using an average concentration of seleniumin SLD bed sediment of 44 ppmSe (see 1994 data).Appendix E2TABLE E2 Concentration of selenium in bed sedim e nt, su spended sedim e nt, and plankton in natural channels

. Sediment in natural channels subj ected to intermittent agricultural drai nage di scharge from Grassl and Drai nage Probl em Area 1) 1950’sSept., 1996 from Agatha Canal and Camp 13 Sl ough; 2) October, 1996- continuing from SLD. All sites a re downstream of discharge except as noted. Bed Sediment ppm Se (value or range) (dry w e ight) Suspended Sediment ppm Se (value or range) (dry w e ight) Plankton ppm Se (value or range) (dry w e ight)
Agatha Canal , CDFG, 1988 1

. 0 1

. 4 3

. 8 Camp 13 Sl ough, 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 Sl ough, CDFG 200m dow n stream of SL D (i nacti v e)* 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 Sl ough (1992-1993, USFWS; Henderson et al ., 1995) 600 yards upstream of SL D di scharge immediately downstream (120 m) of SLD (inactive)* 6.6 miles downstream of SLD (inactive) 0.15-0.75 (average of all sites) Mud Sl ough (1993-Sept.,1996; USB R , 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 Sl ough (WY 1997; USB R 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 Sl ough seasonal backw a ter (l ow fl ow deposi ti onal area) (1993-1996; USB R , 1995) 0.3-0.6 Mud Sl ough seasonal backw a ter (l ow fl ow deposi ti onal area) (March, 1997; USB R et al ., 1998) 0.4-1.5 Sal t Sl ough, CDFG near hw y 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 Sal t Sl ough (1992-1993, USFWS; Henderson et al ., 1995) 0

. 2

- 0

. 4 5 Sal t Sl ough (1993-Sept., 1996; USB R , 1995) 0

. 2

- 1

. 3 Sal t Sl ough (WY 1997; USB R et al ., 1997) 0

. 1 2

- 0

. 9 4 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 Joaqui n Ri ver (CDFG) at Vernal i s (Ai r port B l vd.; Maz e B l vd; al l belo w Sta n isla us Riv er) 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.

Appendix E 3

## APPENDIX F

Supplemental Spreadsheets

## APPENDIX F Supplemental Spreadsheets

TABLES
F1. This scenario assum e s that all freshwater exports are from the Sacram ento River and that all SJR inflow enters the Bay-Delta. Sac R inflow is outflow index m i nus SJR discharge. Se concentration in the SJR is m a intained at 2 μ g Se/L. A total of 32,935 lbs of Se is released annually. Flow data are from 1997. F2. This scenario assum e s that all freshwater exports are from the Sacram ento River and that all SJR inflow enters the Bay-Delta. Sac R inflow is outflow inde x m i nus SJR discharge. Se concentration in the SJR is

m a intained at 1 μ g Se/L. A total of 16,468 lbs of Se is released annually. Flow data are from 1997. F3. Calculation of particulate Se concentrations ( μ g Se/g) from inputs of the Sacram ento 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 ( μ g Se/g) from inputs of the Sacram ento 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 ( μ g Se/g) from inputs of the Sacram ento 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. Bioaccum u lation of Se by a generic bivalve under various scenarios. Forecasts are for a wet year during the high flow season. F7. Bioaccum u lation of Se by a generic bivalve under various scenarios. Forecasts are for a wet year during the low flow season. F8. Bioaccum u lation of Se by a generic bivalve under various scenarios. Forecasts are for a critically dry year during the low flow season. F9. Bioaccum u lation of Se by a generic bivalve under various scenarios. Forecasts are for a targeted SJR load of approxim a tely 7,000 lbs Se annually (3,400 or 3,590 lbs Se per six m onths).

Appendix F 1Table 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. Concentration at Concentration Volumes Contribution Load Load Concentration Volume Volume Volume Carquinez Strait FW Endmember Sum Sum lbs Se billion ug ug Se/L billion L MAF Avg cfs at 20 psu ug Se/L billion liters billion ug Month
January 256565 Total OF 1,448 657 0.04 16412.84 13.31 224096 Sac R. 10,492 4756 2 2378.04 1.93 32469 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.15 0.29 18,792 5,464
February 119090 Total OF 562 255 0.04 6368.24 5.16 86950 Sac R. 10,386 4708 2 2353.94 1.91 32140 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.29 0.57 8,723 5,014

March 33831 Total OF 135 61 0.04 1533.94 1.24 20944 Sac R. 4,164 1888 2 943.85 0.77 12887 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.40 0.81 2,479 2,000
April 13734 Total OF 63 29 0.04 718.56 0.58 9811 Sac R. 1,268 575 2 287.32 0.23 3923 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.33 0.65 1,007 655
May 12261 Total OF 47 21 0.04 528.06 0.43 7210 Sac R. 1,632 740 2 369.94 0.30 5051 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.45 0.90 899 812

June 8762 Total OF 36 16 0.04 406.48 0.33 5550 Sac R. 1,038 470 2 235.25 0.19 3212 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.42 0.84 643 538July 9350

Total OF 47 21 0.04 536.56 0.44 7326 Sac R. 654 296 2 148.24 0.12 2024 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.27 0.54 686 369
August 9031 Total OF 48 22 0.04 540.37 0.44 7378 Sac R. 534 242 2 121.07 0.10 1653 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.24 0.48 662 315
September 4555 Total OF 17 8 0.04 192.84 0.16 2633 Sac R. 621 282 2 140.77 0.11 1922 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.51 1.02 335 341

October 4571 Total OF 14 7 0.04 163.84 0.13 2237 Sac R. 754 342 2 170.94 0.14 2334 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.60 1.19 336 400

November 6270 Total OF 26 12 0.04 299.92 0.24 4095 Sac R. 703 319 2 159.30 0.13 2175 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.41 0.83 460 382

December 18914 Total OF 108 49 0.04 1228.97 1.00 16780 Sac R. 690 313 2 156.29 0.13 2134 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.15 0.30 1,386 413

32,935 Total Selenium Exported from SJR (lbs)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. Concentration at Concentration Volumes Contribution Load Load Concentration Volume Volume Volume Carquinez Strait FW Endmember Sum Sum lbs Se billion ug ug Se/L billion L MAF Avg cfs at 20 psu ug Se/L billion liters billion ug Month
January 256565 Total OF 1,448 657 0.04 16412.84 13.31 224096 Sac R. 5,246 2378 1 2378.04 1.93 32469 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.08 0.16 18,792 3,086
February 119090 Total OF 562 255 0.04 6368.24 5.16 86950 Sac R. 5,193 2354 1 2353.94 1.91 32140 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.15 0.30 8,723 2,660

March 33831 Total OF 135 61 0.04 1533.94 1.24 20944 Sac R. 2,082 944 1 943.85 0.77 12887 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.21 0.43 2,479 1,057
April 13734 Total OF 63 29 0.04 718.56 0.58 9811 Sac R. 634 287 1 287.32 0.23 3923 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.18 0.36 1,007 367
May 12261 Total OF 47 21 0.04 528.06 0.43 7210 Sac R. 816 370 1 369.94 0.30 5051 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.25 0.49 899 442

June 8762 Total OF 36 16 0.04 406.48 0.33 5550 Sac R. 519 235 1 235.25 0.19 3212 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.24 0.47 643 303July 9350

Total OF 47 21 0.04 536.56 0.44 7326 Sac R. 327 148 1 148.24 0.12 2024 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.16 0.32 686 221
August 9031 Total OF 48 22 0.04 540.37 0.44 7378 Sac R. 267 121 1 121.07 0.10 1653 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.15 0.29 662 194
September 4555 Total OF 17 8 0.04 192.84 0.16 2633 Sac R. 311 141 1 140.77 0.11 1922 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.30 0.60 335 200

October 4571 Total OF 14 7 0.04 163.84 0.13 2237 Sac R. 377 171 1 170.94 0.14 2334 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.34 0.68 336 229

November 6270 Total OF 26 12 0.04 299.92 0.24 4095 Sac R. 351 159 1 159.30 0.13 2175 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.24 0.48 460 223

December 18914 Total OF 108 49 0.04 1228.97 1.00 16780 Sac R. 345 156 1 156.29 0.13 2134 SJR 0 0 62.5 0.00 0.00 SLD 113 51 50 1.03 0.00 Refineries 0.09 0.19 1,386 257

16,468 Total Selenium Exported from SJR (lbs)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.

Concentration Particulate Concentration at Concentration Concentration Load Volume Kd = 10,000 Kd=3,000 Kd = 1,000 Carquinez Strait FW Endmember ug Se/L lbs Se per MAF Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember at 20 psu ug Se/L in source 6 months 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. 0.04 1,850 17 Sac R. 1 5,440 2 SJR 50 6,800 0.05 SLD 50 680 0.005 Refineries 1.400 2.800 0.420 0.840 0.140 0.280 0.14 0.28
b) SLD at full capacity (300cfs), 62.5 ppb Se (18,700 lbs in six months); SJR reaches Bay-Delta.

0.04 1,850 17 Sac R. 1 5,440 2 SJR 62.5 18,700 0.11 SLD 50 680 0.005 Refineries 2.600 5.100 0.780 1.530 0.260 0.510 0.26 0.51
c) SLD at full capacity (300 cfs), 150 ppb Se (44,880 lbs in six months); SJR reaches Bay-Delta. 0.04 1,850 17 Sac R. 1 5,440 2 SJR 150 44,820 0.11 SLD 50 680 0.005 Refineries 5.100 10.200 1.530 3.060 0.510 1.020 0.51 1.02
d) SLD at full capacity (300cfs), 300 ppb Se (89,760 lbs in six months); SJR reaches Bay 0.04 1,850 17 Sac R. 1 5,440 2 SJR 300 89,760 0.11 SLD 50 680 0.005 Refineries 9.400 18.800 2.820 5.640 0.940 1.880 0.94 1.88

Targeted SJR load 7,180 lbs annually; 3,590 lbs in six months; full conveyance to the Bay-Delta.

0.04 1,850 17 Sac R. 1.2 3,590 1.1 SJR 0 0 0 SLD 50 680 0.005 Refineries 0.600 1.200 0.180 0.360 0.060 0.120 0.06 0.12
A "restoration scenario" for the SJR; (No SLD extension, refinery cleanup).

0.04 1,850 17 Sac R. 0.5 3,060 2.25 SJR 0 0 0 SLD 50 680 0.005 Refineries 0.500 1.100 0.150 0.330 0.050 0.110 0.05 0.11Table 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.

Concentration Particulate Concentration at Concentration Concentration Load Volume Kd = 10,000 Kd=3,000 Kd = 1,000 Carquinez Strait FW Endmember ug Se/L lbs Se per MAF Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember at 20 psu ug Se/L in source 6 months 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. 0.04 250 2.3 Sac R. 2 3 0.001 SJR 50 6,800 0.05 SLD 50 680 0.005 Refineries 6.000 12.100 1.800 3.630 0.600 1.210 0.6 1.21
b) SLD at full capacity (300cfs), 62.5 ppb Se (18,700 lbs in six months); little SJR reaches Bay-Delta.

0.04 250 2.3 Sac R. 2 5 0.001 SJR 62.5 18,700 0.11 SLD 50 680 0.005 Refineries 14.900 29.900 4.470 8.970 1.490 2.990 1.49 2.99
c) SLD at full capacity (300 cfs), 150 ppb (44,880 lbs in six months); little SJR reaches Bay-Delta. 0.04 250 2.3 Sac R. 2 5 0.001 SJR 150 44,820 0.11 SLD 50 680 0.005 Refineries 34.900 69.700 10.470 20.910 3.490 6.970 3.49 6.97
d) SLD at full capacity (300 cfs), 300 ppb Se ( 89,760 lbs in six months); little SJR reaches Bay-Delta. 0.04 250 2.3 Sac R. 2 5 0.001 SJR 300 89,760 0.11 SLD 50 680 0.005 Refineries 69.000 138.000 20.700 41.400 6.900 13.800 6.9 13.80

Targeted SJR load of 6,800 lbs annually; 3,400 lbs in six months; full conveyance to the Bay-Delta.

0.04 250 2.3 Sac R. 2.5 3,400 0.5 SJR 0 0 0 SLD 50 680 0.005 Refineries 2.800 5.700 0.840 1.710 0.280 0.570 0.28 0.57
A "restoration scenario" for the SJR (No SLD extension, refinery cleanup).

0.04 250 2.3 Sac R. 0.5 1,020 0.75 SJR 0 0 0 SLD 50 680 0.005 Refineries 1.200 2.300 0.360 0.690 0.120 0.230 0.12 0.23Table 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.

Concentration Particulate Concentration at Concentration Concentration Load Volume Kd = 10,000 Kd=3,000 Kd = 1,000 Carquinez Strait FW Endmember ug Se/L lbs Se per MAF Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember at 20 psu ug Se/L in source 6 months 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. 0.04 141 1.3 Sac R. 2 3 0.0005 SJR 50 6,800 0.05 SLD 50 680 0.005 Refineries 10.300 20.700 3.090 6.210 1.030 2.070 1.03 2.07
b) SLD at full capacity (350 cfs), 62.5 ppb Se (18,700 lbs Se in six months); little SJR reaches Bay-Delta.

0.04 141 1.3 Sac R. 2 3 0.0005 SJR 62.5 18,700 0.11 SLD 50 680 0.005 Refineries 25.400 50.700 7.620 15.210 2.540 5.070 2.54 5.07
c) SLD at full capacity (300 cfs), 150 ppb Se (44,880 lbs in six months); little SJR reaches Bay-Delta. 0.04 141 1.3 Sac R. 2 5 0.001 SJR 150 44,880 0.11 SLD 50 680 0.005 Refineries 59.300 118.700 17.790 35.610 5.930 11.870 5.93 11.87
d) SLD at full capacity (300 cfs), 300 ppb Se (89,760 lbs in six months); little SJR reaches Bay-Delta. 0.04 141 1.3 Sac R. 2 3 0.0005 SJR 300 89,760 0.11 SLD 50 680 0.005 Refineries 117.600 235.300 35.280 70.590 11.760 23.530 11.76 23.53

Targeted SJR load of 7,180 lbs annually (3,590 lbs in six months); full conveyance to Bay-Delta.

0.04 250 2.3 Sac R. 2.5 3,400 0.5 SJR 0 0 0 SLD 50 680 0.005 Refineries 4.300 8.600 1.290 2.580 0.430 0.860 0.43 0.86
A "restoration scenario" for the SJR (No SLD extension, refinery cleanup).

0.04 174 1.6 Sac R. 0.5 381 0.28 SJR 0 0 0 SLD 50 680 0.005 Refineries 1.200 2.400 0.360 0.720 0.120 0.240 0.12 0.24Table F6. Bioaccumulation of Se by a generic bivalve under various scenarios. IR=0.2 Ke=0.03 AE4=0.8 AE3=0.63 AE2=0.55 AE1=0.35 AE = assimilation efficiency; Kd = distribution (partitioning) coefficient; Ke = rate constant of loss; IR = ingestion rate 3B 3A 2B 2A 1B 1A Kd = 10,000 Kd=3,000 Kd = 1,000 Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember 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. 1.400 2.800 0.420 0.840 0.140 0.280 Particles 0.4

0.8 AE1 1.9 3.9 AE2 7.4 14.7 AE3 9.3 18.7 AE4

SLD at full capacity (300 cfs), 62.5 ppb Se (18,700 lbs Se in six months); SJR reaches Bay-Delta 2.600 5.100 0.780 1.530 0.260 0.510 Particles 0.8

1.5 AE1 3.6 7.0 AE2 13.7 26.8 AE3 17.3 34.0 AE4
SLD at full capacity (300 cfs); 150 ppb Se (44,880 lbs in six months); SJR reaches Bay 5.100 10.200 1.530 3.060 0.510 1.020 Particles 1.5

3.0 AE1 7.0 14.0 AE2 26.8 53.6 AE3 34.0 68.0 AE4
Prior to refinery cleanup (No SLD extension) 1.100 2.180 0.330 0.660 0.110 0.220 Particles 0.48

0.96 AE1 2.27 4.54 AE2 8.66 17.17 AE3 11.00 21.80 AE4Table F7. Bioaccumulation of Se by a generic bivalve under various scenarios. IR=0.2 Ke=0.03 AE4=0.8 AE3=0.63 AE2=0.55 AE1=0.35 AE = assimilation efficiency; Kd = distribution (partitioning) coefficient; Ke = rate constant of loss; IR = ingestion rate 3B 3A 2B 2A 1B 1A Kd = 10,000 Kd=3,000 Kd = 1,000 Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember 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. 6.0 12.1 1.8 3.6 0.6 1.2 Particles 1.8

3.5 AE1 8.3 16.6 AE2 47.3 63.5 AE3 60.0 80.7 AE4

SLD at full capacity (300 cfs), 62.5 ppb Se (18,700 lbs Se in six months); little SJR reaches Bay-Delta 14.9 29.9 4.5 9.0 1.5 3.0 Particles 4.3

8.7 AE1 20.5 41.1 AE2 117.34 157.0 AE3 149.00 199.3 AE4
SLD at full capacity (300 cfs), 150 ppb Se (44,880 lbs in six months); little SJR reaches Bay-Delta 34.9 69.7 10.5 20.9 3.5 7.0 Particles 10.2

20.3 AE1 48.0 95.8 AE2 274.84 365.9 AE3 349.00 464.7 AE4
Prior to refinery cleanup (No SLD extension) 2.000 3.900 0.600 1.170 0.200 0.390 Particles 0.88

1.71 AE1 4.13 8.04 AE2 15.75 30.71 AE3 20.00 39.00 AE4Table F8. Bioaccumulation of Se by a generic bivalve under various scenarios. IR=0.2 Ke=0.03 AE4=0.8 AE3=0.63 AE2=0.55 AE1=0.35 AE = assimilation efficiency; Kd = distribution (partitioning) coefficient; Ke = rate constant of loss; IR = ingestion rate 3B 3A 2B 2A 1B 1A Kd = 10,000 Kd=3,000 Kd = 1,000 Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember 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. 10.3 20.7 3.1 6.2 1.0 2.1 Particles 2.9

6.1 AE1 14.2 28.4 AE2 81.1 108.7 AE3 103.0 138.0 AE4

SLD at full capacity (300 cfs), 62.5 ppb Se (18,700 lbs Se in six months); little SJR reaches Bay-Delta. 25.4 50.7 7.6 15.2 2.5 5.1 Particles 7.3

14.9 AE1 34.8 69.7 AE2 200.03 266.2 AE3 254.00 338.0 AE4
SLD at full capacity (300 cfs), 150 ppb Se (44,880 lbs in six months); little SJR reaches Bay-Delta. 59.0 119.0 17.8 35.6 5.9 11.9 Particles 17.2

34.7 AE1 81.6 163.2 AE2 464.6 624.8 AE3 590.0 793.3 AE4
Prior to refinery cleanup (No SLD extension). 2.700 5.300 0.810 1.590 0.270 0.530 Particles 1.18

2.32 AE1 5.57 10.93 AE2 21.26 41.74 AE3 27.00 53.00 AE4Table F9. Bioaccumulation of Se by a generic bivalve under various scenarios. IR=0.2 Ke=0.03 AE4=0.8 AE3=0.63 AE2=0.55 AE1=0.35 AE = assimilation efficiency; Kd = distribution (partitioning) coefficient; Ke = rate constant of loss; IR = ingestion rate 3B 3A 2B 2A 1B 1A Kd = 10,000 Kd=3,000 Kd = 1,000 Carquinez Strait FW Endmember Carquinez Strait FW Endmember Carquinez Strait FW Endmember 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 4.30 8.60 1.29 2.58 0.43 0.86 Particles 1.3

2.5 AE1 5.9 11.8 AE2 33.9 45.2 AE3 43.0 57.3 AE4

Wet Year; Low Flow Season 2.80 5.70 0.84 1.71 0.28 0.57 Particles 0.8

1.7 AE1 3.9 7.8 AE2 22.05 29.9 AE3 28.00 38.0 AE4
Wet Year; High Flow Season 0.60 1.20 0.18 0.36 0.06 0.12 Particles 0.2

0.4 AE1 0.8 1.7 AE2 4.7 6.3 AE3 6.0 8.0 AE4