i

Technical Support Document 

for the 

Proposed 

Aquatic Life and Aquatic-Dependent 

Wildlife Selenium Water Quality Criteria

For the San Francisco Bay and Delta

(June 2016)
ii

Proposed 

Aquatic Life and Aquatic-Dependent Wildlife 

Selenium Water Quality Criteria

For the San Francisco Bay and Delta

June, 2016

Special thanks to Theresa Presser and Sam Luoma of the United States Geological Survey, Tom 

Maurer, Bill Beckon, and Joe Skorupa of the U.S. Fish and Wildlife Service, and Joe Dillon of the 

National Marine Fisheries Service for providing invaluable insight.

US Environmental Protection Agency Region 9

Water Division

75 Hawthorne Street

San Francisco, CA 94105

Prepared by Diane E. Fleck, P.E., Esq. and Eugenia McNaughton, Ph.D.
iii

Table of Contents 

EXECUTIVE SUMMARY.........................................................................................................viii

CHAPTER 1 INTRODUCTION..................................................................................................1

A. Purpose.................................................................................................................1

B. Background...........................................................................................................1

C. Chemistry..............................................................................................................4

D. Effects on Biota....................................................................................................4

CHAPTER 2 SELENIUM MODELING......................................................................................7

A. Overview of the USGS Ecosystem-Scale Selenium Model.............................8

B. USGS Modeling of the San Francisco Bay and Delta....................................11

a. Overview of Species-Specific Variables ............................................12

b. Overview of Environment-Specific Variables ...................................16

c. Summary of USGS Modeling of the San Francisco Estuary.............19

CHAPTER 3 SELENIUM BENCHMARK EFFECT CONCENTRATIONS................................21

A. Summary of Benchmarks Considered...........................................................21

B. FWS Sources: FWS Species Reports...............................................................23

a. Species at Risk from Selenium Exposure in the San Francisco 

Estuary; Final Report (USFWS, 2008)........................................23

b. Selenium Effect Levels for Selected Representative/Surrogate 

Species (USFWS, 2009)...............................................................27

c. Evaluation of Toxicity of Selenium to White and Green Sturgeon

(USFWS, 2012).............................................................................31

C. EPA Sources: CWA Section 304(a) National Recommended Water Quality 

Criterion for Selenium and Mallard Bird Studies ............................................37
iv

a. Freshwater Fish Tissue Criterion Element (USEPA, 2016)...............37

b. Bird Egg Tissue Criterion (USEPA, 2011a)..........................................47

D. Benchmarks for EPA Use in Ecosystem-Scale Selenium Model.................51

CHAPTER 4 EPA MODELING AND PROPOSED WATER QUALITY CRITERIA..................52

A. Designated Uses...............................................................................................52

B. EPA Development of Water Quality Criteria................................................53

a. Modeling Variables...............................................................................54

i. Species-Specific Variables......................................................54

ii. Environment-Specific Variables............................................69

iii. Summary of Variables............................................................72

b. Modeling Results..................................................................................73

C. Proposed Criteria..............................................................................................76

a. Applicable Waters; Magnitude, Duration and Frequency...............76

b. Acute and Intermittent Criteria..........................................................78

D. Summary............................................................................................................82

REFERENCES.........................................................................................................................83
v

Appendix A. Administrative Report: Ecosystem-Scale Selenium Modeling in Support of Fish 

and Wildlife Criteria Development for the San Francisco Bay-Delta Estuary, 

California; by Theresa S. Presser and Samuel N. Luoma; U.S. Geological Survey, 

Menlo Park, California; December, 2010.

Appendix B. Species at Risk from Selenium Exposure in the San Francisco Estuary; Final Report 

to the Environmental Protection Agency; by William N. Beckon and Thomas C. 

Maurer; U.S. Fish and Wildlife Service, Sacramento, California; March, 2008.

Appendix C. Selenium Effect Levels for Selected Representative/Surrogate Species; by William 

Beckon; U.S. Fish and Wildlife Service, Sacramento, California; July 31, 2009.

Appendix D. Evaluation of the Toxicity of Selenium to White and Green Sturgeon; by William 

Beckon; U.S. Fish and Wildlife Service, Sacramento, California; March, 2012.

Appendix E. Additional Details for the Derivation of USGS Trophic Transfer Factor for 

Potamocorbula amurensis 

Appendix F. EPA Modeling Results for Proposed Criteria

Appendix G. Comparative Modeling Results (All Transects) 

Appendix H. Partitioning Coefficients (Kds) 

Appendix I. Uncertainty/Sensitivity Analysis 
vi

List of Tables

Chapter 2

Table 2-1 Summary of Modeling Variables.....................................................................20

Chapter 3

Table 3-1 List of FWS Species of Concern (Adapted from USFWS, 2008)...................22

Table 3-2 Summary of EC10 EPA and FWS Benchmarks Considered..........................23

Table 3-3 Probable Critical Life Stages (Adapted from USFWS, 2008)........................26

Table 3-4 Summary of FWS-Recommended EC10 Selenium Benchmark Values 

 for Representative or Surrogate Species (Adapted from USFWS, 2009).......27

Table 3-5 Summary of FWS-Recommended EC10 Selenium Benchmarks for 

White and Green Sturgeon (Adapted from USFWS, 2012)..............................33

Table 3-6 Summary of 304(a) Recommended Freshwater Selenium Ambient Chronic 

Water Quality Criterion for the Protection of Aquatic Life (USEPA, 2016)...38

Table 3-7 Lowest Four Reproductive-Effect Egg/Ovary GMCVs 

(Adapted from USEPA, 2016)...............................................................................39

Table 3-8 Lowest Four Reproductive-Effect Whole Body GMCVs 

(Adapted from USEPA, 2016)...............................................................................39

Table 3-9 Lowest Four Reproductive-Effect Muscle GMCVs 

(Adapted from USEPA, 2016)...............................................................................40

Table 3-10 Effects of Dietary Selenium Exposure on Egg Selenium Concentrations 

and Hatchability in Mallards (Adapted from Ohlendorf, 2003)......................48

Table 3-11 Selenium and Hatching Data for Mallard Clutches Collected from the 

Davis Wastewater Treatment Facility (USFWS, 2011)......................................49
vii

Chapter 4

Table 4-1 Model Variables.................................................................................................54

Table 4-2 Summary of Life Stages and Diet Mixes of Representative Species 

Most at Risk............................................................................................................63

Table 4-3 Trophic Transfer Factors (TTFs).......................................................................64

Table 4-4 Summary of Diet Mixes and TTFs for Representative Species 

Most at Risk...........................................................................................................67

Table 4-5 Summary of Species-Specific Variables.........................................................68

Table 4-6 Hydrologic Variables.........................................................................................70

Table 4-7 Available Transects and Calculated Kd Values...........................................71

Table 4-8 Summary of EPA Modeling Variables.............................................................72

Table 4-9 Summary of Representative Scenarios and Results.....................................75

Table 4-10 Representative Values of the Proposed Intermittent Water 

Concentration Criterion........................................................................................80

Table 4-11 Proposed Selenium Water Quality Criteria for the San Francisco Bay 

and Delta.................................................................................................................81

List of Figures

Figure 1-1 Map of the San Francisco Bay and Delta System

(Adapted from USGS, 2010) .................................................................................3

Figure 2-1 Ecosystem-Scale Selenium Model

(Adapted from USGS, 2010 Figure 6)..................................................................10

Figure 4-1 Illustration of an Intermittent Spike Exposure.............................................79
viii

EXECUTIVE SUMMARY

This document provides the U.S. Environmental Protection Agency’s scientific basis and 

recommendations for site-specific selenium water quality criteria for California’s San Francisco 

Bay and Sacramento-San Joaquin River Delta. The proposed criteria are designed to protect 

aquatic life and aquatic-dependent (avian) wildlife, including federally listed threatened and 

endangered species, from reproductive and developmental effects of elevated levels of 

selenium in the aquatic environment. The existing water quality criteria, promulgated in 1992 

in the National Toxics Rule, do not reflect the latest science on selenium fate and biological 

uptake. This document considers updated science in developing the revised criteria values. 

The recommended criteria consist of fish tissue values, prey (clam) tissue values, and 

dissolved and particulate water column values. All proposed values are considered comparably 

protective. The water column and clam tissue values are based on detailed modeling of the 

estuary using the USGS Ecosystem-Scale Selenium Model (Presser and Luoma, 2010), a model 

specifically developed to predict the fate and biological uptake of selenium in the San Francisco 

estuary. The proposed values are presented in the table below.

Proposed Selenium Water Quality Criteria for the San Francisco Bay and Delta

Media Type

 

 Tissue

 

 Water Column1

Criteria

Fish Whole 

Body or

Muscle

Clam 

Dissolved 

Chronic Intermittent Exposure2

Particulate

Chronic

Magnitude 8.5 μg/g dw

whole body

or

11.3 μg/g dw 

muscle 

15 μg/g dw 0.2 μg/L WQCint =

0.2 μg/L − Cbkgrnd(1 − f int)

f int

1 μg/g dw

Duration Instantaneous 

measurement

Instantaneous 

measurement

30 days Number of days/month with 

an elevated concentration

30 days

Frequency Not to be 

exceeded

Not to be 

exceeded

Not more than 

once in three 

years 

Not more than once in three 

years 

Not more than 

once in three 

years 

1 Water column values are based on dissolved total selenium (includes all oxidation states, i.e., selenite, selenate, organic 

selenium and any other forms) in water.

2 Where Cbkgrnd is the average background selenium concentration in μg/L, and fint is the fraction of any 30-day period 

during which elevated selenium concentrations occur, with fint assigned a value ≥ 0.033 (corresponding to one day).

Note 1: The criteria apply to all waters of the San Francisco Bay and Delta in which the salinity is greater than 1 part per

thousand 95% or more of the time. 

Note 2: A translator of 1 shall be used to determine total recoverable selenium values from dissolved selenium criteria 

values for use in deriving water quality-based effluent limitations for point sources.
1

CHAPTER 1 INTRODUCTION 

A. Purpose 

The purpose of this document is to provide the U.S. Environmental Protection Agency’s

(EPA or Agency) scientific basis for its proposed site-specific selenium water quality criteria for 

California’s San Francisco Bay and Delta estuary ecosystem. The criteria are designed to protect 

aquatic life and aquatic-dependent wildlife including federally listed threatened and 

endangered species. Pursuant to Clean Water Act section 303(c) and EPA’s implementing 

regulations at 40 CFR 131.11(a), water quality criteria must be based on sound scientific 

rationale and must contain sufficient parameters or constituents to protect designated uses; for 

waters with multiple use designations, the criteria must support the most sensitive designated 

uses. The site-specific selenium criteria are intended to be protective of the State’s established 

aquatic life and wildlife designated uses which include: migration of aquatic organisms; 

spawning, reproduction and early development of fish; estuarine habitat; warm and cold 

freshwater habitats; wildlife habitat; and rare, threatened or endangered species.

The information provided herein does not substitute for the Clean Water Act or EPA 

regulation, nor is this document a regulation itself. Thus, this document cannot, and does not, 

impose any legally binding requirements on EPA, the State of California, authorized Tribes, the 

regulated community, or any other party, and might not apply to a particular situation or 

circumstance.

B. Background

Under Clean Water Act (CWA) section 304(a), EPA is required to publish water quality 

criteria guidance values for priority toxic pollutants, for states and tribes to consider in 

developing water quality standards. Over the years, EPA has developed a number of pollutant 

criteria documents for the protection of human health and aquatic life. These guidance values 

are termed CWA section 304(a) national recommended water quality criteria, and are 

informally referred to as “national recommended criteria” or “304(a) criteria.” National 

recommended criteria for aquatic life protection have traditionally been developed as water 

column concentrations that reflect the toxicity of water-only exposure of the pollutant to 

aquatic biota. Water column concentrations can be implemented directly to control and limit 

discharges. However, for pollutants such as selenium that accumulate in aquatic biota through 

diet and where toxicity is exhibited through dietary exposure, tissue concentrations can better 

represent levels of toxicity, particularly for higher order species if the pollutant bioaccumulates 

through the food chain. Since tissue concentrations may be difficult to implement directly, it is 

useful to translate tissue concentrations to water column values that reflect the 

bioaccumulation, i.e., a water column concentration that is related to the tissue concentration
2

of the predator species of concern that is accumulating the selenium. Therefore, EPA has 

developed a national recommended criterion for selenium that incorporates both tissue-based 

values and translations to water column values in order to facilitate the monitoring and 

regulation of pollutant discharges. 

The national recommended tissue criterion incorporates fish tissue values based on the 

empirically measured relationship between reproductive effects and fish tissue values from 

dietary exposure from a range of field and laboratory studies (USEPA, 2016). Using the U.S. 

Geological Survey (USGS) Ecosystem-Scale Selenium Model1(Presser and Luoma, 2010), EPA 

also included water column values associated with the fish tissue values for lentic and lotic 

systems (USEPA, 2016). 

The currently applicable aquatic life water quality criteria for selenium in the San 

Francisco Bay and Delta are those that were promulgated as part of the National Toxics Rule 

(NTR) (57 FR 60848, December 22, 1992, as amended by 60 FR 22228, May 4, 1995; codified at 

40 CFR 131.36). The aquatic life chronic criterion value is 5.0 micrograms per liter (μg/L) (total 

recoverable). The NTR criteria are based on EPA’s 1987 national aquatic life selenium 

freshwater criteria recommendations, Ambient Water Quality Criteria for Selenium - 1987, EPA440/5-87-008, and are represented in terms of water column concentrations. The 1987 

national recommended criteria were derived from observed field conditions at a contaminated 

lake, Belews Lake, North Carolina, a cooling water reservoir that had been affected by selenium 

loads from a coal-fired power plant, and reflect water column and dietary exposure of selenium 

(USEPA, 1987). 

Since the most significant exposure pathway of selenium to species of concern in the 

San Francisco Bay and Delta is through diet, the currently applicable criteria for selenium from 

the NTR no longer adequately protect species in the estuary. This document provides the basis 

for EPA’s proposed site-specific water quality criteria for selenium protective of aquatic life and 

aquatic-dependent wildlife for the San Francisco Bay and Delta to address bioaccumulation 

through dietary exposure.

EPA is proposing the site-specific criteria apply to all salt and estuarine waters of the San 

Francisco Bay and Delta (see Figure 1-1 Map of the San Francisco Bay and Delta System). These 

waters are located within the jurisdictions of the San Francisco Bay Regional Water Quality 

 

1 The model is a predictive tool to delineate the fate and biological uptake of selenium in an aquatic ecosystem, 

and is discussed in detail in Chapter 2 of this document. 
3

Control Board (SFRWQCB) and the Central Valley Regional Water Quality Control Board 

(CVRWQCB) of the State of California. 

Figure 1-1 Map of the San Francisco Bay and Delta System (Adapted from USGS, 2010)
4

C. Chemistry 

In the Periodic Table, selenium is a non-metal, even though it is often considered a 

metalloid. Selenium exists in several allotropic (variant molecular structural) forms, and its 

most stable form, crystalline hexagonal selenium, is a metallic gray substance, exhibiting metallike characteristics, including photoconductivity and photovoltaic properties. Selenium often 

occurs naturally in organic carbon-enriched sediments, and is readily mobilized in the 

environment and transformed into bioavailable forms. It bioaccumulates in organisms over 

time and is assimilated into the food chain. 

Selenium occurs naturally in sediments of marine origin, and can enter the aquatic 

environment when water comes into contact with selenium–bearing deposits. Aquatic 

environmental problems occur when selenium is mobilized through human activities, including 

agricultural irrigation, mountain top mining, and the processing of fossil fuels such as petroleum 

refining. Once selenium is converted, it tends to remain in a bioavailable form which 

contributes to its build up in the biotic environment over time (USEPA, 2011b). Under highly 

anoxic conditions (e.g., buried sediments), it can be reduced to elemental selenium, but does 

not readily convert to the elemental form from a bioavailable form (USEPA, 2011b). Depending 

on environmental conditions, one or another selenium species such as selenate, selenite and 

organo-selenium, which differ in transformation rates and bioavailability, may predominate. 

The least bioavailable form, selenate, can be reduced by some organisms to selenite, a more 

bioavailable form, which can then be accumulated as organo-selenium, the most bioavailable 

form of selenium (USEPA, 2011b).

D. Effects on Biota

Although selenium is an essential micronutrient for bacteria and animals, it is a dosesensitive nutrient, and the range between essential and toxic levels in many organisms is 

narrow (Chapman et al., 2009). Selenium can be toxic to organisms at very low levels of chronic 

exposure (Lemly, 1997). It has been a long-standing hypothesis that selenium toxicity occurs 

through biochemical pathways where selenium may not be distinguished from sulfur, with 

excess selenium substituting into proteins and altering protein structure and function (see 

USGS Linking Selenium Sources to Ecosystems: Local and Global Perspectives, Modeling at 

http://wwwrcamnl.wr.usgs.gov/Selenium/modeling.htm ). More recent studies indicate that 

selenium may affect organisms via oxidative stress (USEPA, 2016). The role of seleniuminduced oxidative stress in embryo toxicity and teratogenesis (embryonic malformations) 

appears to be related to impacts on metabolic enzyme (glutathione) homeostasis. In a review 

of bird studies, Hoffman (2002) reported that avian exposure to selenium altered ratios of 

reduced to oxidized glutathione and thus increased measurements of oxidative cell damage. 

Palace et al. (2004) suggested that, in rainbow trout embryos, oxidative stress due to elevated 
5

selenium levels results in pericardial and yolk sac edema. For a more detailed discussion of the 

mechanism of toxicity at the biochemical level, including the role of oxidative stress, see Janz et 

al. (2010). Exposure to elevated selenium in fish and other wildlife causes reduced growth, and 

reduces reproductive success through effects that lower embryo survival, most notably from 

teratogenesis (Eisler, 1985 in USFWS, 2008; Stewart et al., 2004 in USEPA, 2011b). 

A well-documented case of selenium toxicity to wildlife occurred in the 1980s, when 

agricultural runoff high in selenium collected in a reservoir consisting of shallow ponds in the 

Kesterson Wildlife Refuge, part of the San Luis Wildlife Refuge in the Central Valley of 

California. Built in the early 1970s as part of the San Luis Drain system to discharge agricultural 

runoff from the west side of the San Joaquin River basin to the San Francisco Delta, Kesterson 

was to be a temporary holding area or terminus within the Valley until the drain could be 

extended into the Delta. By 1982, toxic levels of selenium from agricultural irrigation drainage 

moved from the aquatic environment into the food chain (see USGS Understanding Our Planet 

Through Chemistry at http://minerals.cr.usgs.gov/gips/na/elemap.html ). Widespread fish 

mortality was observed, as well as an unusually high percentage of avian embryo and hatchling 

deformities such as missing eyes, shortened, twisted or missing legs, and elongated or missing 

beaks, all characteristic of selenium poisoning (USGS Linking Selenium Sources to Ecosystems: 

Local and Global Perspectives, Irrigation at 

http://wwwrcamnl.wr.usgs.gov/Selenium/irrigation.htm ). In 1983, a 64% rate of deformity 

and death of embryos and hatchlings of wild aquatic birds was recorded. The destruction of 

wildlife at Kesterson brought the effects of selenium bioaccumulation and assimilation to 

national attention (see also Ohlendorf et al., 1986a, 1986b, and 1986c). 

Selenium can accumulate in the aquatic food web through various routes and at various 

rates. Some aquatic food webs are very efficient at taking in and transferring selenium up the 

food chain. At the bottom of the food chain, microorganisms (bacteria and algae) can 

bioaccumulate selenium to levels that greatly exceed water column concentrations, and some 

invertebrates, namely filter feeding clams, can very efficiently accumulate selenium from 

suspended organic and inorganic particulate material and bed sediment. Since exposure to 

selenium primarily occurs through diet, an organism’s exposure to selenium is affected by the 

concentration of selenium in its food sources. In the San Francisco Bay and Delta, clam-based 

food webs accumulate selenium at a much higher rate than insect-based food webs.

Potamocorbula amurensis (P. amurensis)2 or Corbula, an introduced clam species, can now be 

 

2 Also commonly known as Corbula amurensis (C. amurensis). See: World Register of Marine Species at

http://www.marinespecies.org/aphia.php?p=taxdetails&id=397175 on 2014-09-17; and see the Integrated 

Taxonomic Information System on-line database at: 

http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=81746.
6

found throughout the San Francisco estuary, primarily in subtidal areas, across the full range of 

bay salinities (<1 to 33 parts per thousand, ppt) (Carlton et al., 1990; Thompson and Parchaso, 

2010). Corbula are abundant in San Pablo Bay, and Suisun Bay and Marsh, and accumulate 

selenium at roughly three times the rate of supplanted native clam species (Cohen, 2011 at 

http://www.exoticsguide.org; Stewart et al., 2004). In San Francisco Bay, predator species that 

prefer to feed on Corbula, such as diving birds and sturgeon, are exposed to higher levels of 

bioaccumulated selenium than species that feed mainly on insects or higher order species 

within an insect-based food web.

The risk of impacts or vulnerability of a species to selenium is determined by a 

combination of factors such as the species’ exposure (including exposure through diet and 

habitat), toxicological sensitivity3, and population status. Other important factors include the 

duration and timing of the exposure and life stage of the species. For example, white sturgeon 

spend much of their lives in Bay and Delta waters, but may be overall less toxicologically 

sensitive to selenium in their diet than green sturgeon (De Riu et al., 2014, USFWS, 2012). On 

the other hand, adult green sturgeon are believed to spend less time than white sturgeon in the 

estuary (USFWS, 2008 and 2012). Concerns have been raised about the sensitivity of juvenile 

salmon, whose preferred habitat includes the Delta and San Joaquin River (USFWS, 2008 and 

2009). The juvenile or the developing stage of a species, a critical life stage, may be more

vulnerable to selenium exposure. Exposure to selenium-laden prey during these stages could 

have a significant impact on the survival and growth of the species. 

The availability of selenium under different physical and biological conditions explains

why water column concentrations may not by themselves be sufficient indicators of 

toxicological effect. In addition, hydrologic conditions and water chemistry affect the degree to 

which selenium is taken up into the food chain at a given site. Lentic water systems, where 

waters are calm and flushing is limited, enhance the production of bioavailable forms of 

selenium (selenite). Lotic water systems, where waters are flowing and flushing is rapid, limit 

selenium uptake given the rapid movement of the water and the predominant form of 

selenium (selenate) (Nagpal and Howell, 2001, and Adams et al., 2000 in Simmons and 

Wallschlager, 2004). Where different types of water bodies are contiguous, impacts to 

downstream waters shall be taken into account (40 CFR 131.10(b)). All of these species-specific 

and hydrologic factors have been considered in determining appropriate site-specific water 

quality criteria for selenium in the San Francisco Bay and Delta.

 

3

 Toxicological sensitivity to selenium refers to toxicity effects due only to increased levels of selenium, usually 

determined under laboratory controlled conditions. Different fish species can have very different inherent 

toxicological sensitivity to selenium (Janz et al., 2010).
7

CHAPTER 2 SELENIUM MODELING

EPA has been working collaboratively with the U.S. Fish and Wildlife Service (FWS) and 

the National Marine Fisheries Service (NMFS) (collectively, the Services) to gather information 

about threatened and endangered species’ vulnerability to selenium, and with USGS to model 

the biological movement of selenium in the estuary. The Services provided detailed 

information concerning critical species and benchmark effect concentrations that are important 

in the modeling (see Chapter 3). USGS first published a selenium fate, transport and biological 

uptake methodology in Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: 

Ecological Effects of a Proposed San Luis Drain Extension, USGS Open-File Report 00-416 (USGS, 

2000). This publication was revised and superseded by Professional Paper 1646 (USGS, 2006). 

As discussed in Professional Paper 1646, the methodology was validated using field data and 

peer reviewed through the USGS Fundamental Science Practices review process before 

publication4. The methodology outlined in Professional Paper 1646 is the basis of the 

Ecosystem-Scale Selenium Model, which is explained in Presser and Luoma (2010). When the 

Services, USGS, and EPA met in September 2002 to discuss the development of selenium 

criteria for the San Francisco estuary, the agencies agreed that the USGS methodology, 

originally developed to evaluate selenium loads to the estuary through the proposed San Luis 

Drain extension, offered the best available predictive tool to understand the fate and biological 

uptake of selenium in the Bay and Delta, and that it would be appropriate to use in the 

development of site-specific aquatic life and aquatic-dependent wildlife criteria.

Starting in 2003, EPA provided funding for the USGS to model selenium fate and 

biological uptake in the estuary, using the Ecosystem-Scale Selenium Model. USGS completed 

its report Ecosystem-Scale Selenium Modeling in Support of Fish and Wildlife Criteria 

Development for the San Francisco Bay-Delta Estuary, California, Administrative Report (the 

USGS report) and submitted it to EPA in December, 2010 (USGS, 2010; Appendix A). The 

modeling was validated by comparing existing site-specific field data sets from 1998 – 2001 to 

predicted selenium concentrations in prey (specifically Corbula), water and suspended 

particulate material. The predicted selenium concentrations compared well with observed 

concentrations (USGS, 2010 pages 24 – 25 and Tables 14, 15, and 16). The report underwent

review through the USGS Fundamental Science Practices process prior to publication.

 

4

The USGS review process includes extensive technical review and comment by experts not associated with the 

work and a thorough reconciliation document, prior to public release of the final document. The USGS technical 

peer review process is outlined in U.S. Geological Survey Fundamental Science Practices Circular 1367, at 

http://www.usgs.gov/quality_integrity/.
8

USGS used site-specific data from various sources, and species-specific data from FWS in 

two reports: Species at Risk from Selenium Exposure in the San Francisco Estuary, and Selenium 

Effect Levels for Selected Representative/Surrogate Species (USFWS, 2008 and USFWS, 2009, 

Appendices B and C, respectively). The USGS report illustrates how selenium moves through 

the San Francisco ecosystem using site-specific hydrologic and species-specific information for 

the estuary. EPA relied on the Ecosystem-Scale Selenium Model, the USGS report, the FWS 

reports, and other materials to develop the analyses contained in this document, on which the 

proposed criteria for the estuary are based (see Chapter 4).

A. Overview of the USGS Ecosystem-Scale Selenium Model5

As selenium bioaccumulates and assimilates into and up through the food web via 

predator-prey food chains, the most important route of exposure to wildlife is through diet. 

Therefore, to be scientifically credible and for regulatory purposes, modeling the fate and 

biological uptake of selenium in an aquatic environment for the protection of aquatic species 

and aquatic-dependent species must consider diet. The Ecosystem-Scale Selenium Model 

conceptualizes and quantifies the variables that predict how selenium moves from the water 

environment to wildlife species. The model uses biogeochemical and physiological factors from 

field and laboratory studies, accounting for selenium speciation, loading, transformation 

between dissolved and particulate selenium, bioavailability and bioaccumulation, and trophic 

transfer and assimilation to higher order species.

Using the model, selenium concentrations in different media can be linked to translate 

predator tissue concentrations to dissolved water column, particulate water column, and/or 

prey food tissue concentrations. The flexibility of the model promotes a more complete 

understanding of how selenium behaves in site-specific ecosystems. It takes into account the 

specific food web of the species of interest, as well as site-specific biogeochemical conditions 

such as selenium partitioning between dissolved and particulate forms in the aquatic 

environment. This last variable is critical to determining selenium uptake through 

phytoplankton and bacteria at the bottom of the food web. Since the efficiency of selenium to 

be taken up into the aquatic environment by particular food webs varies widely, choosing the 

appropriate ecosystem (i.e., food web) and environmental variables, such as partitioning 

conditions, is key to determining the extent of bioaccumulation and assimilation to highertrophic level wildlife species. 

 

5

Some information in this section is paraphrased and/or summarized from A Methodology for Ecosystem-Scale 

Modeling of Selenium, published in Integrated Environmental Assessment and Management (IEAM), Volume 6, 

Number 4, pp 685-710, Presser and Luoma, May 26, 2010. 
9

The model considers sources of selenium, such as agricultural drainage, oil refinery 

effluent, and mining discharge; dissolved selenium speciation (selenate, selenite, and organoselenium); particulate selenium speciation (elemental selenium, adsorbed selenite and/or 

selenate, and organo-selenium); and receiving water type or transformational environment

such as wetlands, marshes, ponds, streams, rivers, and estuaries. The model also considers the 

bioavailability potential of different media such as sediment, detritus, phytoplankton, and 

periphyton; invertebrate-specific bioaccumulation potential and trophic transfer factors to fish 

or aquatic birds using species-specific physiological parameters including ingestion rate, 

assimilation efficiency, efflux rate, and growth; health effects endpoints such as reproduction, 

teratogenesis, decreased growth, and decreased survival; predator life cycles using speciesspecific energetics (body weight and ingestion rate), life stage (breeding, larval, adult), 

distribution (resident, mobile, migratory), timing (route, duration), and feeding behavior (prey 

availability and preference, etc.); and demographics including loss of individuals, population 

reduction, and community change (Presser and Luoma, 2010 Table 1).

The linked approach to environmental variables synthesizes the site-specific fate, 

bioaccumulation and assimilation of selenium within a particular ecosystem. Figure 2-1,

Ecosystem-Scale Selenium Model, is a generalized schematic of variables and linkages involved 

(USGS, 2010 Figure 6). For a detailed discussion of the model, see A Methodology for 

Ecosystem-Scale Modeling of Selenium, published in Integrated Environmental Assessment and 

Management (IEAM), Volume 6, Number 4, on May 26, 2010 (Presser and Luoma, 2010).
10

Figure 2-1 Ecosystem-Scale Selenium Model (Adapted from USGS, 2010 Figure 6)
11

B. USGS Modeling of the San Francisco Bay and Delta6

Using site-specific information for the San Francisco Bay and Delta, USGS ran the 

Ecosystem-Scale Selenium Model under several different hydrologic scenarios and ecological 

endpoints for the Bay and Delta system to help identify protective selenium values and 

associated critical flow and loading conditions. The various scenarios and endpoints illustrate 

the variability and sensitivity of the system under different conditions, which informs the 

process to define the best representation of the system for deriving protective regulatory 

values based on site-specific conditions. A brief summary is presented here; details of the USGS 

modeling can be found in the USGS report in Appendix A (USGS, 2010). 

The estuary modeling focused on the area of the Bay from the Golden Gate Bridge 

through the central and northern Bay and Delta to Rio Vista on the Sacramento River and to 

Stockton on the San Joaquin River (see Figure 1-1 Map of the San Francisco Bay and Delta 

System). The South Bay area (Lower San Francisco Bay and South San Francisco Bay) is 

shallower and slower moving than the central and northern parts of the Bay. It exchanges 

water with other parts of the Bay, and shares similar estuarine processes, species, and habitats 

with the central and northern parts of the Bay and Delta. The South Bay provides habitat for 

the important species evaluated in the modeling. Therefore, protective selenium values based 

on the modeling should be appropriate for the entire Bay and the Delta system.

The Sacramento and San Joaquin Rivers are the main sources of inflow to the Delta. The 

Sacramento River is the dominant inflow under current flow management conditions. The 

rivers mix with seawater in the Delta and with internal selenium sources. The model considers 

the total river inflow from the Sacramento and San Joaquin Rivers, San Joaquin River water 

diversions and exports, and the total outflow of the estuary to the Pacific Ocean (or Net Delta 

Outflow Index, or NDOI, which is related to residence time for freshwater in the Delta and Bay). 

The model quantifies selenium concentrations in water, suspended particulate matter, 

and prey tissue that would be present, given a certain selenium concentration in a predator 

species under specific environmental conditions. For a given predator tissue selenium 

concentration (e.g., 8.5 micrograms of selenium per gram of tissue dry weight), the choice of 

species (e.g., adult white sturgeon) determines the food web to be modeled. Once a food web 

is chosen, the selenium concentrations of species within the food web can be determined using 

trophic transfer factors, which relate selenium concentrations in species to concentrations in 

 

6

Some Information in this section is paraphrased and/or summarized from the USGS report in Appendix A (USGS, 

2010).
12

their food. Invertebrate concentrations at the bottom of the food web can be linked to their 

food source concentrations, e.g., the concentration of selenium in clams can be linked to the 

concentration of selenium in suspended particulate material. Suspended particulate selenium 

concentrations can be linked to dissolved selenium concentrations by environmental 

partitioning coefficients. Determining the protective water column selenium concentration 

requires that the appropriate range of site-specific partitioning coefficients be used in the 

modeling.

Model variables are either species-specific, i.e., relating to the species of concern, or 

environment-specific, i.e., relating to the physical environment of the system in which the 

species is found. The species-specific variables include:

 Choice of species to protect and their critical life stage or stages;

 Food Web of the species of concern, to define prey/predator pairs in their diet; 

 Diet Mix and Trophic Transfer Factors (TTFs) to define the relative amounts of prey in 

the species’ diet (diet mix), and to define how much selenium bioaccumulates and 

assimilates into and through the species’ food chain (TTFs); and

 Effect Concentration Guidelines to define how much selenium may be harmful to the 

species of concern.

The environment-specific variables include:

 Salinity to constrain locations and thus potential pathways for loading, transformation, 

and exposure; 

 Partitioning Coefficients or Kds to quantify how much selenium is available to enter the 

base of a food web under specific hydrologic conditions; and

 Flow Year Type and Flow Season to reflect appropriate hydrologic conditions.

a. Overview of Species-Specific Variables

Wildlife Species, Critical Life Stages and Food Web: Since hundreds of wildlife species 

are present in the San Francisco estuary, FWS identified the species most at-risk due to 

elevated levels of selenium in a report, Species at Risk from Selenium Exposure in the San 

Francisco Estuary (USFWS, 2008). The FWS report considered both migratory7 and indigenous 

bird and fish species, and identified a smaller list of the most potentially vulnerable species (see 

Chapter 3). For each at-risk species, the FWS report included information about the critical life 

 

7 The San Francisco estuary is located along the Pacific Flyway and is a stopover for many avian species.
13

stage or stages, such as adult female reproduction (including egg laying), adult migration, and 

juvenile growth and development. The FWS analysis also contained detailed information about 

diet, including whether it was primarily clam-based or included insects and other prey items 

such as amphipods. If diet was primarily clam-based, the FWS report included an approximate 

percentage of clams in the species’ diet. 

USGS categorized the at-risk species by food chain (clam- or insect-based) and modeled

each category separately: clam-eating fish; clam-eating birds; and insect-eating fish (see 

Chapter 3, Table 3-1). Each category included at least one threatened or endangered species 

listed under the Endangered Species Act (ESA) (16 U.S.C. §1531 et seq.). The species considered

most at-risk that are federally listed are the California Ridgway’s rail (Rallus longirostris)

8

, a 

clam-eating bird; green sturgeon (Acipenser medirostris), a clam-eating fish; and (juvenile) 

Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss), both insecteating fish (USFWS, 2008). Clam-eating species are considered at-risk because of the presence 

of the invasive clam Corbula.

Corbula, a small bivalve (25 millimeters [mm] or less), was discovered in Suisun Bay in 

the northern part of San Francisco Bay after a major flood in the spring of 1986 that removed 

parts of the benthic community in the estuary (Cohen, 2011). Its increase and spread coincided 

with a multi-year dry period that began in the summer of 1986. Corbula is now found to be 

abundant throughout the Bay and most of the Delta. Adults can be found at salinities from 1 to 

33 ppt, with long-term survival greatest at salinities over 5 ppt, and recruits from 2 to 30 ppt; 

these ranges encompass the Bay and most of the northern estuary in most seasons and years 

(Cohen, 2011; Thompson and Parchaso, 2010; California Department of Water Resources 

Benthic BioGuide at http://www.water.ca.gov/bdma/BioGuide/ ). Corbula is also a frequent 

and dominant bivalve species in the South Bay (Thompson and Parchaso, 2010). It is most often 

observed in subtidal waters, but can also be found in intertidal mudflats (Cohen, 2011; 

Thompson and Parchaso, 2010; California Department of Water Resources Benthic Bio Guide at 

http://www.water.ca.gov/bdma/BioGuide/). Because this clam species is very efficient in 

accumulating selenium from its environment (Stewart et al., 2004), the species most at risk are 

believed to be clam-eating fish and clam-eating birds.

Diet Mix: Diet mix is the amount of each type of prey in a species’ diet. To evaluate the 

sensitivity of the model, USGS modeled different diet scenarios: an all-clam (100% clam) diet 

and a 50% clam/50% amphipod diet for clam-eating fish and clam-eating birds, and an all-insect 

 

8 The California Ridgway’s rail was formerly known as the California clapper rail (Chesser et al., 2014).
14

(100% insect) diet for insect-eating fish9. Other considerations included how long and during 

what life stages the species reside in the estuary. For example, although white sturgeon 

migrate upstream to spawn, they spend most of their life in the estuary. Sturgeon are longlived (green up to 50, white up to 100 years), and have a two-year internal egg maturation 

period. The longevity and extended reproductive cycle of white sturgeon may increase their 

dietary exposure to selenium from Corbula in the estuary, and may contribute to selenium 

loading in eggs (USGS, 2010 citing Linville, 2006). 

Trophic Transfer Factors: The model uses trophic transfer factors or TTFs to model the 

uptake or bioaccumulation of selenium from one trophic level to the next in a food chain. TTFs

define the relationship between selenium concentrations in an animal and in its food, and are 

species-specific or, lacking specific data may incorporate an appropriate category of animal

with known feeding habits, e.g., forage fish (USGS, 2010). 

TTFs can be determined from physiological parameters using a biodynamic equation or 

derived from field data. The biodynamic equation considers the selenium concentration in the 

animal, exposure time, assimilation efficiency from ingested particles, the ingestion rate of 

particles, the selenium concentration of ingested particles, the efflux (excretion) rate, and the 

growth rate of the animal (USGS, 2010).

If derived from matched data sets of field concentrations, TTFs can be estimated by 

dividing the concentration of selenium in the animal by the concentration of selenium in its 

prey species (food source), or TTF(species) = C(species) / C(prey). For example: 

TTF (invertebrate) = C (invertebrate) / C (suspended particulate matter) 

where the Cs are the concentrations of selenium in the animal (invertebrate) and in its food 

source (suspended particulate matter10), respectively (USGS, 2010). If the species has a mixed 

diet that includes more than one prey species, the concentration of selenium in its prey species 

can be weighted for each species. The higher the TTF value, the more the animal accumulates 

selenium from its food source. 

Information from one method can be compared or combined with information from 

another to refine or verify outcomes for specific species. Once TTFs are known, they can be 

 

9 The detailed dietary information provided in the FWS report (USFWS, 2008) for the species most at-risk is 

considered and discussed in Chapter 4, EPA Modeling and Proposed Water Quality Criteria.

10 USGS defines suspended particulate material (spm) as a mixture of living and non-living material (USGS, 2010). 
15

combined to represent step-wise bioaccumulation of selenium from particulate material 

through an invertebrate to a predator fish or bird species (USGS, 2010). 

Bioaccumulation of selenium from suspended particulate matter to invertebrate species 

varies widely. In general bivalves accumulate selenium more efficiently than other 

invertebrates (Presser and Luoma, 2010), and Corbula accumulates selenium much more 

efficiently than other bivalves in the estuary (Stewart et al., 2004; USGS, 2010). 

Since bioaccumulation rates differ widely among invertebrates and accurate 

characterization is critical to modeling success, USGS developed site-specific TTFs for Corbula in 

the estuary. USGS used a mechanistic equation for quantifying the biodynamics of Corbula, and 

estuary-specific data for their food source of suspended particulate material (USGS, 2010 pages 

21 – 23 and equations 14, 15 and 16). The mean TTF for Corbula from suspended particulate 

material in the estuary is 17.1, and the range across the estuary is 14 – 26 (USGS, 2010). Since 

the modeling is representative of the estuary, USGS used a rounded mean TTF value of 17 (see 

Appendix E Additional Details for the Derivation of USGS Trophic Transfer Factor for 

Potamocorbula amurensis). 

A discussion of other TTFs used in the modeling for the estuary is included in the USGS 

report. Calculated TTFs for various freshwater and marine species are summarized in Presser 

and Luoma (2010) (see Table 3 and Supporting Information). 

Selenium Benchmark Effect Concentrations: A benchmark is the concentration of a 

pollutant that relates to a level of adverse effect in the population of an animal or a category of 

animal (e.g., pelagic fish or aquatic birds). Selenium benchmarks are often expressed as a 

concentration of selenium in the predator species’ tissue. Benchmarks for fish tissue can be 

expressed as an egg or ovary, whole body or muscle concentration. Benchmarks for bird tissue 

are expressed as an egg concentration. Benchmarks are expressed in micrograms per gram 

(μg/g) or milligrams per kilogram (mg/kg) in dry weight (dw), e.g., 8.5 μg/g dw or 8.5 mg/kg dw. 

Studies use both; they represent the same unit and are used interchangeably in this document.

Benchmarks or effect concentrations (ECs) can be specified at different levels of effect 

and for different endpoints. ECs are the concentrations of selenium that may negatively affect 

up to a certain percentage of the species population, i.e., an EC05 level may affect up to 5% of 

the population, and an EC10 level may affect up to 10% of the population. Endpoints include 

those associated with reproductive effects and those associated with non-reproductive effects. 

For selenium, reproductive effect endpoints are those associated with maternal diet and 

transfer, and most often include reproductive failure (larval mortality for fish, hatchability for 
16

birds) and larval and juvenile deformity (teratogenesis); non-reproductive effect endpoints are 

those associated with diet and most often include reduction in or abnormal juvenile growth and 

development. Hatchlings and juvenile fish born with deformities and/or experiencing stunted 

growth and development are unlikely to survive to adulthood. They are much less likely to 

successfully reproduce, reducing the overall success of the species population in the ecosystem. 

Therefore, both reproductive and non-reproductive effects are important take into 

consideration. 

For several at-risk species, FWS provided information about selenium benchmarks, or 

selenium effect concentrations (USFWS, 2009, 2012). Mallard ducks (Anas platyrhincos) were 

chosen as the surrogate species for all aquatic-dependent birds given the lack of available data 

on listed and/or at-risk birds, and the relative abundance of data as to the toxicological 

sensitivity of mallards to selenium (USFWS, 2009). FWS provided selenium effect 

concentrations as a concentration of selenium in the species tissue (whole body for fish and egg 

tissue for birds), and as a concentration of selenium in the diet (USFWS, 2009, 2012). 

USGS modeled the three food web categories found in the San Francisco Bay and Delta 

(clam-eating fish, clam-eating birds, and insect-eating fish), using the FWS values for EC0, EC05, 

and EC10 effect concentrations as endpoints11 (USGS, 2010 Table 17 for clam-eating fish, Table 

18 for clam-eating birds and Table 19 for insect-eating fish). The results identified associated 

water column, particulate, and prey selenium concentrations for the different scenarios.

b. Overview of Environment-Specific Variables

Salinity: The two food webs in the estuary (clam- and insect-based) were independently 

modeled using salinity-specific transects in order to represent the dominant habitat used by 

each predator/prey pair (USGS, 2010). Landward gradient modeling represents the insectbased food web in the Delta from Benicia to Rio Vista and to Stockton for insect-eating fish such 

as juvenile Chinook salmon and steelhead. Seaward gradient modeling represents the clambased food web in the Bay from the Golden Gate Bridge through Suisun Bay to Chipps Island for 

clam-eating fish and clam-eating birds such as sturgeon and diving birds (USGS, 2010). A 

focused seaward gradient approach was also modeled for the area of Suisun Bay and Carquinez 

Strait, where critical habitat for sturgeon12 and important habitat for diving birds13 are located. 

 

11

 Chapter 3, Selenium Benchmark Effect Concentrations, discusses in detail the selenium effect concentration 

values used in the EPA modeling on which the proposed criteria are based.

12 Critical habitat for green sturgeon specifically includes Suisun Bay and San Pablo Bay, as well as the SacramentoSan Joaquin Delta (see Endangered and Threatened Wildlife and Plants: Final Rulemaking To Designate Critical 
17

This approach was used to compartmentalize the modeling to reduce uncertainties associated 

with ocean and freshwater influences, and to focus on the restricted area where the refineries 

discharge selenium and the area of critical and important habitat for clam-eating fish and bird 

species. Corbula (a dominant prey species) are abundant in this area (Cohen, 2011).

Partitioning Coefficients: Environmental partitioning factors or coefficients (Kds) are 

used to quantify the transformation process to different forms of selenium, and are site-specific 

(USGS, 2010). A Kd is defined as the ratio of the selenium concentration of particulate material 

to the dissolved selenium concentration in the water: 

Kd = Cparticulate material / Cwater

where Cparticulate material is in micrograms of selenium per kilogram of material in dry weight (μg/kg 

dw), and Cwater is in micrograms of selenium per liter of water (μg/L) (USGS, 2010). Particulate 

material is a mixture of living and non-living particulates and may include phytoplankton, 

periphyton, detritus, inorganic suspended material, biofilm, sediment and attached vascular 

plants (USGS, 2010; Presser and Luoma, 2010). Kd represents the efficiency with which 

dissolved selenium may be converted to particulate selenium material. The potential for phase 

transformation from dissolved to particulate selenium is important because selenium enters 

the food web primarily through particulate material (Presser and Luoma, 2010 citing Luoma et 

al., 1992; Presser and Luoma, 2010; and Stewart et al., 2010). The dominant chemical species 

or form of selenium (organo-selenium, elemental selenium, or adsorbed selenium) depends on 

the physical-chemical environment, which in turn affects its bioavailability to invertebrates

(USGS, 2010). The form of dissolved selenium also influences the phase transformation 

reaction. A detailed discussion of phase transformations is included in the USGS report.

All available, relevant data (USGS, 2010 Table 7) were included in calculating Kd values 

across the estuary (USGS, 2010 Tables 8, 9, and 10). Salinity-specific data were used to 

calculate Kds for the two salinity gradients within the estuary: the seaward gradients from the 

Golden Gate Bridge through Suisun Bay to Chipps Island for the clam-based food web, and the 

landward gradients from Benicia to Rio Vista and to Stockton (through the Delta) for the insectbased food web (USGS, 2010). Specific Kds were calculated for the focused seaward gradients 

 

Habitat for the Threatened Southern Distinct Population Segment of North American Green Sturgeon, 74 FR 52300, 

November 9, 2009). 

13 Important habitat for California Ridgway’s rail (previously California clapper rail) includes tidal and brackish 

marshes around San Francisco Bay (see Endangered and Threatened Wildlife and Plants; Final Recovery Plan for 

Tidal Marsh Ecosystems of Northern and Central California, 79 FR 10830, February 26, 2014). This includes Suisun 

Marsh and other tidal and brackish areas in Suisun Bay. 
18

(the area of Suisun Bay and Carquinez Strait) for the clam-based food web (USGS, 2010). Data 

from Cutter and Cutter (2004) and Doblin et al. (2006) were used to develop Kd values for the 

seaward and focused seaward transects, and from Lucas and Stewart (2007) to develop Kd

values for landward transects (USGS, 2010). The transect data sets used to determine Kd values 

consisted of samples taken one meter below the surface from 13 to 20 sites, and included 

salinity, dissolved selenium concentration and speciation, and suspended particulate material 

selenium concentration and speciation. Mean Kds and ranges of Kd values for each transect 

were calculated (USGS, 2010). To reduce uncertainty further, a temporal component was 

assigned to each dataset. Each transect was assigned a freshwater residence time, a water year 

type, and a flow season (USGS, 2010). The mean Kd value for each of four representative 

seaward transects and focused seaward transects was used to model the clam-based food 

chain in the estuary, and the mean for each of four representative landward transects was used 

to model the insect-based food chain in the estuary (USGS, 2010). 

Water Year Type and Flow Season: USGS collects data on surface waters from 

streamflow gaging stations throughout the United States and publishes them in annual reports 

(see USGS Annual Water Data Reports at http://wdr.water.usgs.gov/). “Water years” run from 

October 1st through September 30th. The observed average long-term values are the average 

flow values of a stream or water body from data collected since the early 1930s, when

sufficient numbers of streamflow gages were placed across the nation to collect representative 

data. Water years are labeled by their relative ranking of the yearly average flows within that 

80+ year history. The years are classified as normal (falling within a range of observed longterm average values), above normal, much above normal, or highest. Below normal may be 

classified as below normal, much below normal, or lowest (USGS, 2012). 

For San Francisco Bay and Delta, data were available for below normal, above normal, 

and wet (much above normal) years. The data used for modeling the clam-based food web 

(seaward transects) reflected above normal and wet water years; data used for modeling the 

insect-based food web (landward transects) reflected below normal and above normal water 

years. Since data were not available for critically dry and dry water years, the results may be 

less conservative than if drier conditions had been modeled.

Flow season is categorized as either low or high; low flow season refers to the time 

between June and the end of November when stream flows from runoff are usually at their 

lowest, and high flow season refers to the time between December and the end of May, when 

stream flows from runoff are usually at their highest. The San Francisco Bay and Delta 

modeling included data from both low and high flow seasons. 
19

Both water year type and flow season affect partitioning coefficients; the higher the 

flow (above normal and wet water years, and high flow seasons), the shorter the residence 

time and the lower the partitioning coefficient, resulting in less selenium being available to 

enter the food web. Conversely, the lower the flow (below normal and dry water years, and 

low flow seasons), the longer the residence time, the higher the partitioning coefficient, 

resulting in more selenium being available to enter the food web. Scenarios were run using 

water year types and flow seasons for which data were available. 

c. Summary of USGS Modeling of the San Francisco Estuary

Species-specific and site-specific information for the San Francisco estuary used in the 

Ecosystem-Scale Selenium Model illustrates the fate, bioaccumulation and assimilation of 

selenium in the aquatic environment. The species- and site-specific information is critical to the 

development of appropriate scenarios representative of the estuary. Table 2-1 Summary of 

Modeling Variables present that information. In Chapters 3 and 4, we discuss the variables that 

EPA used to populate the model to determine the proposed criteria for the estuary.
20

Table 2-1 Summary of Modeling Variables

Species-Specific Variables Considerations Sub-Categories USGS Choices

1. Most At-Risk Species Critical Life Stages;

Federal Status; 

Diet (General Food Web); 

Diet Mix (prey species).

1. Clam-Based 

Food Web - Fish

Trophic Transfer Factors (TTFs) & Diet Mix (%):

TTF – Amphipods

TTF – Clams - 100%

TTF – Amphipod/Clam - 50%/50%

TTF – Fish

2. Clam-Based 

Food Web - Birds

TTF – Amphipods

TTF – Clams - 100%

TTF – Amphipod/Clam - 50%/50%

TTF – Bird Egg

3. Insect-Based 

Food Web – Fish

TTF – Insects – 100%

TTF – Fish 

2. Effect Concentration

 (EC)

Endpoints: 

Larval Mortality - Fish;

Hatchability - Birds;

Deformity – Fish & Birds;

Reduction in Growth & 

Development – Fish & Birds.

1. Whole Body – Fish 

Percent of Population Affected:

EC05

EC10

2. Egg Tissue- Bird 

EC0 

EC05

EC10 

3. Diet – Fish & Birds

EC0 

EC05

EC10

Environment-Specific 

Variables Considerations Sub-Categories

1. Water Year Type Effect on Partitioning 

Coefficients

1. Critically Dry

(All available data)

2. Dry

3. Below Normal 

4. Normal

5. Above Normal

6. Wet

7. Critically Wet

2. Flow Season Effect on Partitioning 

Coefficients

1. Low

(All available data)

2. High

3. Partitioning Coefficient

 (Kd)

Salinity Gradient;

Residence Time (NDOI)

Transect Set:

1. Seaward Mean Value of each transect

2. Landward Mean Value of each transect

3. Focused Seaward Mean Value of each transect 
21

CHAPTER 3 SELENIUM BENCHMARK EFFECT CONCENTRATIONS 

As explained in Chapter 2, EPA, the Services and the USGS have been working together 

using the Ecosystem-Scale Selenium Model to develop water quality criteria protective of 

aquatic life and aquatic-dependent wildlife including federally listed species for the San 

Francisco estuary. This chapter considers which selenium benchmark effect concentration 

values EPA chose to use in the Ecosystem-Scale Selenium Model to develop site-specific criteria 

for the San Francisco Bay and Delta.

An important variable in the Ecosystem-Scale Selenium Model is the selenium effect 

concentration, EC, or benchmark, for the species of concern. The EC is the concentration of a 

pollutant that relates to a level of adverse effect in the population of an animal or a category of 

animal (see Chapter 2). Consistent with EPA’s recent national recommendation to states and 

tribes for a setting selenium water quality criterion, EC10 levels of effect are considered for this 

analysis (USEPA, 2016). The Ecosystem-Scale Selenium Model was developed using whole body 

fish tissue values (Presser and Luoma, 2010), therefore, we consider whole body fish tissue 

concentrations to use in the model for the San Francisco estuary. 

A. Summary of Benchmarks Considered

FWS Sources: EPA considered several benchmark recommendations from FWS. At the 

request of EPA, FWS completed an analysis of species most at risk in the estuary (USFWS, 2008) 

(see Table 3-1 List of FWS Species of Concern), as well as draft site-specific benchmark values 

for aquatic life (represented by two food webs in the estuary: clam-eating fish and insect-eating 

fish) and aquatic-dependent wildlife (represented by clam-eating birds in the estuary) (USFWS, 

2009). FWS also completed a more detailed species-specific analysis of benchmark 

recommendations for (clam-eating) white and green sturgeon (USFWS, 2012). All fish species 

considered most at risk are indigenous to the estuary, and all bird species are either indigenous 

or migratory, since the estuary is an important stopover along the Pacific Flyway.

EPA Sources: For aquatic life in the San Francisco Bay and Delta, EPA considered all 

available science, including the fish tissue values in EPA’s national recommended freshwater 

aquatic life criterion for selenium (USEPA, 2016). These values are intended to be protective of 

aquatic life under a variety of conditions in water bodies across the United States. EPA’s 

document incorporates a comprehensive review of selenium effects data currently available in 

the literature for freshwater species, including anadromous fish species. The freshwater fish 

tissue values used in the national recommended criterion are based on data from qualityassured studies to ensure representativeness and reduce uncertainty, while data from other 
22

relevant studies are noted and discussed14. The studies used to develop the national 

recommended chronic criterion are evaluated here to consider whether they are 

representative of species in the San Francisco estuary, and thus whether the freshwater fish 

tissue values are appropriate for use as benchmark values in the model for the estuary to 

develop site-specific water quality criteria. For aquatic-dependent wildlife (clam-eating birds), 

EPA considered the egg tissue value that the State of Utah adopted and EPA Region 8 approved 

for Gilbert Bay of the Great Salt Lake (USEPA, 2011a). During the development of this bird egg 

tissue criterion, an expert panel reviewed all currently available bird egg data; the studies used 

to develop the bird egg tissue value are evaluated here to determine whether they are 

representative of species in the San Francisco estuary, and thus whether the bird egg tissue 

value is appropriate for EPA to use as a benchmark value in the model for the estuary.

 Table 3-1 List of FWS Species of Concern (Adapted from USFWS, 2008) 

Species (Indigenous/Migratory)

Food Web

(Clam or Insect) 

Federal Status under the 

Endangered Species Act 

Clam-eating Fish

Sturgeon: Green & White (Indigenous)

Acipenser medirostris & A. transmontanus Clam (≤ 40%)

Threatened - Green Sturgeon; 

Not Listed - White Sturgeon

Sacramento Splittail (Indigenous)

Pogonichthys macrolepidotus Clam (≤ 34%) Concerned

Clam-eating Birds

California Ridgway’s Rail (Indigenous) 

(formerly California clapper rail)

Rallus longirostris obsoletus

Clam (≤ 64%) Endangered

Scaup: Greater & Lesser (Migratory)

Aythya marila & A. affinis Clam (80-96%)* Not Listed

Scoter: White-Winged, Surf, & Black (Migratory)

Melanitta fusca, M. perspicillata, & M. nigra Clam (75-86%)* Not Listed

Insect-eating Fish

Chinook Salmon (Indigenous)

Oncorhynchus tshawytscha Insect Threatened & Endangered 

Steelhead Trout (Indigenous) 

O. mykiss Insect Threatened 

Delta Smelt (Indigenous) 

Hypomesus transpacificus Insect Threatened

* When wintering in the estuary. Since nesting and breeding occurs after migration to Alaskan and Canadian 

tundra, potential selenium exposure from Bay and Delta clams may not be relevant to breeding. 

A summary of the categories of species considered for the San Francisco Bay and Delta 

and FWS and EPA EC10 benchmark values are presented in Table 3-2 Summary of EC10 EPA and 

FWS Benchmarks Considered.

 

14 See EPA Guidelines for Ensuring and Maximizing the Quality, Objectivity, Utility, and Integrity, of Information 

Disseminated by the Environmental Protection Agency, commonly known as EPA Data Quality Guidelines (USEPA, 

2002). 
23

Table 3-2 Summary of EC10 EPA and FWS Benchmarks Considered

Category 

 EC10

EPA Benchmark

EPA

Source

 EC10

FWS Benchmark

FWS

Source

Clam-eating 

fish

8.5 mg/kg dw

(whole body)

USEPA, 2016

3.86-9.65 mg/kg dw White Sturgeon 

(whole body)

Using Linville, 2006 and Tashjian et al., 

2006

USFWS, 2012

1.97-3.71 mg/kg dw Green Sturgeon

(whole body)

Using Linares-Casenave et al., 2010, 

Linville, 2006, and Tashjian et al., 2006

Clam-eating 

birds

12.5 mg/kg dw

(egg tissue)

USEPA, 

2011a

7.73 mg/kg dw (Mallard surrogate)

(egg tissue)

USFWS, 2009

Insect-eating 

fish

8.5 mg/kg dw

(whole body)

USEPA, 2016

1.84 mg/kg dw Chinook Salmon

(whole body)

Using Hamilton, et al., 1990; 

2.19 mg/kg dw Rainbow Trout 

(whole body) 

Using Hilton et al., 1980

USFWS, 2009

B. FWS Sources: FWS Species Reports

a. Species at Risk from Selenium Exposure in the San Francisco Estuary; Final Report 

(USFWS, 2008): Since hundreds of species of wildlife are present in the San Francisco Bay and 

Delta, EPA asked FWS to provide a list of species most at risk (i.e., vulnerable) in the Bay and 

Delta due to elevated levels of selenium. In general, some species are affected by selenium in 

their environment because they are either more toxicologically sensitive to increased selenium 

levels than other species and/or because they are exposed to significantly elevated selenium 

levels through diet preferences (i.e., bioaccumulated selenium concentrations through prey 

species). FWS completed a report, Species at Risk from Selenium Exposure in the San Francisco 

Estuary; Final Report (USFWS, 2008). The report looks at the species in the estuary and their 

sensitivity and exposure to selenium, and includes an analysis of each species’ diet (prey 

species) with a focus on how much of each species’ diet consists of clams.

FWS compiled an initial list of approximately 45 species that live in or around the 

estuary for evaluation; federally threatened and endangered species were given priority. FWS 

then narrowed the list to 13 species considered to be most at risk from selenium exposure. 

This list includes seven bird and six fish species; all of the species are aquatic or aquaticdependent species, and five (four fish and one bird) species are listed as threatened or 

endangered under the Endangered Species Act (USFWS, 2008). 
24

The 13 most at-risk species fall into three general food-web categories based on their 

diet: clam-eating fish, clam-eating birds, and insect-eating fish (see Table 3-1 List of FWS 

Species of Concern). Since the invasive clam species Corbula is abundant throughout the 

estuary and efficiently accumulates selenium, the species thought to be most at risk are clameating birds and clam-eating fish. One species, the bald eagle (Haliaeetus leucocephalus), was 

not considered for further evaluation (and is not included in Table 3-1) because its diet is not 

predominantly clam-based,

15 nor is the eagle more vulnerable to elevated selenium levels in its 

environment than the other aquatic-dependent bird species considered in the analysis (USFWS, 

2008). 

Clam-Eating Fish: FWS found that the clam-eating fish species most at risk from 

selenium dietary exposure in the estuary are green sturgeon (Acipenser medirostris) listed as 

federally threatened, white sturgeon (A. transmontanus), and Sacramento splittail

(Pogonichthys macrolepidotus). FWS estimated the diet of white sturgeon to be approximately 

40% clam-based, and although not firmly established, the diet of green sturgeon to be similar 

(USFWS, 2008; USFWS, 2012). 

FWS concluded that green sturgeon are likely to be more toxicologically sensitive to the 

effects of selenium in their diet than white sturgeon, and juvenile sturgeon, both white and 

green, may be more sensitive than adult sturgeon (USFWS, 2012). Since data exist for white 

sturgeon, while limited data exist for green sturgeon, white sturgeon are considered as a 

surrogate for listed green sturgeon and differences are noted where known. Both species are 

anadromous, i.e., they are born in freshwater and return to brackish and marine waters as 

juveniles. Both white and green sturgeon are known to migrate and spawn in the Sacramento 

River, and both have been caught on the San Joaquin River upstream of Stockton; new data 

confirm that white sturgeon also spawn in the San Joaquin River system (Jackson and 

Eenennaam, 2013). It is currently understood that white sturgeon spend a considerable 

amount of time over a lifetime in the estuary, and some are year-round residents; green 

sturgeon also spend time in the estuary (from first to third years) but eventually move into 

open ocean waters (USFWS, 2008).

FWS estimated the diet of Sacramento splittail to be up to 34% clam-based (USFWS, 

2008). Affected critical life stages from selenium exposure for clam-eating fish species include 

 

15

 Approximately 23% of the bald eagle diet consists of waterfowl (USFWS, 2008). Assuming the worst-case 

scenario, that all waterfowl consumed are clam-eating waterfowl, the other bird species considered most at-risk 

(California Ridgway’s rail, scoter and scaup) are at a higher risk of adverse effect, as FWS estimated these species 

consume more than twice as much clam-based food (see Table 3-1 List of FWS Species of Concern).
25

impaired reproduction (toxicity to eggs, including larval mortality and deformity) and impaired 

juvenile growth and development (USFWS, 2008) (see Table 3-3 Probable Critical Life Stages).

Clam-Eating Birds: FWS identified the clam-eating birds most at risk from selenium 

dietary exposure in the estuary as the California Ridgway’s rail (Rallus longirostris obsoletus), 

listed as federally endangered, and the diving ducks: the greater scaup (Aythya marila), lesser 

scaup (A. affinis), white-winged scoter (Melanitta fusca), surf scoter (M. perspicillata), and black 

scoter (M. nigra) (USFWS, 2008). California rails are year-round residents of the estuary, and 

FWS estimated their diet to be as much as 64% clam-based.16 Affected critical life stages from 

selenium exposure include impaired reproduction (toxicity to embryos, including egg 

hatchability and deformity) (USFWS, 2008). Scoters and scaups are migratory birds that spend 

the winter in the estuary, and fly north to breed in the spring. FWS estimated their diet to 

range from 75% to 96% clam-based while wintering in the estuary (USFWS, 2008). The FWS 

report finds that affected critical life stages from selenium exposure may include impaired 

reproduction (toxicity to embryos, including egg hatchability and deformity) and impaired 

migration (reduced ability to successfully reach breeding grounds). Research indicates that surf 

scoter and greater scaup accumulate elevated levels of selenium in muscle and liver while 

overwintering in Suisun Bay (De La Cruz, 2010 and De La Cruz et al., 2008), and that these levels 

might impair their ability to migrate successfully to breeding areas in Alaska and Canada 

(Ohlendorf and Heinz, 2011).

Insect-Eating Fish: The FWS report found that the insect-eating fish species (or species 

in an insect-eating fish food chain) most at risk from selenium dietary exposure in the estuary 

are Chinook salmon (Oncorhynchus tshawytscha) listed as federally endangered17 (Sacramento 

River winter-run Evolutionary Significant Unit [ESU]) and threatened (Central Valley spring-run 

ESU), steelhead trout (O. mykiss) listed as federally threatened, and Delta smelt (Hypomesus 

transpacificus) also listed as federally threatened. Chinook salmon and steelhead trout are 

anadromous, and both are considered highly toxicologically sensitive to selenium levels in their 

environment (USFWS, 2008). Affected critical life stages include impaired reproduction (toxicity 

to eggs, including larval mortality and deformity) and impaired juvenile growth and 

 

16 California rails are littoral feeders and consume various types of clams. Corbula, which are predominantly found 

in subtidal waters, are estimated to be no more than 20% of the rail’s diet. See Chapter 4. 

17 The National Marine Fisheries Service has identified 17 Evolutionary Significant Units (ESU) of Chinook salmon in 

California, Oregon, Washington and Idaho; three use the estuary: the Sacramento River winter-run ESU; the

Central Valley spring-run ESU; and the Central Valley fall/late-fall run ESU (USFWS, 2008). 
26

development18 (USFWS, 2008). However, none of the species are known to consume Corbula,

(or consume fish species that consume Corbula) so their dietary exposure of selenium in the 

estuary is likely lower than other species that are known to consume Corbula (USFWS, 2008). 

Table 3-3 Probable Critical Life Stages (Adapted from USFWS, 2008) 

Species Probable Critical Life Stage 

Clam-eating Fish 

Sturgeon: Green & White 

(anadromous)

Adult Female/Reproduction (egg/larval mortality; deformity);

Juvenile (growth and development)

Sacramento Splittail

Adult Female/Reproduction (egg/larval mortality; deformity); 

Juvenile (growth and development)*

Clam-eating Birds

California Ridgway’s Rail Adult Female/Reproduction (egg hatchability; deformity)

Scaup: Greater & Lesser

Adult Female/Reproduction (egg hatchability; deformity);

Adult Male & Female/Migration

Scoter: White-Winged, 

 Surf, & Black

Adult Female/Reproduction (egg hatchability; deformity); 

Adult Male & Female/Migration

Insect-eating Fish

Chinook Salmon (anadromous)

Adult Female/Reproduction (egg/larval mortality; deformity);

Juvenile/Migration (growth and development)

Steelhead Trout (anadromous)

Adult Female/Reproduction (egg/larval mortality; deformity); 

Juvenile/Migration (growth and development)

Delta Smelt

Adult Female/Reproduction (egg/larval mortality; deformity);

Juvenile (growth and development)

* Juvenile splittail (ages 0 to 2 years) range in length from 25 mm to 200 mm (1 to 8 inches) (USFWS, 2008). 

Splittail are bottom feeders, and although Corbula are small (averaging 0.5 inches), younger splittail juveniles

may consume fewer mollusks than older juveniles.

Summary: The FWS report narrows the list of vulnerable species to 13. These species 

can be categorized by food chain: clam-eating fish, clam-eating birds, and insect-eating fish, 

with each category including at least one federally listed species. Therefore, the analysis 

focuses on these three categories of species and the representative species within each 

category. For clam-eating fish, target species are white and green sturgeon and splittail, and 

the FWS estimates their diets to be approximately 40% and 34% clam-based, respectively. 

Green sturgeon are federally listed as endangered. For clam-eating birds, target species are the 

California Ridgway’s rail which is federally listed as endangered, and the five species of 

migratory diving ducks, the scoters and scaups. FWS estimates the rail diet to be approximately 

64% clam-based, and the scoters and scaups to be approximately 75-96% clam-based when 

 

18 Adult Chinook salmon and steelhead spend most of their lives in the open ocean, and only in-migrate through 

the Bay and Delta to natal waters just prior to spawning; they are unlikely to consume food from the estuary. 

Juvenile salmon and steelhead out-migrate through the estuary on their way to the ocean. During that time, they 

may consume food items from the estuary that are low in selenium (insects, zooplankton, etc.) for a short period 

of time. See more detailed discussion in Chapter 4. 
27

overwintering in the estuary. For insect-eating fish, target species are Chinook salmon, listed as 

endangered, and steelhead trout and delta smelt, both listed as threatened. 

b. Selenium Effect Levels for Selected Representative/Surrogate Species (USFWS, 

2009): In July 2009, FWS provided recommended benchmark values for representative and/or 

surrogate species19 living in the San Francisco estuary to EPA (USFWS, 2009). Representative or 

surrogate species include mallard ducks (Anas platyrhynchos) for clam-eating birds, white 

sturgeon (A. transmontanus) and green sturgeon (A. medirostris) for clam-eating fish, and 

Chinook salmon (O. tshawytscha) and rainbow trout (O. mykiss) for insect-eating fish. The 

report includes benchmark values for EC0, EC05 and EC10 for whole body tissue (for fish) and 

egg tissue (for birds). Since FWS provided EPA with detailed benchmark values for white and 

green sturgeon in a more recent report (USFWS, 2012), this section discusses the benchmarks 

for clam-eating birds and insect-eating fish. Benchmarks for sturgeon, the representative 

species for clam-eating fish, are discussed in the next section. Table 3-4 summarizes the 

relevant EC10 FWS recommended bird egg tissue and fish whole body benchmark values for 

clam-eating birds and insect-eating fish, respectively. 

Table 3-4 Summary of FWS-Recommended EC10 Selenium Benchmark Values for 

Representative or Surrogate Species (Adapted from USFWS, 2009)

Species

Selenium 

Tissue Value 

μg/g dw

Effect Dietary Exposure 

duration (days)

Form of 

Selenium

(in food)

Model Data 

Source*

Mallard 

duck

7.73

(egg tissue)

Hatchability > 40

(parental)

Seleno-DLmethionine

Beckon et al., 

2008 

(biphasic)

Heinz et al., 

1989

Chinook 

salmon

1.84

(whole body)

Mortality 90

(juvenile)

Seleno-DLmethionine

Brain and 

Cousens, 

1989

(biphasic)

Hamilton et 

al., 1990

Rainbow 

trout

2.19

(whole body)

Reduction 

in growth

140

(juvenile)

Sodium 

selenite

Beckon et al., 

2008

(biphasic)

Hilton et al., 

1980

* The Hamilton et al., 1990 study and the Hilton et al., 1980 study are not used in USEPA, 2016 to derive criteria 

values due to data quality concerns.

Clam-Eating birds: Since toxicity studies have not been performed on any of the avian 

species identified as most at-risk, the FWS report uses mallard ducks as the surrogate species 

for clam-eating birds (USFWS, 2009). FWS relies on a detailed dietary study by Heinz et al. 

 

19 Data do not exist for some of the at-risk species living in the estuary. In those cases, we rely on data from other 

species (i.e., surrogate species) that we believe will respond in a manner similar to how the at-risk species would 

respond to the same environmental condition, and discuss where differences might occur.
28

(1989) that investigated the reproductive success of several groups of mallards that were fed 

diets containing different concentrations of selenium; the data collected included selenium egg 

and liver concentrations. Mallard ducks are commonly found in the San Francisco Bay area, and 

live in fresh, brackish and salt waters (National Geographic at 

http://animals.nationalgeographic.com/animals/birds/mallard-duck/). FWS uses the egg 

concentration data from the Heinz (1989) study to determine an EC10 egg value.

In 2008, Tetra Tech, Inc. (Tetra Tech), in association with the Western States Petroleum 

Association (WSPA), completed a detailed review of all available avian studies, in an effort to 

assist the San Francisco Regional Water Quality Control Board in completing a selenium TMDL 

for the North San Francisco Bay (Tetra Tech, 2008). The Tetra Tech review indicated that 

although many avian toxicity studies on selenium have been conducted to determine dietary 

benchmarks and several of these studies are associated with reproductive success, only a few 

studies measured egg selenium concentrations.20 Tetra Tech reviewed studies available in the 

literature on the reproductive success of avian species including chickens, mallards, pheasants, 

and screech owls; these studies indicate that mallards are the most sensitive of the species 

studied. Key reproductive studies on mallards include Heinz, et al., 1987, and 1989, Heinz and 

Hoffman 1996, and 1998, and Stanley et al., 1994, and 1996 (Tetra Tech, 2008). 

In the 2009 report, FWS selected the Heinz et al. (1989) study on mallards and applied a 

biphasic (log-logistic2)

21 model to the egg selenium concentration data (USFWS, 2009 and 

Beckon et al., 2008). A biphasic model is one in which the dependent variable is maximal or 

minimal at an intermediate level of the independent variable, i.e., the relationship is depicted 

either as a hill-shaped or valley-shaped curve (Beckon et al., 2008). Using a biphasic model on 

the Heinz et al. (1989) data, FWS estimated an EC10 bird egg value of 7.73 μg/g dw (USFWS, 

2009). 

Insect-Eating fish: For rainbow trout, a representative species for insect-eating juvenile 

fish, FWS calculated a whole body EC10 value using the data from the Hilton et al. (1980) study, 

using a biphasic model (USFWS, 2009 and Beckon et al., 2008). In the Hilton study, juvenile 

rainbow trout were fed diets spiked with six different concentrations of selenium ranging from 

between 0.07 and 13.06 μg/g dw over 20 weeks (140 days). Over the course of the study, fish 

were sacrificed and data were collected including carcass, liver and kidney selenium 

 

20 Research on selenium toxicity indicates that for most bird species, similar to fish species, reproductive endpoints 

appear to be more sensitive than non-reproductive endpoints (USFWS, 2009 and Tetra Tech, 2008). 

21

 The term log-logistic2(i.e., log-logistic squared) reflects a model that is formed by the multiplicative combination 

of two log-logistic models (Beckon et al., 2008).
29

concentrations. Fish that were fed the higher concentration selenium diets exhibited reduced 

growth, food avoidance and mortality. 

FWS took the carcass, liver and kidney data from Hilton et al. (1980) to calculate whole 

body selenium concentrations, and performed a regression analysis against weight (USFWS, 

2009 Figure 11). The FWS analysis indicated that juvenile rainbow trout exhibit reduced growth 

at diets containing 13.06 μg/g dw of selenium, and that effects (10%) began to be observed at 

whole body concentrations of approximately 2 μg/g dw. Using a biphasic model, FWS 

calculated a whole body EC10 value for reduction of growth (non-reproductive effect) in 

juvenile rainbow trout of 2.19 μg/g dw (USFWS, 2009). 

For Chinook salmon, FWS calculated a whole body EC10 value with data from Hamilton 

et al. (1990), using the biphasic model (USFWS, 2009 and Brain and Cousens, 1989). In the 

Hamilton study, juvenile Chinook salmon were exposed to three different types of diets for 90 

days at various concentrations: a control diet containing meal with low-selenium mosquitofish 

collected from a reference site; a diet containing meal with high-selenium mosquitofish 

collected from the San Luis Drain in California (the SLD diet); and a diet containing meal with 

low-selenium mosquitofish fortified with seleno-DL-methionine (the SeMet diet). For the SLD 

and the SeMet diets, fish were fed six different concentrations of selenium, ranging from 3.2 

μg/g dw to 35.4 μg/g dw of selenium (Hamilton et al., 1990). Mortality in each test group was 

recorded daily, and growth was recorded and whole body tissue samples were taken at 30-day 

intervals. The authors reported that there was a positive correlation between whole-body 

concentrations of selenium and increased concentrations of dietary selenium, regardless of diet 

type. However, between 60 and 90 days, mortality in all three dietary scenarios increased 

noticeably; for the control scenario, percent survival decreased from 99% to 67%; for the SLD 

diets, percent survival decreased from 89 - 97% to 18 - 51%. For the SeMet diets, percent 

survival decreased from 63 – 100% to 11 - 73% (Hamilton et al., 1990).

FWS used the 90-day data on percent survival and whole body concentrations for the 

SLD diet and SeMet diet scenarios, and performed a regression analysis using a biphasic model 

(USFWS, 2009 Figure 9 and Table 6). The model yielded a whole body EC10 value for mortality 

(non-reproductive effect) in Chinook salmon of 1.84 μg/g dw (USFWS, 2009).

Summary: In all three analyses, FWS used a biphasic model. For clam-eating birds, FWS 

used (mallard) data from Heinz, et al. (1989) and applied a biphasic model (Beckon et al., 2008) 

to derive an EC10 egg tissue value of 7.73 μg/g dw (USFWS, 2009). For insect-eating fish, FWS 

used (rainbow trout) data from Hilton et al. (1980) and applied a biphasic model (Beckon et al., 

2008) to derive an EC10 whole body fish tissue value of 2.19 μg/g dw; and (Chinook salmon) 
30

data from Hamilton et al. (1990) and applied a biphasic model (Brain and Cousens, 1989) to 

derive an EC10 whole body fish tissue value of 1.84 μg/g dw (USFWS, 2009). 

Biphasic relationships occur in toxicology, and reflect the type of effect that selenium 

has on many species, i.e., selenium is a micronutrient having a negative effect at zero or very 

small (deficient) concentrations, a positive effect at small or moderate concentrations, and a 

negative effect at higher concentrations. Biphasic modeling may be more appropriate than loglogistic modeling if sufficient data points are available in both the lower and higher dose 

regions, and the measured effect occurs in both a deficient and in an excess of the constituent, 

e.g., impaired growth for selenium (non-reproductive effects).22 However, if sufficient data are 

not available in the deficit range, the resulting modeled chronic values in the excess range may 

be biased. Most studies in the published literature on selenium were not set up experimentally 

or intended to capture the appropriate effects and range of doses in the deficit region that are 

necessary for biphasic modeling. EPA reviewed the data sets for the published studies for 

which FWS used a biphasic model, and did not find they included appropriate or sufficient data 

for utilization of a biphasic model. Therefore, EPA supports the use of a standard log-logistic 

model to determine EC10 values with data sets from published literature, including the data 

sets for the studies discussed above, and does not use biphasic models to calculate chronic 

values.

For bird egg tissue modeling using mallard data, EPA supports the use of standard loglogistic modeling as was done for Gilbert Bay of the Great Salt Lake in Utah, using all available 

appropriate data (USEPA, 2011a). This is discussed in more detail in section C. 

Hilton et al. (1980) fed juvenile rainbow trout a diet consisting of a casein-torula yeast 

supplemented with selenium as sodium selenite (inorganic selenium). As discussed in USEPA 

(2016) for the Ogle and Knight (1989) study with fathead minnow, the reduction in growth 

observed with fish fed at higher dietary inorganic selenium concentrations may be due to 

reduced palatability of the food, since much of the food remained uneaten, i.e., the diet mix 

contained an unrealistic fraction of inorganic selenium, causing food avoidance. This is a 

common observation in early selenium studies, including the Hilton study (USEPA, 2016). The 

reduced growth at the higher dietary concentration in Hilton et al. is likely due to the observed 

food avoidance, an artifact of unrealistic spiking of the diet with inorganic selenium in the 

experimental protocol (USEPA, 2016). Therefore, the results of the study would not be 

appropriate for deriving chronic values. Additionally, the range of tested concentrations was 

 

22

 Reproductive effects such as embryonic mortality or malformations are known to occur after excessive doses of 

dietary selenium, but not when there is a dietary deficiency; therefore, reproductive effects should only be 

modeled using a log-logistic model (Beckon et al., 2008).
31

wide, so that the NOEC and LOEC are unacceptably far apart (USEPA, 2016). Lastly, since 

reproductive toxicity tests are available for the genus Oncorhynchus, they are preferable to 

non-reproductive effect studies. As concluded by selenium experts at the 2009 Pellston

conference (Chapman et al. 2009), the most important toxicological effects of selenium in fish 

arise following maternal transfer of selenium to eggs during vitellogenesis, resulting in selenium 

exposure when hatched larvae undergo yolk absorption. Such effects include larval mortality or 

permanent developmental malformations, such as skeletal and craniofacial deformities. 

In Hamilton (1990), mortality in juvenile Chinook salmon increased in all three test 

groups between 60 and 90 days including the control group as indicated by a 1% mortality at 60 

days and a 33% mortality at 90 days. EPA reviewed the data and determined that the health of 

the fish was likely compromised between 60 and 90 days. Therefore, the results of the 90-day 

endpoint were excluded from the analysis for the national recommended selenium criterion 

(USEPA, 2016). The control mortality of 1% was acceptable at 60 days. The Aquatic Life 

Guidelines (USEPA, 1985) and the Manual of Instructions for Preparing Aquatic Life Water 

Quality Criteria Documents (Stephan, 1987) recommend that excessive control mortality be 

treated as an exclusionary threshold in data quality assessments for regulatory purposes such 

as deriving water quality criteria. EPA performed a regression on the 60-day weight and whole 

body concentrations, and derived a whole body EC10 value of 7.355 μg/g dw for the SeMet diet 

for reduced growth, and a whole body EC10 value of 11.14 μg/g dw for the SLD diet for reduced 

growth. These are the only two EC10 Species Mean Chronic Values (SMCVs) acceptable to use 

for deriving non-reproductive endpoints for the genus Oncorhynchus, and the Genus Mean 

Chronic Value (GMCV) is 9.052 μg/g dw23 (USEPA, 2016 Table 6.2). 

Given the concerns with using a biphasic model and data quality concerns with Hilton et 

al. (1980) and Hamilton et al. (1990), the FWS-recommended benchmark values for clam-eating 

birds and insect-eating fish would not be appropriate for use in the Ecosystem-Scale Selenium 

Model for deriving site-specific criteria for the San Francisco Bay and Delta.

c. Evaluation of Toxicity of Selenium to White and Green Sturgeon (USFWS, 2012): As 

a follow-up to the FWS report on effect levels for selected species, FWS provided additional 

detail and supporting information for the clam-eating fish tissue values. FWS determined that 

white and green sturgeon were pivotal species for determining aquatic life water quality 

standards for selenium in the estuary, and then examined the available studies and data on the 

two sturgeon species to estimate selenium benchmarks (USFWS, 2012). 

 

23 These results are discussed under Non-Reproductive Effect Studies in section C, EPA Sources: CWA Section 

304(a) National Recommended Water Quality Criterion for Selenium and Mallard Bird Studies. 
32

FWS identified four key studies (Linville, 2006; Linares-Casenave et al., 2010; Silvestre et 

al., 2010; and Tashjian et al., 2006), and used the data and information to develop the report, 

Evaluation of the Toxicity of Selenium to White and Green Sturgeon (USFWS, 2012). In Linville 

(2006) (University of California, Davis, Ph.D. dissertation) white sturgeon larvae from the San 

Francisco estuary were exposed to elevated levels of selenium in two separate experiments: 

one in which L-selenomethionine was injected into yolk sacs just after hatching 

(microinjection), and the other in which gravid females were fed selenized yeast for up to 6 

months before they deposited their eggs (maternal transfer) (USFWS, 2012 and Linville, 2006). 

FWS performed a regression on the data from the Linville (2006) microinjection study to 

determine the 5% and 10% larval mortality effect levels, and used data from the Linville (2006) 

maternal transfer study and the Tashjian et al. (2006) study to translate the larval mortality 

effect levels to egg, muscle and whole body effect levels. FWS translated the microinjection 

larval effect levels to egg concentrations using the relationship in the Linville (2006) maternal 

transfer study (USFWS, 2012 Figure 3). Similarly, FWS translated the microinjection larval effect 

levels to muscle concentrations using the relationship found in the Linville (2006) maternal 

transfer study (USFWS, 2012 Figure 4). Muscle concentrations were translated to whole body 

concentrations using the relationship in Tashjian et al. (2006) on juvenile white sturgeon 

(USFWS, 2012 Figure 5). 

FWS also performed a regression on the data from the maternal transfer study to 

determine the 5% and 10% larval developmental effect levels (USFWS, 2012). FWS then 

translated the developmental effect levels to egg, muscle and whole body effect levels, using 

the relationships calculated from the data in the maternal transfer study and the data in 

Tashjian et al., in the same way as the larval mortality effect levels from the microinjection 

study were translated (USFWS, 2012).

To develop benchmarks for green sturgeon, FWS used data from the Linares-Casenave 

et al. (2010) microinjection study to determine green sturgeon larval mortality effect levels, 

which were then translated to egg, muscle and whole body using the relationships previously 

developed for white sturgeon using Linville (2006) and Tashjian et al. (2006). Lastly, FWS used 

data from the Linares-Casenave microinjection studies on green and white sturgeon to develop 

a sensitivity ratio, which was then applied to the results of the Linville maternal transfer study 

on white sturgeon to calculate effect levels of maternal transfer on green sturgeon. FWS 

determined that green sturgeon are more than twice as sensitive as white sturgeon to selenium 

(USFWS, 2012). They noted that other studies confirm that green sturgeon are more sensitive 

to selenium at environmentally relevant concentrations than white sturgeon (USFWS, 2012 

citing Kaufman et al., 2008, Linares-Casenave et al., 2010, and Silvestre et al., 2010). 
33

The FWS EC10 sturgeon whole body and egg tissue effect concentrations24 are 

summarized in Table 3-5 Summary of FWS-Recommended EC10 Selenium Benchmarks for 

White and Green Sturgeon.

Table 3-5 Summary of FWS-Recommended EC10 Selenium Benchmarks for White and Green 

Sturgeon (Adapted from USFWS, 2012)

Species

Concentration of 

Se in whole body

(μg/g dw)

Concentration of 

Se in egg tissue

(μg/g dw)

Effect Study Type Data Source

White 

Sturgeon

3.86 6.83

Larval

Mortality Microinjection

Linville, 2006;

Tashjian et al., 2006

9.65 15.8

Larval 

abnormality Maternal Diet

Linville, 2006;

Tashjian et al., 2006

Green 

Sturgeon

1.97 3.70 Larval 

Mortality Microinjection

Linares-Casenave et 

al., 2010; 

Linville, 2006; Tashjian 

et al., 2006

3.71* 6.59* Larval 

abnormality

Maternal Diet*

(estimated 

from sensitivity 

ratio)

Linares-Casenave et 

al., 2010;

Linville, 2006; Tashjian 

et al., 2006

* Benchmarks are projected using a sensitivity ratio that was developed by comparing the results of microinjection 

studies on green and white sturgeon (Linares-Casenave et al., 2010) and applying the sensitivity ratio to the results 

of the Linville (2006) maternal transfer study on white sturgeon (whole body values derived using data from 

Tashjian et al., 2006).

The FWS report acknowledges that although the best available information was used, 

some of the studies (Linares-Casenave et al. [2016] and Silvestre et al. [2010]) may have limited 

relevance, as the progeny of only a single individual could be used in the study as the species is 

federally listed as threatened. Additionally, the report notes that the analysis focuses on a 

single endpoint (either mortality or abnormalities), but in nature, mortality and deformity 

effects are additive such that the surviving individuals suffer developmental impairment; 

therefore, they postulate that their analysis may underestimate the extent of the effects of 

selenium to sturgeon (USFWS, 2012). 

The microinjection studies (Linville and Linares-Casenave et al.) represent an artificial 

route of exposure that can add uncertainty with respect to metabolism and distribution of 

selenium in the body. Microinjection is a more efficient route of exposure (higher absorption 

efficiency) and likely leads to less excretion of selenium than maternal exposure through 

 

24 A complete summary of FWS benchmarks can be found on page 2 of the USFWS report, and includes EC05 and 

EC10 benchmarks for whole body, muscle and egg tissue.
34

ingestion of contaminated prey. In addition, microinjection represents a “bolus” dose of 

selenomethionine to the developing embryo, and the metabolic controls associated with 

maternal transfer to the egg are completely bypassed. Metabolic rates may also vary across 

the species based on the exposure route, i.e., there is uncertainty whether relative sensitivity 

would remain the same via other routes due to absorption and assimilation efficiency. To help 

evaluate these issues, EPA had an external peer review performed on the FWS analysis.

Peer Review of FWS Report: External Peer Review of Sturgeon Study (ERG, 2012): 

Experts in the field of selenium and/or aquatic ecotoxicology reviewed the FWS study on white 

and green sturgeon (USFWS, 2012) (ERG, 2012). The charge asked the experts to consider 

whether the studies cited provided the best available information on green and white sturgeon 

for determining mortality and abnormality benchmarks; whether the use of microinjection 

studies and maternal transfer studies was comparable and appropriate for the purpose of the 

report; whether each step in the analysis was reasonable and appropriate, and explained in 

sufficient detail; whether the assumptions and conclusions in each step of the analysis were 

reasonable and supported by the data; and lastly, given the available data, whether the experts 

would recommend any alternative analyses to estimate benchmarks for mortality or 

abnormalities.

The conclusions of the experts were consistent in affirming that the report relied on the 

best available data. In general, they agreed that the maternal transfer studies were more 

relevant and represented a better depiction of exposure in the field than the microinjection 

studies, which tend to overestimate toxicity; and that the Linville (2006) maternal transfer 

study, although not published, is the most relevant study. The reviewers noted that while 

regressions performed using white sturgeon data for tissue-to-tissue relationships are relevant 

for that species, the relationships should be used with caution for related species, even one as 

close as green sturgeon, because tissue-to-tissue relationships vary between species. They 

noted that this issue may be especially relevant to these sturgeon species, since white sturgeon 

spend more time in the estuary, while green sturgeon spend more time in the ocean, and have 

adapted to slightly different environments. Lastly, the reviewers noted that although the study 

reflected an appropriate and thorough analysis given the available data, the limited data in 

each of the studies, and especially those related to green sturgeon, are associated with a high 

degree of uncertainty, and therefore the results should be used with caution in estimating 

benchmark values. 

After considering these issues, EPA finds the Linville (2006) maternal transfer study 

results to have more weight than the microinjection study results. The FWS analysis indicates 

an EC10 whole body value for white sturgeon of 9.65 μg/g dw for reproductive effects (larval 
35

abnormalities) using the maternal diet results from Linville (USFWS, 2012). Similarly, the FWS 

analysis indicates an EC10 egg tissue value for white sturgeon of 15.8 μg/g dw for reproductive 

effects using the maternal diet results from Linville (USFWS, 2012). This value was calculated 

from the regression performed on larval developmental effects data from the maternal transfer 

study, translated to an egg tissue value using data from the same maternal transfer study. This 

is the most direct translation in the analysis, and therefore less subject to bias. The resulting 

egg tissue value is also consistent with EPA’s national recommended EC10 fish tissue egg/ovary 

criterion value of 15.1 mg/kg dw (USEPA, 2016). 

The results of the Linares-Casenave et al. (2010) microinjection study on both white and 

green sturgeon indicate that green sturgeon may be more sensitive to selenium than white 

sturgeon. Other studies have observed the same relative sensitivities (Kaufman et al., 2008; 

Silvestre et al., 2010; and De Riu et al., 2014). De Riu et al. (2014), a recent study on juvenile 

green and white sturgeon from San Francisco Bay published after the FWS sturgeon report, 

suggests that although juvenile green sturgeon may be more sensitive than juvenile white 

sturgeon to increasing dietary selenium concentrations, initial whole body concentrations (i.e., 

background concentrations in the controls) were 7.2 ± 0.3 μg/g dw in green sturgeon and 4.8 ±

0.5 μg/g dw in white sturgeon; and after several weeks, the controls had similar concentrations 

ranging from 6.5 to 7.1 μg/g dw for green sturgeon and 5.6 to 7.3 μg/g dw for white sturgeon. 

These control concentrations are close to EPA’s national recommended EC10 whole body 

criterion value of 8.5 μg/g dw (USEPA, 2016), and suggest that juvenile green and white 

sturgeon have similar sensitivities to selenium at these whole body concentrations. The De Riu 

et al. study is discussed in more detail later in this chapter. 

EPA Analysis of Linville (2006) White Sturgeon Study (USEPA, 2016): EPA 

independently analyzed the reproductive endpoint data from the maternal transfer portion of 

the Linville (2006) study. The analysis is included in EPA’s derivation of the national 

recommended criterion for selenium (USEPA, 2016), discussed in the following section.

Linville evaluated the effect of elevated dietary selenium on the health and 

reproduction of white sturgeon (A. transmontanus). Adult female white sturgeon 

(approximately 5 years old) were fed either a control diet (no added selenium; 1.4 mg/kg 

selenium) or a diet spiked with selenized yeast (34 mg/kg selenium) for six months in a 

freshwater flow through system. At the end of the dietary exposure, females were induced to 

spawn and eggs were fertilized with non-exposed male milt. Large cohorts of fertilized eggs 

from individual females were collected and separately hatched. After hatching (stage 36), 

n=500 sets of larvae were randomly distributed into each of six flow through chambers. 

Progeny from two control females and the three treatment females were examined for length, 
36

weight, edema and deformities. Three of the chambers were earmarked for stage 40 

evaluations and 3 for stage 45 evaluations, with stage 36 samples for selenium analysis and 

abnormality (edema, skeletal deformities) evaluation being taken at the time of distribution. 

Mortality was monitored as fish matured to the desired stage. At stage 40 and 45, samples 

were collected for selenium analysis and abnormality evaluations. For deformities, one sample 

of n=30 progeny was taken from each chamber for five of the cohorts (2 control, 3 treated).

No selenium effects were observed for length or weight of larvae but effects were 

observed for both edema and skeletal deformities. Selenium concentrations in eggs from the 

control fish were 1.61 and 2.68 mg/kg dw, and were 7.61, 11, and 20.5 mg/kg dw in eggs from 

the treatment fish. EPA evaluated larval survival and abnormality frequency at stage 45. 

Because the mortalities for each cohort were recorded up to the sample collection time for 

abnormalities, a combined effects variable was derived based on the total proportion of 

hatched larvae which were both alive and without any abnormalities at stage 45. This can be 

calculated as PS*(1-PA), where PS is the proportion survival in the test chambers and PA is the 

proportion of the sample of surviving larvae with abnormalities. The larvae hatched from these 

eggs had respectively 0, 0, 13.3, 0 and 27.8% occurrence of the combined effects of edema and 

deformities; and were 99.7, 99.7, 86.4, 99.7 and 66.2% alive and without abnormalities.

Estimation of the EC10 was conducted using weighted nonlinear regression analysis with 

the threshold sigmoidal model equation (TRAP version 1.30a)

25

. The binary data available in 

this study would normally be analyzed using the tolerance distribution analysis in TRAP, 

however, the combined survival/abnormalities effects variable in this study precludes its use 

because of the different sample sizes for survival and abnormality evaluation. When there are 

insufficient data for TRAP to fit an effects/exposure curve, an interpolation is conducted with 

the same TRAP equation, but constrained to provide interpolation between two points. 

Binomial confidence limits were calculated to evaluate significant differences among 

data points and between data points and fitted curves (see Linville summary in USEPA, 2016 

Appendix C). Since such confidence limits cannot be directly calculated for the combined 

effects variable, confidence limits were estimated for the percent survival and percent 

abnormalities for each cohort by combining the upper and lower confidence limits of the 

individual effects variable using the same equation previously mentioned above. These 

confidence limits are only slightly exaggerated because the survival confidence limits are very 

narrow compared to the abnormality confidence limits.

 

25 TRAP will fit a sigmoidal toxic response versus an exposure variable relationship to standard toxicity data. For 

more information, see EPA’s website at https://archive.epa.gov/med/med_archive_03/web/html/trap.html .
37

Since the study yielded only one definite partial effect, TRAP cannot be used to estimate 

a concentration-response curve. Instead, TRAP was used to interpolate between the last two 

points to estimate the EC10 (see Linville summary in USEPA, 2016 Appendix C for detail). The 

resultant TRAP slope is 2.96 and the interpolated EC10 is 15.6 mg/kg.

The white sturgeon egg/ovary EC10 of 15.6 mg/kg dw is included in the data set for the 

derivation of the national recommended freshwater selenium criterion (USEPA, 2016). The 

species is a commercially and recreationally important fish species in California and in the 

Pacific Northwest. This species also provides taxonomic surrogacy for other sensitive sturgeon 

species that are threatened or endangered, including green sturgeon.

C. EPA Sources: CWA Section 304(a) National Recommended Water Quality Criterion for 

Selenium and Mallard Bird Studies

a. Freshwater Fish Tissue Criterion Element (USEPA, 2016): In June, 2016, EPA 

published the national recommended criterion document, Aquatic Life Ambient Water Quality 

Criterion for Selenium – Freshwater 2016 (USEPA, 2016). This national recommended criterion 

has four elements: two fish tissue-based elements and two water column-based elements. The 

fish tissue elements consist of an EC10 egg or ovary tissue value of 15.1 mg/kg dw, and an EC10 

whole body or muscle tissue value of 8.5 and 11.3 mg/kg dw, respectively. The whole body, 

muscle and water column elements are determined from the egg/ovary element. This is 

consistent with the Pellston International Expert Workshop sponsored by the Society of 

Environmental Toxicology and Chemistry (SETAC) on selenium in 2009 that affirmed that tissue 

concentrations are an appropriate media to measure selenium toxicity, since the main route of 

exposure of selenium to aquatic biota is dietary, and analyses demonstrate that reproductive 

effects through maternal transfer from diet result in more sensitive (lower) endpoints than nonreproductive effects through diet (USEPA, 2016). Another key finding of the SETAC workshop 

was that relationships between selenium tissue concentrations in egg/ovary and water can be 

linked by site-specific bioaccumulation measurements and modeling.

The national recommended criterion also includes water column elements. These 

consist of a set of chronic water column values, one for lentic systems and one for lotic 

systems, and an intermittent exposure water column value based on an equation using either 

the lentic or lotic chronic water column value and a time variable. The chronic water column 

values for lentic and lotic systems are translated from the egg/ovary value, using an equation 

that represents how selenium accumulates through the food chain, as influenced by the overall 

hydrologic and ecosystem conditions represented by the two waterbody types. The equation is 

based on the Ecosystem-Scale Selenium Model discussed in Chapter 2. The criterion elements 
38

are summarized in Table 3-6 Summary of Freshwater Selenium Ambient Water Quality Criterion 

Elements for the Protection of Aquatic Life. 

Table 3-6 Summary of 304(a) Recommended Freshwater Selenium Ambient Chronic Water 

Quality Criterion for the Protection of Aquatic Life (USEPA, 2016)

Media Type Fish Tissue1 Water Column4

Criterion 

Element

Egg/Ovary2Fish Whole Body 

or Muscle3

Monthly 

Average 

Exposure

Intermittent Exposure5

Magnitude 15.1 mg/kg dw 8.5 mg/kg dw 

whole body 

or 

11.3 mg/kg dw 

muscle (skinless, 

boneless filet)

1.5 μg/L in lentic 

aquatic systems

3.1 μg/L in lotic 

aquatic systems

WQCint =

WQC30−day − Cbkgrnd(1− f int)

f int

Duration Instantaneous 

measurement6

Instantaneous 

measurement6

30 days Number of days/month with an 

elevated concentration

Frequency Not to be 

exceeded

Not to be 

exceeded

Not more than once 

in three years on 

average

Not more than once 

in three years on 

average

1 Fish tissue elements are expressed as steady-state.

2 Egg/Ovary supersedes any whole-body, muscle, or water column element when fish egg/ovary concentrations are 

measured.

3

Fish whole-body or muscle tissue supersedes water column element when both fish tissue and water 

concentrations are measured. 

4Water column values are based on dissolved total selenium in water and are derived from fish tissue values via 

bioaccumulation modeling. Water column values are the applicable criterion element in the absence of steadystate condition fish tissue data.

5 Where WQC30-day is the water column monthly element, for either a lentic or lotic waters; Cbkgrnd is the average 

background selenium concentration, and fint is the fraction of any 30-day period during which elevated selenium 

concentrations occur, with fint assigned a value ≥ 0.033 (corresponding to 1 day). 

6

Fish tissue data provide instantaneous point measurements that reflect integrative accumulation of selenium over 

time and space in fish population(s) at a given site.

The egg/ovary tissue criterion element of 15.1 mg/kg dw is calculated using the four 

lowest EC10 GMCVs from a database of acceptable freshwater fish studies, based on the 

methodology outlined in the 1985 Aquatic Life Guidelines.

26

 Since reproductive endpoints were 

found to be the most sensitive endpoints, studies of reproductive effects were considered. 

Twelve fish reproductive toxicity studies of sufficient quality and covering eight fish genera 

 

26 As outlined in the 1985 Aquatic Life Guidelines, the Final Chronic Value (FCV) of 15.1 mg/kg dw was determined 

from a regression analysis of the four most sensitive GMCVs and an extrapolation to the 5th percentile of the 

distribution represented by the tested genera. 
39

were available that yielded endpoints including larval mortality, larval edema and 

skeletal/cranial deformities (teratogenicity) through maternal transfer from dietary exposures. 

The four most sensitive genera are, in order of most to least sensitive, Acipenser (white 

sturgeon), Lepomis (bluegill sunfish), Salmo (brown trout), and Oncorhynchus (rainbow and 

cutthroat trout). The genera and GMCVs are listed in Table 3-7 Lowest Four ReproductiveEffect Egg/Ovary GMCVs.

Table 3-7 Lowest Four Reproductive-Effect Egg/Ovary GMCVs (Adapted from USEPA, 2016)

Relative Sensitivity Rank Genus GMCV (mg Se/kg dw egg/ovary)

1 Acipenser 15.6

2 Lepomis 20.6

3 Salmo 21.0

4 Oncorhynchus 25.3

Fish whole body and muscle criterion element values were developed because fish egg 

or ovary tissue is only available in females at certain times of the year while fish whole body 

and muscle tissue data are more commonly available. The whole body and muscle tissue values 

are based on the egg/ovary tissue concentration. The whole body tissue value of 8.5 mg/kg dw

is calculated using the same methodology using the four lowest whole body EC10 GMCVs of the 

same set of reproductive effect studies. The four most sensitive genera are, in order of most to 

least sensitive, Acipenser (white sturgeon), Lepomis (bluegill sunfish), Oncorhynchus (rainbow 

and cutthroat trout), and Salmo (brown trout). The genera and GMCVs are listed in Table 3-8 

Lowest Four Reproductive-Effect Whole Body GMCVs.

Table 3-8 Lowest Four Reproductive-Effect Whole Body GMCVs (Adapted from USEPA, 2016)

Relative Sensitivity Rank Genus GMCV (mg Se/kg dw whole-body)

1 Acipenser 9.2

2 Lepomis 9.9

3 Oncorhynchus 11.6

4 Salmo 13.2

The muscle tissue criterion element value of 11.3 mg/kg dw is calculated using the four 

lowest muscle EC10 GMCVs of the same set of reproductive effect studies. The four most 

sensitive genera are in order of most to least sensitive, Acipenser (white sturgeon), 

Oncorhynchus (rainbow and cutthroat trout), Lepomis (bluegill sunfish), and Salmo (brown 

trout). The rankings for the muscle criterion element differ from both the egg/ovary rankings 

and the whole body rankings. This is because the factors used to convert the egg/ovary to 
40

muscle concentrations or to whole body concentrations vary across species.27 Although the 

muscle criterion element and the whole body criterion element are of different magnitude, 

they both represent the same level of protection as they were both converted from the 

egg/ovary criterion element as the starting point. The genera and GMCVs are listed in Table 3-9

Lowest Four Reproductive-Effect Muscle GMCVs. 

Table 3-9 Lowest Four Reproductive-Effect Muscle GMCVs (Adapted from USEPA, 2016)

Relative Sensitivity Rank Genus GMCV (mg Se/kg dw muscle)

1 Acipenser 11.9

2 Oncorhynchus 14.3

3 Lepomis 15.9

4 Salmo 18.5

If a review of the species used in the underlying studies indicates the species are 

representative of those that live in the Bay and Delta (i.e., if the same species live in the estuary 

or are appropriate surrogates for species that live in the estuary), the fish tissue criterion 

elements may be appropriate to use as benchmarks in the Ecosystem-Scale Selenium Model. 

Species used to determine the egg/ovary element are white sturgeon (Acipenser 

transmontanus), bluegill sunfish (Lepomis macrochirus), brown trout (Salmo trutta) and 

rainbow and cutthroat trout (Oncorhynchus mykiss and O. clarki lewisi). Although these are 

the lowest four genera, nine species covering eight genera were included in the analysis. 

Genera and species used to determine the whole body and muscle elements are the same four 

genera (and species) used to determine the egg/ovary element, but are ranked in a slightly 

different order. A discussion of each of the species by genera follows.

Acipenser: The study on white sturgeon (A. transmontanus) that is used to determine 

the egg/ovary, whole body and muscle tissue element values is the maternal transfer Linville 

(2006) study discussed in the previous section. This study yielded an egg/ovary EC10 GMCV of 

15.6 mg/kg dw, the lowest value of the four GMCVs used to determine the egg/ovary tissue 

element value; and a whole body EC10 GMCV of 9.2 mg/kg dw, and a muscle EC10 GMCV of 

11.9 mg/kg dw, each the lowest value of the four GMCVs used to determine the whole body 

and muscle tissue element values, respectively (USEPA, 2016). 

The genus Acipenser includes two species indigenous to the San Francisco Bay and 

Delta: white sturgeon (A. transmontanus) and green sturgeon (A. medirostris); green sturgeon 

(Southern Distinct Population Segment, DPS) are listed as threatened under the ESA (CA DFG, 

2001; Threatened Status for Southern Distinct Population Segment of North American Green 

 

27 For a complete discussion, see EPA’s national recommended freshwater aquatic life criterion for selenium,

Aquatic Life Ambient Water Quality Criterion for Selenium – Freshwater 2016 (USEPA, 2016).
41

Sturgeon, 71 FR 17757, April 7, 2006). They are the only two sturgeon species occurring on the 

U.S. West Coast, and the San Francisco estuary is listed as critical habitat for the Southern DPS 

of green sturgeon (Final Rulemaking to Designate Critical Habitat for the Threatened Southern 

Distinct Population Segment of the North American Green Sturgeon, 74 FR 52300, October 9, 

2009). 

In California, white sturgeon are only found on the Klamath River and in the San 

Francisco estuary (Sacramento and San Joaquin Rivers) where most are located (CA DFG, 2001; 

Jackson and Eenennaam, 2013). White sturgeon are the largest freshwater-inhabiting fish in 

North America, and can grow to over 13 feet and weigh over 1,300 pounds. White sturgeon 

have been fished from the estuary since the 1860s; commercial fishing peaked in 1887 with 

1.65 million pounds of catch, but because of overfishing, only 0.2 million pounds of catch were 

caught by 1901 (CA DFG, 2001). The commercial fishing of white sturgeon in the estuary 

stopped in 1917, and throughout the 1900s, the population of white sturgeon in the estuary 

fluctuated, including periods of rebound (after wetter years) and decline (after drier years) (CA 

DFG, 2001). Sport fishing of white sturgeon is currently very popular, but in order to manage 

the population, size limitations are imposed.28 Researchers are tagging, tracking and 

conducting studies on both white and green sturgeon to support recovery efforts (CA DFG, 

2001; IEP, 2011). Both sturgeon species are ecologically and economically very important to 

the San Francisco estuary system. 

Lepomis: The studies on bluegill sunfish (L. macrochirus) used in determining the 

egg/ovary, whole body and muscle tissue elements yielded an egg/ovary EC10 GMCV of 20.6 

mg/kg dw, the second lowest value of the four GMCVs used to determine the egg/ovary tissue 

element value, a whole body EC10 GMCV of 9.9 mg/kg dw, the second lowest value of the four 

GMCVs used to determine the whole body tissue element value, and a muscle EC10 GMCV of 

15.9 mg/kg dw, the third lowest of the four GMCVs used to determine the muscle tissue

element value (USEPA, 2016). Bluegill sunfish and a close relative, redear sunfish (L. 

microlophus), both live in the more freshwater reaches of the estuary, although neither are 

indigenous (USGS at http://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=390 and

http://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=385; SacDelta.com at 

http://www.sacdelta.com/fishing/). Bluegill are more common and are found throughout the 

northern parts of the estuary (Wang, 1986) possibly due to their relatively low salinity tolerance 

(< 5 ppt) (Stuber et al., 1982), although some populations of bluegill that are native to coastal 

 

28 Currently, fishing for white sturgeon is open year-round (with some restrictions). Catch must be between 40 and 

60 inches (fork length), and no more than one per day and three per year per person. See California Department 

of Fish and Wildlife at https://www.wildlife.ca.gov/Fishing/Ocean/Regulations/Fishing-Map/SF-Bay#sturgeon, 

updated April 2, 2016.
42

rivers can be found in salinities of up to 10 ppt and sometimes 12 ppt (Wallus and Simon, 2008; 

Peterson et al., 1993). 

Bluegill and redear cross or hybridize with each other to produce viable offspring (USGS 

at http://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=385; Inspired by Nature, Inc. at 

http://www.ibnature.com/few-facts-on-sun-fish). Although bluegill diet consists mainly of 

aquatic insects and plant matter, they can be bottom feeders (Inspired by Nature, Inc. at 

http://www.ibnature.com/few-facts-on-sun-fish; Michigan Department of Natural Resources at 

http://www.michigan.gov/dnr/0,4570,7-153-10364_18958-45644--,00.html), while redear are 

mostly bottom feeders and are highly molluscivorous (USGS at 

http://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=385 ). Species of fish that are bottom 

feeders, especially molluscivorous species, are at greatest risk in the San Francisco estuary from 

effects of selenium bioaccumulation. 

Salmo: The study on brown trout (S. trutta) that is used to determine the egg/ovary and 

whole body and muscle tissue elements yielded an egg/ovary EC10 GMCV of 21.0 mg/kg dw, 

the third lowest value of the four GMCVs used to determine the egg/ovary tissue element 

value, a whole body EC10 GMCV of 13.2 mg/kg dw and a muscle EC10 of 18.5 mg/kg dw, each 

the highest of the four GMCVs used to determine the whole body and muscle tissue element 

values, respectively (USEPA, 2016). The genus Salmo includes only two species that live in 

North America, Atlantic salmon, S. salar, and brown trout, S. trutta. The distribution of the 

remaining 40 or so species within the genus Salmo is mostly European and Asian (FishBase, A 

Global Information System on Fishes at 

http://fishbase.sinica.edu.tw/identification/SpeciesList.php?genus=Salmo). Brown trout are 

historically native to Europe, western Asia and northern Africa, but since their introduction to 

North America in the late 1800s, they are now found throughout the United States (Animal 

Diversity Web at http://animaldiversity.ummz.umich.edu/accounts/Salmo_trutta/) including 

throughout California (California Department of Fish and Wildlife at 

http://www.dfg.ca.gov/fish/resources/WildTrout/WT_BrownDesc.asp). Anadromous brown 

trout, also called sea-run brown trout or sea trout (Fishbase at 

http://fishbase.sinica.edu.tw/summary/Salmo-trutta.html), can be found in the San Francisco 

delta (SacDelta.com at http://www.sacdelta.com/fishing/), but are not common (Schroeter and 

Moyle, 2006). Young adult sea-run brown trout or smolts have been found in the Sacramento 

River portion of the delta (Schroeter and Moyle, 2006 citing Moyle, 2002). Sea-run brown trout 

and freshwater brown trout are the same species.

Oncorhynchus: The studies evaluated and used to determine the egg/ovary, whole body 

and muscle tissue element values include several studies on salmonids, including rainbow trout 
43

(O. mykiss) and Westslope cutthroat trout (O. clarki lewisi). The document calculates an 

egg/ovary EC10 SMCV for rainbow trout as 24.5 mg/kg dw, an egg/ovary EC10 SMCV for 

cutthroat trout as 26.2 mg/kg dw, and an egg/ovary GMCV (for Oncorhynchus) as 25.3 mg/kg 

dw (the geomean of the two SMCVs) (USEPA, 2016). This is the highest value of the four 

GMCVs used to determine the egg/ovary tissue element value. The studies on cutthroat and 

rainbow trout yielded a whole body EC10 GMCV of 11.6 mg/kg dw, the third lowest of the four 

GMCVs used to determine the whole body tissue element value, and a muscle EC10 GMCV of 

14.3 mg/kg dw, the second lowest of the four GMCVs used to determine the muscle tissue 

element value (USEPA, 2016). 

Rainbow trout are the more sensitive of these two species in this genus. Steelhead 

trout are anadromous rainbow trout, living part of their lives in estuarine and/or marine 

waters, returning to freshwaters to mate and spawn, while resident rainbow trout live their 

entire lives in freshwater or spend very short periods of time in estuarine and near-shore 

marine waters (Alaska Department of Fish and Game at 

http://www.adfg.alaska.gov/index.cfm?adfg=steelhead.main; NOAA Fisheries Office of 

Protected Resources at http://www.nmfs.noaa.gov/pr/species/fish/steelheadtrout.htm). 

Steelhead trout and rainbow trout are the same species. There are no major physical 

differences between rainbow and steelhead, and juveniles are indistinguishable; adults appear 

different given their different life histories (Alaska Department of Fish and Game at 

http://www.adfg.alaska.gov/index.cfm?adfg=steelhead.main). 

Both rainbow and steelhead are native to the San Francisco estuary and connecting 

tributaries, and were historically abundant (Leidy et al., 2005; USFWS, 2008). Populations in 

the estuary have significantly declined over the last 50 years (Leidy et al., 2005), and two ESUs 

are currently listed as threatened: the Central California Coast ESU which includes populations 

in the San Francisco Bay (62 FR 43937, August 18, 1977); and the California Central Valley ESU 

which includes populations in the eastern delta regions (63 FR 13347, March 19, 1998). 

Steelhead are in the Salmonidae family. Salmonids are an important part of the economically 

significant recreational fishing industry in the Bay area, generating millions of dollars of revenue 

annually (Battelle Memorial Institute, 2008). 

Cutthroat trout are close relatives of rainbow/steelhead trout and naturally occurring 

hybrids have the physical markings of both (Alaska Department of Fish and Game at 

http://www.adfg.alaska.gov/index.cfm?adfg=steelhead.main). The rainbow/cutthroat hybrids 

are viable and fertile, and of the 14 recognized subspecies of cutthroat, all have been impacted 

by hybridization (USGS at http://www.nrmsc.usgs.gov/science/feature/hybrid_trout). Coastal 

cutthroat trout (O. clarki clarki) are a subspecies of cutthroat trout (O. clarki), and are
44

anadromous but prefer to remain close to their natal streams (Washington Department of Fish 

and Wildlife at http://wdfw.wa.gov/fishing/salmon/cutthroat.html); they are found in northern 

coastal California regions north of the San Francisco estuary, but not in the estuary (California 

Department of Fish and Wildlife at 

http://www.dfg.ca.gov/fish/resources/WildTrout/WT_CCutDesc.asp). 

Other information considered in the determination of the egg/ovary, whole body and 

muscle tissue element values included information on Micropterus salmoides (largemouth 

bass). The study on largemouth bass (M. salmoides) yielded an egg/ovary EC10 GMCV of 26.3 

mg/kg dw, the fifth lowest value of the eight genera in the dataset. Largemouth bass are 

commonly found in the San Francisco delta (California Department of Water Resources at 

http://www.water.ca.gov/aes/predators/largemouthbass.cfm; USGS at 

http://nas.er.usgs.gov/queries/FactSheet.aspx?speciesID=401; SacDelta.com at 

http://www.sacdelta.com/fishing/; Trails.com at 

http://www.trails.com/tcatalog_trail.aspx?trailid=XFA053-039; and CVRWQCB, 2010). 

Largemouth bass are non-native; they were introduced into California in the late 1800s as a 

sport fish (California Department of Water Resources at 

http://www.water.ca.gov/aes/predators/largemouthbass.cfm). Sport fishing is a very 

important industry in the San Francisco Bay area, and bass, including largemouth bass, are an 

important source of recreation and economic revenue in the San Francisco delta (California 

Department of Water Resources at 

http://www.water.ca.gov/aes/predators/largemouthbass.cfm; Trails.com at 

http://www.trails.com/tcatalog_trail.aspx?trailid=XFA053-039; and California Department of 

Fish and Wildlife at https://www.wildlife.ca.gov/Fishing/Inland/Black-Bass ). 

Summary of Genera: All species used to determine the egg/ovary, whole body and 

muscle tissue elements may be found in the San Francisco estuary except cutthroat trout, 

which is found in waters north of the estuary, and each of these species that are found in the 

estuary are important to the health of the estuary. These species include: white sturgeon, 

bluegill sunfish29; steelhead/rainbow trout; and brown trout. White sturgeon, as well as green 

sturgeon, are indigenous, and both are ecologically and economically important to the estuary. 

Although brown trout are not common in the estuary, others species such as largemouth bass, 

which is represented in the dataset, are prevalent. Although neither largemouth bass nor 

bluegill are native, they are economically important to the sport fishing industry in the region. 

Native steelhead are part of the Salmondae family; all salmon species in the estuary are 

essential as salmon fishing is a large part of the recreational and commercial fishing industry in 

 

29

 A closely related species to bluegill sunfish, the redear sunfish (a molluscivorous species), is also found in the 

estuary, but was not one of the species used to develop the national recommended criterion. 
45

the Bay area. Steelhead are also ecologically important; two ESUs that have historically lived in 

the estuary are currently listed as threatened. It is important to the economy as well as the 

ecology of the region to increase the population of this species. 

Non-Reproductive Effect Studies: In EPA’s recent 304(a) recommended criterion 

document, a thorough analysis of dietary studies of non-reproductive endpoints, e.g., juvenile 

survival and growth was completed. This analysis indicates that EC10 values are above the 

EC10 values for reproductive endpoints, and therefore adverse non-reproductive effects will be 

prevented if adverse reproductive effects are prevented (USEPA, 2016). 

Relevant non-reproductive studies evaluated in the 304(a) criterion document include 

the study by Tashjian et al. (2006) on white sturgeon (A. transmontanus). This study indicates 

an EC10 whole body value of 15.08 mg/kg dw for reduction in body weight (juvenile growth);

this value is higher than the fish tissue whole body criterion element value of 8.5 mg/kg dw

(USEPA, 2016). Thus, non-reproductive effects to white sturgeon should be prevented by the 

EC10 whole body element value. 

A dietary study on Sacramento splittail (P. macrolepidotus), by Teh et al. (2004), 

indicates a No Observed Effect Concentration (NOEC) and Lowest Observed Effect 

Concentration (LOEC) for juvenile deformities of 10.1 and 15.1 mg/kg dw, respectively, in 

muscle tissue. The Maximum Acceptable Toxicant Concentration (MATC), which is the 

geometric mean of the NOEC and LOEC (and considered to be the chronic value) is 12.34 mg/kg 

dw. Since the national recommended criterion includes an EC10 muscle tissue element value of 

11.3 mg/kg dw, the muscle tissue element should be protective of non-reproductive endpoints 

to splittail, as found in the Teh et al. study (USEPA, 2016).

Other relevant non-reproductive studies include a study on Chinook salmon (O.

tshawytscha) (Hamilton et al., 1990) (discussed in section B) and other studies on rainbow 

trout/steelhead. Both Chinook salmon and rainbow/steelhead trout are important ecological 

species, and important to the recreational and commercial industry in the estuary. Although

the studies were considered, they were not used in the development of criteria values due to 

quality concerns with the studies including poor control survival and/or confounding factors 

(e.g., other pollutants in diet) (USEPA, 2016). For these and other studies, including studies on 

bluegill, information indicated that the whole body SMCVs were not lower than the 

reproductive-effect EC10 whole body element value of 8.5 μg/g dw, the national recommended 

criterion (USEPA, 2016).
46

For the Hamilton et al. (1990) study, EPA reviewed the results of the 60-day test on 

juvenile Chinook salmon, and derived a whole body EC10 GMCV of 9.052 μg/g dw for nonreproductive effects (reduced growth) (USEPA, 2016). Chinook salmon are anadromous, and 

like other Pacific anadromous salmonid species, spend most of their juvenile and all of their 

adult lives in the ocean, returning to natal inland freshwaters only to spawn. They do not feed 

during in-migration, and they are semelparous so there is little dietary selenium exposure to 

adults from bay, estuarine or even freshwater sources. The EC10 GMCV for non-reproductive 

effects calculated at 60 days (Hamilton et al., 1990) is close to the whole body element criterion 

value of 8.5 μg/g dw for reproductive effects; therefore, the whole body element criterion 

value should be protective for Pacific juvenile anadromous salmonid species that may be 

exposed to bay and estuarine selenium sources during out-migrating to the ocean (USEPA, 

2016).

Relative Sensitivity Studies: An issue of importance for the San Francisco estuary is the 

issue of whether indigenous green sturgeon (listed as threatened) are more sensitive to 

selenium than indigenous white sturgeon, to help explain why green sturgeon populations are 

declining. De Riu et al. (2014) fed juvenile green and white sturgeon (~30 g body weight) diets 

containing a range of selenium concentrations (selenomethionine added to diet formulation; 

2.2 mg/kg selenium in control diet [no added selenium] and 19.7, 40.1 and 77.7 mg/kg 

selenium in three treatment diets). Several endpoints were monitored over an 8-week 

exposure period including survival and percent body weight increase (% BWI). White sturgeon

juveniles had no mortalities through the highest dietary treatment. Green sturgeon juveniles 

had 0%, 7.7% and 23.1% mortality with the three dietary treatments. TRAP analysis (threshold 

sigmoid nonlinear regression) of the green sturgeon survival data resulted in a whole body EC10 

value of 28.93 mg/kg dw. EC10 values were lower for % BWI using TRAP. For % BWI, the whole 

body EC10 value for green sturgeon was 16.36 mg/kg dw, and for white sturgeon, 23.94 mg/kg 

dw.

Also notable, in the control treatments, the background concentrations of selenium in 

the juvenile green and white sturgeon were elevated at 7.2, 6.5 and 7.1 mg/kg dw (green 

sturgeon whole body), and 4.8, 7.3 and 5.6 mg/kg dw (white sturgeon whole body) at test 

initiation, and after four and eight weeks of exposure, respectively. 

De Riu et al. (2014) suggests green sturgeon may be more sensitive to selenium than 

white sturgeon and that the EPA whole body concentration of 8.5 mg/kg dw (USEPA, 2016) will 

be protective, based on the survival and growth data and the observation that the control 

whole body tissue concentrations (up to 7.2 mg/kg dw) are approaching the whole body 

criterion element value. This is important because white sturgeon, as well as juvenile green 
47

sturgeon (up to three to four years of age), spend most of their time in the San Francisco 

estuary. 

b. Bird Egg Tissue Criterion (USEPA, 2011a): Relevant avian studies on mallards were 

identified and used recently to develop bird egg threshold values for the Great Salt Lake in Utah 

(Tetra Tech, Inc., 2008 citing Ohlendorf, 2007; Ohlendorf, 2007). The key studies included

Heinz, et al., 1987, 1989, Heinz and Hoffman 1996, 1998, Stanley et al., 1994, 1996 (Ohlendorf, 

2007). As part of the development process for the threshold values, the Great Salt Lake Science 

Panel30 looked at data from the key studies to determine EC10 dietary concentrations and EC10 

egg selenium concentrations (Tetra Tech, Inc., 2008; Ohlendorf, 2007). Data on hatching 

success were used to determine an EC10 egg selenium concentration of 12.5 μg/g dw31 using a 

logistic regression, and an EC10 of 11.5 μg/g dw15 using a hockey stick regression (Tetra Tech, 

Inc., 2008; Ohlendorf, 2007). Other studies considered in the Great Salt Lake analysis indicate 

relevant egg concentration values ranging from 5.1 μg/g dw to 16 μg/g dw (Ohlendorf, 2007 

Table 2). Although 12.5 μg/g dw based on the logistic regression was chosen as the relevant 

value for the Great Salt Lake, not all members of the Science Panel agreed (Ohlendorf, 2007; 

Skorupa, 2008). EPA approved the State of Utah’s criteria in 2011 (USEPA, 2011a). 

The 12.5 μg/g dw EC10 described in Ohlendorf (2003) was calculated using data from six 

maternal transfer studies for mallard ducks (A. platyrhynchos) in which adults were fed 

selenomethionine for several weeks prior to breeding and throughout the egg laying period. 

Percent egg hatchability and selenium concentrations in eggs were measured. Because of the 

high inter-study variability in the control percent hatch (Table 3-10), egg hatchabilities were 

control-normalized prior to analysis (Ohlendorf, 2003). Following control normalization, the 

effects of selenium concentrations in eggs on mallard egg hatchability were analyzed using a 

two-parameter logistic regression model, with a resulting EC10 of 12.5 μg/g dw. Dietary 

treatment levels, egg selenium concentrations, and unadjusted and control normalized egg 

hatchabilities for the six studies as originally reported in Ohlendorf (2003) are provided in Table 

3-10.

The EC10 value of 12.5 μg/g dw appears protective of mallards upon review of the 

results of a field study conducted by FWS (USFWS, 2011). In this field study, FWS examined the 

relationship between selenium concentrations and proportional hatch in mallard eggs collected 

 

30

 See http://www.deq.utah.gov/ProgramsServices/programs/water/selenium/index.htm for information on the 

process used to develop the selenium water quality criteria in the Great Salt Lake, Utah. 

31

 The logistic egg selenium regression was previously reported in Ohlendorf (2003), and the hockey-stick egg 

selenium regression was previously reported in Adams et al., 2003 (Tetra Tech, Inc., 2008; Ohlendorf, 2007). 
48

in the field between 2000 and 2005. Eggs were collected in Davis, California, from nesting sites 

in fields irrigated with treated sewage water with slightly elevated selenium levels discharged 

by the city. The objective of the study was to generate sufficient data across a range of 

selenium concentrations in the eggs above background levels to facilitate a comparison 

between two alternative hypothesized thresholds of selenium toxicity in mallards based on 

laboratory toxicity testing: a threshold of 6-10 μg/g dw versus a threshold of 16-20 μg/g dw 

(USFWS, 2011).

Table 3-10 Effects of Dietary Selenium Exposure on Egg Selenium Concentrations and 

Hatchability in Mallards (Adapted from Ohlendorf, 2003)

Dietary Selenium

Treatment 

(nominal) (mg/kg)

Egg Se

(mg/kg)

# Hens %Egg

Hatchability

%Egg

Hatchability

(Control 

Normalized)

Reference

Control 0.16 11 65.7 100 Heinz et al., 1987

10 15.2 5 30.9 47.0 Heinz et al., 1987

Control 0.59 32 59.6 100 Heinz et al., 1989

1 2.74 15 70.7 119 Heinz et al., 1989

2 5.28 15 60.0 101 Heinz et al., 1989

4 11.2 15 53.4 89.6 Heinz et al., 1989

8 36.3 15 36.9 61.9 Heinz et al., 1989

16 59.4 9 2.2 3.7 Heinz et al., 1989

Control 1.35 10 41.3 100 Heinz and Hoffman, 1996

10 30.4 15 7.6 18.4 Heinz and Hoffman, 1996

10 29.4 15 6.4 15.5 Heinz and Hoffman, 1996

Control 1.16 12 44.2 100 Heinz and Hoffman, 1998

10 25.1 11 24.0 54.3 Heinz and Hoffman, 1998

Control 1.4 37 88.2 100 Stanley et al., 1994

10 37 35 37.0 22.7 Stanley et al., 1994

Control 0.89 33 62.0 100 Stanley et al., 1996

3.5 11.6 29 61.0 98.4 Stanley et al., 1996

7.0 23.4 34 41.0 66.1 Stanley et al., 1996

Paired hatchability and egg selenium data were available for a total of 96 mallard 

clutches collected between 2000 and 2005 (USFWS, 2011). Selenium concentrations in eggs 

ranged from 1.7 – 14 μg/g dw, with a geometric mean of 4.2 μg/g dw. Hatchability of individual 

clutches ranged from 40 to 100%, and average yearly hatchability ranged from a low of 82% in 

2003 (a year with four clutches collected, one of which had 40% hatchability) to a high of 100% 

in 2005. Average hatchability across all 96 clutches between 2000 and 2005 was 91%. Ranges 

and average selenium concentration and hatchability results are shown in Table 3-11, which is 

reproduced directly from USFWS (2011). 
49

The relationships between selenium concentrations and percent hatchability were 

investigated in a summary of the USFWS (2011) report using correlations and analysis of 

variance (GLEC, 2014). Correlations between egg selenium concentrations and percent 

hatchability were performed separately for each year of the study, and for the entire study 

period. There was no correlation between selenium concentrations and proportional hatch for 

the full 2000 to 2005 dataset. Similarly, there was no correlation between selenium 

concentrations and proportional hatch for individual years with the exception of 2003, where 

there was a statistically significant positive correlation (p = 0.04, r2 = 0.92) between selenium 

concentrations and hatch. The number of clutches found during 2003 was notably lower than 

for all other years (4 of 96), and the anomalous positive correlation was driven by a single 

clutch with 40% hatch at a selenium concentration of 2.1 μg/g dw coupled with three clutches 

with selenium concentrations between 4.5 and 5.7 μg/g dw and hatches between 88% and 

100%. The positive correlation between selenium concentration and percent hatch appears to 

be a consequence of an outlier value with low hatchability combined with a small sample size, 

as clutches from other years during the study were found to have 100% hatch with lower 

selenium concentrations. 

Table 3-11 Selenium and Hatching Data for Mallard Clutches Collected from the Davis 

Wastewater Treatment Facility (USFWS, 2011)

 

 2000

 

 2001 

 

 2002

 

 2003

 

 2004

 

 2005

 All 

 Years

# Clutches 

Collected 23 17 13 4 28 11 96

Mean 

[Se]*

(Range)

4.1

(1.7 -14)

3.4

(2.4 – 5.2)

5.0

(3.2 – 7.3)

4.1

(2.1 – 5.7)

4.7

(1.8 – 11)

3.6

(1.9 – 12)

4.2

(1.7 – 14.0)

Mean % 

Hatch

(Range)

87%

(50.00 -

100)

90%

(66.67 -

100)

98%

(83.33 -

100)

82%

(40.00 –

100)

91%

(50.00 –

100)

100% 91%

(40.00 –

100)

* Geometric mean presented as μg/g 

dry weight.

Analysis of variance (ANOVA) was used to examine whether or not hatchability of eggs 

with selenium concentrations above the lower level (6 μg/g dw) of the mallard egg selenium 

toxicity threshold of 6 - 10 μg/g dw was, as hypothesized by FWS, as follows. The 96 values for 

the entire 2000 to 2005 sampling period were divided into two bins, one with selenium 

concentration less than 6.0 μg/g dw, and one with selenium concentration of 6.0 μg/g dw and 

higher. The less than 6.0 μg/g dw bin consisted of 76 clutches, and the 6.0 μg/g dw and higher 
50

bin consisted of 20 clutches. The geometric mean of the selenium concentration in the less 

than 6.0 μg/g dw bin was 3.47 μg/g dw, and was 8.32 μg/g dw in the 6.0 μg/g dw and greater 

bin. Next, a Kruskal-Wallis (non-parametric ANOVA) test was performed to determine whether 

there were any statistically significant differences in hatch between the two bins. Results of the 

Kruskal-Wallis test revealed no significant differences (p = 0.59) between the two groups, 

suggesting that for these data, 6.0 μg/g dw did not represent a selenium toxicity threshold for 

mallard egg hatchability. The average hatchability for the less than 6.0 μg/g dw bin was 91.4%, 

and the average hatchability for the 6.0 μg/g dw and higher bin was 91.1%.

Summary of EPA Sources: The national criterion consists of egg/ovary, whole body and 

muscle fish tissue elements, which were developed using information on several fish species 

that reside in the San Francisco estuary, or species that are appropriate surrogates for fish 

species that reside in the estuary. Therefore, the egg/ovary, whole body and muscle fish tissue 

element values can be properly considered as benchmark values for reproductive effects, and 

can be used in the Ecosystem-Scale Selenium Model for the development of water quality 

criteria for aquatic species in the San Francisco estuary. A review of the analyses of bird egg 

tissue values indicate that an egg tissue value of 12.5 mg/kg dw is appropriate to use in the 

Ecosystem-Scale Selenium Model for the development of water quality criteria for aquaticdependent wildlife (avian) species in the estuary.

Site-Specific Values: The EPA national recommended criterion values are guidance that 

are nationally applicable; however, they may sometimes be over- or under-protective for 

certain specific water bodies due to local differences in biology and/or water quality. In cases 

where the guidance values are under-protective, EPA’s 1985 Aquatic Life Guidelines allows for 

the lowering of the guidance value when necessary to protect a critically important species, 

such as a recreationally or economically important species32 (USEPA, 1985). Other methods 

may be used such as the Recalculation Procedure to develop site-specific tissue criterion values 

(USEPA, 2016). These methods allow regulatory authorities to create tailored water quality 

criteria that are protective of the specified designated uses based on local species, and can be 

used to develop criteria to protect more sensitive resident species. 

EPA’s national recommended selenium criterion document includes recommended 

calculation procedures for states to develop site-specific water column concentration elements 

that better reflect site-specific conditions. Since the translation of tissue values to water 

column values depends on the target predator species and its diet, and the hydrologic 

 

32 The 1985 guidelines allow for the 5th percentile of the lowest 4 GMCVs (the calculated criterion) to be lowered to 

the SMCV of an economically or recreationally important species.
51

conditions of the waterbody, the water column elements can be strongly dependent on sitespecific conditions. One method to translate a tissue value is to take a mechanistic modeling 

approach, which uses an equation based on the Ecosystem-Scale Selenium Model discussed in 

Chapter 2 (USEPA, 2016). Since this effort to develop site-specific criteria for the San Francisco 

estuary relies on the Ecosystem-Scale Selenium Model using detailed site-specific data, this 

effort generates precise and accurate values for the San Francisco Bay and Delta, and is 

consistent with EPA’s recommended procedure for developing site-specific water column 

concentration elements.

D. Benchmarks for EPA Use in the Ecosystem-Scale Selenium Model

EPA’s 2016 national recommended freshwater selenium criterion has four elements: an 

egg/ovary element, a whole body or muscle element, lentic or lotic water column elements, 

and an intermittent water column exposure element (USEPA, 2016). The San Francisco Bay 

estuary is a large area, extending from the Golden Gate Bridge southeastward to South San 

Francisco Bay, and from the Bridge, northeastward to the San Joaquin and Sacramento Rivers, 

and includes brackish and marine waters with salinities ranging from 1 ppt and higher. The 

national recommended freshwater selenium tissue elements are developed using information 

on several species including anadromous species, most of which reside in the estuary or are 

closely taxonomically related and serve as surrogates for the untested estuarine or marine 

species; therefore the national recommended criterion tissue elements may be appropriately 

considered as benchmark values in the model for the estuary. Since the model uses whole 

body fish tissue values in its calculations, we propose to use the 304(a) recommended whole 

body element in the model, an EC10 value of 8.5 mg/kg dw.

EPA recently reviewed all available bird egg tissue studies for aquatic-dependent avian 

species (USEPA, 2011a), and found the appropriate egg tissue EC10 value is 12.5 mg/kg dw, 

based on studies of mallards. We include this avian egg tissue value in the Ecosystem-Scale 

Selenium Model, and use the results to inform our analysis for determining protective water 

quality criteria for the estuary. 
52

CHAPTER 4 EPA MODELING AND PROPOSED WATER QUALITY CRITERIA 

A. Designated Uses

The site-specific criteria developed in this document (i.e., proposed criteria) are 

intended to be protective of aquatic life and aquatic-dependent wildlife, including federally 

listed threatened and endangered species in the San Francisco Bay and Delta. This is consistent 

with the State’s existing designated (beneficial33) uses for the estuary. Two Regional Water 

Quality Control Boards oversee different areas within the San Francisco Bay and Delta: the San 

Francisco Regional Water Quality Control Board (SFRWQCB) and the Central Valley Regional 

Water Quality Control Board (CVRWQCB). The SFRWQCB oversees all parts of the Bay and the 

western part of the Delta; these areas are the South San Francisco Bay, Lower San Francisco 

Bay, Central San Francisco Bay, San Pablo Bay, Carquinez Strait, Suisun Bay, and the western 

portion of the Sacramento-San Joaquin Delta (SFRWQCB, 2013). The CVRWQCB oversees the 

eastern portions of the Delta, which includes most of the Delta and the confluences of the 

Sacramento and the San Joaquin Rivers (CVRWQCB, 2011). Each of the Regional Water Boards 

has regional water quality plans that include beneficial uses for the waterbodies they oversee 

(SFRWQCB, 2013; CVRWQCB, 2011). 

In 1978, the State Water Resources Control Board (SWRCB), which oversees the 

Regional Water Boards, adopted a comprehensive plan for the estuary, the Water Quality 

Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary. The plan was 

amended in 1991, 1995, and most recently in December, 2006 (SWRCB, 2006). This plan 

supplements the other water quality plans that cover the Bay and Delta (SWRCB Resolution 

2006-0098, Whereas paragraph 8), and includes a comprehensive set of existing beneficial uses 

for all parts of the estuary. Existing beneficial uses in the SWRCB water quality plan for the 

protection of aquatic life and aquatic-dependent wildlife include: 

Warm Freshwater Habitat (WARM) - Uses of water that support warm water ecosystems 

including, but not limited to, preservation of aquatic habitats, vegetation, fish, or wildlife, 

including invertebrates.

Cold Freshwater Habitat (COLD) – Uses of water that support cold water ecosystems including, 

but not limited to, preservation or enhancements of aquatic habitats, vegetation, fish, or 

wildlife, including invertebrates. 

 

33 The State of California uses the term “beneficial uses” instead of the term “designated uses” as used in the Clean 

Water Act.
53

Migration of Aquatic Organisms (MIGR) – Uses of water that support habitats necessary for the 

migration or other temporary activities by aquatic organisms, such as anadromous fish.

Spawning, Reproduction, and/or Early Development (SPWN) – Uses of water that support high 

quality aquatic habitats suitable for reproduction and early development of fish.

Estuarine Habitat (EST) – Uses of water that support estuarine ecosystems including, but not 

limited to, preservation or enhancement of estuarine habitats, vegetation, fish, shellfish, or 

wildlife (e.g., estuarine mammals, waterfowl, shorebirds). 

Wildlife Habitat (WILD) – Uses of water that support estuarine ecosystems including, but not 

limited to, preservation and enhancement of terrestrial habitats, vegetation, wildlife (e.g., 

mammals, birds, reptiles, amphibians, invertebrates), or wildlife water and food sources.

Rare, Threatened, or Endangered Species (RARE) – Uses of water that support habitats 

necessary, at least in part, for the survival and successful maintenance of plant or animal 

species established under State or federal law as being rare, threatened, or endangered.

The SWRCB water quality plan is consistent with the two Regional water quality plans. 

All parts of the San Francisco Bay and Delta have several existing beneficial uses that are 

intended to fully protect aquatic life and aquatic-dependent wildlife. For the protection of 

aquatic life, existing WARM, COLD, MIGR, SPWN, EST and RARE uses apply, and for the 

protection of aquatic-dependent wildlife including birds, existing EST, WILD and RARE uses 

apply (SWRCB, 2006). 

B. EPA Development of Water Quality Criteria

Chapter 2, Selenium Modeling, explains the Ecosystem-Scale Selenium Model, and 

describes the USGS modeling of the San Francisco estuary using the model. Several scenarios 

were run for the Bay and Delta under site-specific environmental conditions with different 

endpoints to illustrate the bioaccumulation of selenium throughout the estuary’s ecosystem

(USGS, 2010). Endpoints included estimated selenium tissue effect concentration values for 

several wildlife species (or surrogate species) known to be living in the estuary modeled 

through the species’ food web. 

Chapter 3, Selenium Benchmark Effect Concentrations, discusses options and choices 

concerning selenium benchmark effect values for EPA to use in the Ecosystem-Scale Selenium 
54

Model to inform the analysis to determine water quality criteria for the estuary. This chapter 

discusses the options and choices for other variables that EPA used in the model to create 

representative scenarios from which to develop criteria. EPA’s intent is to identify and protect 

the most sensitive species in the estuary and to make reasonable assumptions and selections of 

input values for the model variables, and to use the results of our modeling to develop 

protective criteria. Protection of all species in the estuary at all times is not an objective 

because ecosystems can tolerate some stress and occasional adverse effects (USEPA, 1985). A 

range of values for some variables, representing a balance in data availability and quality, is 

used in the model; thus a range of model outputs is presented and discussed. 

a. Modeling Variables

The Ecosystem-Scale Selenium Model integrates two general categories of variables: 

those attributable to species, and those related to the aquatic environment (Table 4-1). Each of 

the variables and values for the variables used in the model for determining water quality 

criteria is discussed below. 

Table 4-1 Model Variables

Species-Specific Variables Environment-Specific Variables

1. General Food Webs 1. Partitioning Coefficients (Kds)

2. Representative Species 2. Hydrologic Water Year Type/Condition

3. Critical Life Stages 3. Flow Season

4. Diet Mixes (for Representative Species)

5. Trophic Transfer Factors (TTFs)

6. Effect Concentrations (ECs)

i. Species-Specific Variables

General Food Webs, Representative Species, Critical Life Stages, and Diet Mixes: 

Clam-Eating Fish: EPA considered the analysis (USFWS, 2008) that identified the following 

clam-eating fish species as most at risk from selenium dietary exposure: green sturgeon 

(Acipenser medirostris) listed as federally threatened; white sturgeon (A. transmontanus); and

the Sacramento splittail (Pogonichthys macrolepidotus) (USFWS, 2008). White sturgeon and 

Sacramento splittail are not federally listed as either threatened or endangered. Critical life 

stages include adult female reproduction and juvenile growth and development for both 

sturgeon and splittail (USFWS, 2008). Green sturgeon appear to be more sensitive to selenium 

in their diet than white sturgeon (USFWS, 2012; Kaufman et al., 2008; Linares-Casenave et al, 

2010; Silvestre et al., 2010), however both juvenile and adult white and green sturgeon may be 
55

similarly sensitive to selenium at environmentally relevant whole body concentrations of 

around 6 to 7 μg/g dw (De Riu et al, 2014). 

Juvenile Sturgeon: Based on the size of juvenile sturgeon found in coastal estuaries and 

their natal upstream freshwaters, studies indicate that both green and white juvenile sturgeon 

spend six months to a year upstream in freshwater34. As with other fish species, it is likely that 

this early life stage is the most sensitive juvenile stage. During this time, diet most likely 

consists of (freshwater) plankton, larval insects, amphipods, and small benthic invertebrates, 

including crabs, clams and shrimp (Moyle, 2002; CA DFG, 2001), which are generally low in 

selenium. When the juveniles are somewhat larger and older, they migrate down into brackish 

areas of the estuary, and likely consume some Corbula. Although the specific timing is 

unknown, juvenile green sturgeon are thought to spend from one to three years in the estuary 

(i.e., from approximately age one to age four), before migrating to ocean waters (NOAA 

Fisheries at 

http://www.westcoast.fisheries.noaa.gov/protected_species/green_sturgeon/green_sturgeon_

pg.html; Moyle, 2002).

Sturgeon are long-lived animals; white sturgeon are believed to have historically lived 

up to 100 years (University of California, Davis at 

http://calfish.ucdavis.edu/species/?ds=241&uid=113), and green sturgeon can live up to 70 

years (USFWS at 

http://ecos.fws.gov/speciesProfile/profile/speciesProfile.action?spcode=E09K). Although 

sturgeon grow rapidly (up to one foot in length) during their first year in freshwater, older 

juveniles grow at a much slower rate, reaching 46 inches35 after 9 to 16 years (CA DFG, 2001). 

The time that older juvenile green sturgeon may spend in the estuary before migrating to the 

ocean is not significant given their lifespan, nor is it the most sensitive or significant period of 

growth. However, in our analysis for the Bay and Delta we consider the effects of dietary 

selenium from Corbula in the estuary on both green and white juvenile sturgeon.

In De Riu et al. (2014), background green and white juvenile sturgeon whole body 

concentrations in the control (fed a diet of 2.2 ± 0.2 mg Se/kg dw) ranged from approximately 

5.6 – 7.3 mg/kg dw; no adverse effects on growth and development (including mortality) were 

 

34 Juvenile sturgeon grow up to one foot (30 cm) in length during their first year of life (CA DFG, 2001). Juvenile 

sturgeon that have been found in Pacific coastal estuaries are all generally much larger (see Nakamoto et al., 1995 

and CA DFG, 2002).

35 White sturgeon can reach 13 feet or more (CA DFG, 2001), and green sturgeon can reach up to 7 feet (NOAA 

Fisheries at http://www.fisheries.noaa.gov/pr/species/fish/green-sturgeon.html). 
56

recorded in the controls. These values are approaching EPA’s national recommended whole 

body fish tissue criterion element value of 8.5 mg/kg dw (USEPA, 2016), and EPA proposes that 

both green and white juvenile sturgeon will be protected by the national whole body tissue 

value. 

Adult sturgeon: Many adult white sturgeon in the San Francisco estuary are year-round 

residents (USFWS, 2008; Moyle, 2002). Thus, our analysis focuses on adult white sturgeon and 

dietary impacts on reproduction from foraging in the estuary. 

Adult green sturgeon are believed to spend the majority of their lives in near shore 

oceanic waters, but are known to forage at times in estuaries and bays (NOAA Fisheries at 

http://www.westcoast.fisheries.noaa.gov/protected_species/green_sturgeon/green_sturgeon_

life_history.html ). Reproductively mature adult green sturgeon have been observed to move 

rapidly through the San Francisco estuary to spawning areas, and, once in freshwaters, spend 

several months there before out-migrating to marine areas (Israel and Klimley, 2008 at 

http://essexpartnership.com/wp-content/uploads/2010/10/GreenSturgeon-_1_.pdf ). In one 

study, tagged mature female green sturgeon moved through the San Francisco estuary in a 

matter of a few days on their way to spawning areas in the Sacramento River (Heublin et al., 

2009 Figures 2, 4 and 6). Although the length of stay of the tagged green sturgeon in the 

Sacramento River varied, they took a few weeks to two months before passing under the 

Golden Gate Bridge to the ocean (Heublin et al., 2009). 

It is likely that for adult green sturgeon to have reproductive impacts from diet, they 

would have to be foraging in the estuary at the time when they were undergoing vitellogenesis 

(nutrient or yolk formation during oogenesis, the formation of egg cells). There is little 

published information about vitellogenesis in green sturgeon. However, the reproductive cycle 

in cultured white sturgeon is lengthy and vitellogenesis can occur over a span of 16 to 18 

months; reproductive cycles in wild sturgeon have been observed to be even longer, but the 

specific reasons for these differences are not known (Doroshov et al., 1997). If vitellogenesis in 

wild green sturgeon is similar, and they forage in the estuary during that critical stage in their 

life history, they may be at an increased risk of exposure, bioaccumulation and maternal 

transfer of selenium to their eggs36. However, since adult green sturgeon only periodically 

forage in the estuary, their diet most likely predominantly reflects prey species from a marine 

ocean environment. Existing information about vitellogenesis in green sturgeon and their 

 

36 It is also unknown whether energy for vitellogenesis comes more from stored body mass (from oceanic diet) or 

from body fat (directly from a current diet), or both. The source of energy for vitellogenesis (stored body mass vs. 

body fat) may determine the source of any selenium deposited into eggs. Additionally, some uncertainty exists 

concerning the rate of deposition of vitellogenin, and the overall process of vitellogenesis in green sturgeon. 

 
57

foraging habits during vitellogenesis does not allow for more precise quantification of this risk. 

Therefore, the focus of this analysis is on the dietary risk to juvenile green and white sturgeon, 

and to adult white sturgeon that remain in the estuary most of their lives. 

Diet: The FWS report states that the diet of white sturgeon in the estuary is 

approximately 40% clam-based; the diet of the green sturgeon in the estuary, although 

unknown, is believed to be similar (USFWS, 2008 Table 2 citing McKechnie and Fenner, 1971). 

More recent sources, reporting observations made after the introduction of Corbula to the 

estuary, indicate a larger percentage of clams, specifically the invasive bivalve Corbula, in white 

sturgeon diet (Brodsky et al., 2014; Zeug et al., 2014). However, some studies have observed 

whole (unopened) and/or live Corbula in the feces of white sturgeon and have suggested that 

not all of the Corbula tissue consumed is digested (Kogut, 2008; Urquhart and Regalado, 1991). 

A recent study by Zeug et al. (2014) found that the gut contents of white sturgeon from the 

estuary contained between 82 and 93% Corbula by volume, but that stable isotope analysis 

found that their assimilated contribution to sturgeon biomass was lower, between 70 to 83%. 

This indicates that although some sturgeon may consume large amounts of Corbula by volume, 

a portion is not digested and assimilated. 

Worms and crustaceans generally make up the balance of the diet, although sturgeon 

may be feeding on smaller fish and clams in greater quantities since the introduction and 

proliferation of Corbula into the estuary (see University of California, Davis, California Fish

Website at http://calfish.ucdavis.edu/species/?ds=241&uid=113; USFWS, 2008; Brodsky et al., 

2014; Zeug et al., 2014; and Feyrer et al., 2003).

To evaluate reproductive and non-reproductive effects in clam-eating fish, we consider 

a diet of 40% Corbula, and 60% crustaceans, insects and other invertebrates for adult white 

sturgeon and juvenile white and green sturgeon. The diet of juvenile green sturgeon while in 

the Bay and Delta is most likely similar to that of white sturgeon. Although Corbula are very 

abundant in sub-tidal waters of the estuary inhabited by adult and juvenile white sturgeon, 

juvenile green sturgeon, and other bottom-dwelling, clam-eating fish species, and sturgeon may 

consume a higher percentage of Corbula by volume, not all is digested and assimilated.

The FWS report indicates that the diet of the Sacramento splittail can be up to 34% 

clam-based (USFWS, 2008); other sources calculate a smaller percentage, even after the 

availability of the splittail’s other benthic food items (i.e., mysid shrimp) declined once Corbula

was introduced into the estuary (Feyrer et al., 2003). The splittail diet consists mainly (70%) of 

detritus, the remainder is various crustaceans including opossum shrimp (mysids), insect larvae, 

earthworms, and other invertebrates, including some (< 10%) bivalves (Feyrer et al., 2003; 
58

University of California, Davis, California Fish Website at 

http://calfish.ucdavis.edu/species/?uid=83&ds=241). Since Sacramento splittail consume less 

Corbula than white sturgeon (approximately 34% clam-based, a portion of which may be 

Corbula), if white sturgeon are protected, then splittail should also be protected. 

Analyses indicate that the most sensitive endpoint arising from dietary exposure of 

selenium is adverse effects on reproduction (see Chapter 3 and USEPA, 2016); therefore, if 

these are prevented in adult female white sturgeon, then adverse non-reproductive effects 

such as reduced growth and development in juvenile white and green sturgeon also should be 

prevented37. 

Clam-Eating Birds: EPA reviewed the information in the FWS report that identified the 

clam-eating birds most at risk from selenium dietary exposure as the California Ridgway’s rail

(Rallus longirostris obsoletus), listed as federally endangered, and the diving ducks: the greater 

scaup (Aythya marila), lesser scaup (A. affinis), white-winged scoter (Melanitta fusca), surf 

scoter (M. perspicillata), and black scoter (M. nigra) (USFWS, 2008). FWS identified the critical 

life stage for rails as reproductive, and for diving ducks as migratory.38

California Ridgway’s rails are year-round residents of the estuary. The FWS report 

indicates their diet may contain up to 90% animal matter, with the remaining diet consisting of 

plant matter, and of the 90% animal matter, up to 64% is comprised of clams and mussels, and 

26% is comprised of insects, crabs, worms and snails (USFWS, 2008). Both scoter and scaup

winter along the Pacific coast of North America including in the San Francisco estuary, then 

migrate north in the spring to their breeding grounds in Alaska and Canada (USFWS, 2008). 

Their diet can range from 75% to 96% clam-based, with the remainder consisting of snails, 

crustaceans, insects, and some plant material (USFWS, 2008). 

California Ridgway’s rails live in the estuary’s tidal salt marshes (see USFWS at 

http://www.fws.gov/refuge/San_Pablo_Bay/LifeTimesofCCR.html), and are littoral feeders, i.e., 

they consume species that are available in the shallow, near shore and intertidal waters. 

Corbula, primarily found in sub-tidal waters, can also be found in intertidal mudflats. To 

evaluate reproductive effects in California Ridgway’s rail, we consider a diet of up to 20% 

Corbula and 40% other mollusks, 30% insects and 10% plant matter. This represents a 90% 

 

37 See also the discussion in Chapter 3 concerning the background (control) whole body concentrations in green 

and white juvenile sturgeon in the De Riu et al. (2014) study. 

38 Although FWS identified the critical life stage as migration for (adult) diving ducks, we also include (adult female) 

reproduction in this analysis for completeness.
59

animal (60% mollusk and 30% insect) diet, and includes some (20%) Corbula in their diet, 

possibly reflecting a conservative (reasonable high end) estimate of Corbula consumption. 

More detailed information on the rail’s diet in the estuary is not currently available. 

Scoter and scaups are migratory birds that winter in various parts of the estuary and fly 

north to boreal forests in the springtime. A study on the movements of surf scoters in 2004 and 

2005 by De La Cruz et al. (2014) found that scoters concentrated in San Pablo Bay during 

December and January39 but their distribution shifted in February and March to the Central 

Bay. The scoters also used Suisun Bay in January and February, then moved into the Central 

Bay in February and March. Some surf scoters congregated along the San Mateo County and 

south Oakland coastlines throughout the winter season. The study noted that scoter diet in San 

Pablo and Suisun Bays consists mostly of clams (Corbula) likely due to its abundance, while in 

the Central Bay it consists of herring roe, Japanese littleneck clams (Venerupis philipinarium) 

and invertebrates found in seagrass beds. The most accurate predictor of scoter presence and 

density in the estuary was herring roe, which is abundant in the Central Bay starting in January, 

continuing into February and March when herring spawn (De La Cruz et al., 2014). Lovvorn et 

al. (2013) looked at the movements and diets of lesser scaup, greater scaup and surf scoter in 

the San Francisco estuary and found similar migratory patterns and diets. 

DeVink et al. (2008), using captive lesser scaup, simulated exposure to spring migration 

(selenium in staging areas) to determine reproductive and physiological effects. The study 

included three treatment scenarios: a control group fed 0.65 μg/g dw selenium reflecting 

observed levels in uncontaminated boreal invertebrates; a second group fed 7.7 ± 0.2 μg/g dw 

selenium, and a third group fed 14.9 ± 0.5 μg/g dw selenium (actual treatment concentrations), 

to simulate observed mussel concentrations in the St. Lawrence River (7.5 μg/g dw) and in Lake 

Michigan (15 μg/g), respectively. The groups were fed the treatment diets for 4 weeks (30 

days), to simulate stopover exposure on the Great Lakes; elevated selenium was removed from 

diet shortly before egg-laying began. Results showed that body mass, breeding probability and 

clutch initiation dates were not affected, and that selenium concentrations in eggs from the 

two treatment groups decreased rapidly, down to a threshold value of 9 μg/g dw by 8 and 12 

days after treatment ceased for the 7.7 and 14.9 μg/g dw dietary selenium groups, respectively. 

The study concluded that the limited duration of exposure to dietary selenium in spring staging 

environments is not sufficient to affect reproduction or body mass in scaup that migrate to 

uncontaminated breeding areas. The results may reflect the ability of females to depurate 

excess selenium at breeding sites where dietary selenium is low, or the possibility that 

 

39

 Migratory waterfowl arrive in the San Francisco Bay area during the fall starting in October (USFWS at 

http://www.fws.gov/refuge/Don_Edwards_San_Francisco_Bay/seasons_of_wildlife/index.html).
60

contaminated birds may not be breeding (DeVink et al., 2008). The study noted that scaup 

departing from the Great Lakes take a minimum of 21 days to reach breeding grounds where 

they initiate nesting, and during that time excess selenium is likely depurated before egg 

formation. 

In the San Francisco estuary, although migratory ducks may be eating a high selenium 

diet during the first part of the winter in San Pablo and Suisun Bays, they are eating a low 

selenium diet after moving into the Central Bay where they consume herring roe and 

invertebrates, before migrating north in March and April. De La Cruz et al. (2009) documented 

that it took approximately 47 days for scoters to reach breeding grounds once they left the 

estuary. Over that time, it is likely that selenium will be depurated and neither physiological 

nor reproductive impairments will occur. However, this risk has not been quantified, and 

therefore we include migratory diving ducks in our analysis.

Although the diet of scoters and scaups consists of up to 75 to 96% clam during their 

stopover, they are part-time residents of the estuary. Therefore, to evaluate reproductive and 

migratory life stages, we consider a yearly diet of 45% Corbula, 5% other plant/animal material 

from the estuary, and 50% food material from outside the estuary. This reflects a diet 

consisting of up to 90% Corbula for the approximately six months of the year that they reside in 

the estuary, i.e. from about October to April, (1⁄2 of 90% = 45%) and a diet in the upper end of 

the estimated range of clams consumed, most of which is Corbula40. Although concentrated 

consumption of Corbula occurs during the winter in the estuary, it precedes northern migration 

by at least a month, and is not consumed during breeding. Although unknown, prey items 

consumed from northern breeding areas do not likely contain concentrations of selenium 

similar to those found in Corbula from the estuary. 

Insect-Eating Fish: EPA considered the FWS analysis which identified the insect-eating 

fish species most at risk from selenium dietary exposure as Chinook salmon (Oncorhynchus 

tshawytscha) listed as Federally endangered, and steelhead trout (O. mykiss) and Delta smelt 

(Hypomesus transpacificus), both listed as Federally threatened (USFWS, 2008). For smelt, 

affected critical life stages include reproduction, and for all three species, juvenile growth and 

development (USFWS, 2008). 

Juvenile Salmonids: Both Chinook salmon and steelhead trout are anadromous species, 

spending their lives in ocean waters and migrating to freshwaters to reproduce. Juvenile 

Chinook (or King) salmon spend from 3 months to 2 years in freshwater (depending on whether 

 

40 In a study by Richman and Lovvorn (2004), during the 1998-99 and 1990-2000 winters, 96 percent of the dry 

mass of the esophagus contents of 13 lesser scaup in San Pablo Bay consisted of Corbula (USFWS, 2008).
61

they are ocean-type or stream-type), then move into estuaries as smolts, to acclimate to 

saltwater before migrating to ocean waters (NOAA Fisheries at 

http://www.nmfs.noaa.gov/pr/species/fish/chinook-salmon.html). They spend the majority of 

their life, usually 2 to 4 years, at sea before returning to their natal freshwaters to reproduce 

(NOAA Fisheries at http://www.nmfs.noaa.gov/pr/species/fish/chinook-salmon.html). Chinook 

salmon are semelparous, i.e, they breed once before dying. 

Juvenile steelhead spend from one to three years in freshwater before moving into 

estuaries to acclimate; they then migrate to the ocean where most of their growth occurs 

(USFWS at http://ecos.fws.gov/speciesProfile/profile/speciesProfile.action?spcode=E08D). 

They spend one to four years at sea before returning to natal freshwaters to spawn (USFWS at 

http://ecos.fws.gov/speciesProfile/profile/speciesProfile.action?spcode=E08D). Steelhead are 

iteroparous, i.e., they breed more than once – usually twice – before dying. 

Juveniles of both species, while in the estuary as smolts and acclimating to more saline 

water, eat mostly terrestrial and aquatic insects and insect larvae when young and small, and 

also small fish as they grow (NOAA Fisheries at 

http://www.nmfs.noaa.gov/pr/species/fish/chinook-salmon.html; Moyle, 2002). 

Juvenile Chinook salmon and steelhead spend varying amounts of time in the estuary 

before migrating to the ocean. Fall-run Chinook are known to spend a few weeks or months in 

estuaries, while spring-run Chinook can spend up to 18 months in estuarine water (State of 

Oregon at http://www.oregon.gov/dsl/SSNERR/docs/EFS/EFS30salmon.pdf). Similarly, 

steelhead can spend several weeks to a few months in estuaries before migrating to the ocean 

(NMFS, 2012). Since juvenile salmonids may be more sensitive to selenium than other fish 

species, this analysis looks at the dietary effects of selenium on juvenile salmonids. 

Adult Salmonids: Anadromous salmonids such as Chinook salmon and steelhead trout 

generally use the estuary as a migratory corridor between their oceanic habitat and natal 

freshwaters where they reproduce. Mature female Chinook salmon in the Klamath River basin 

were observed to pass very quickly through the estuary (in less than 24 hours) to reach 

freshwaters (Strange, 2013). Salmon species, once they leave the ocean to migrate to 

freshwaters, do not feed, and often they will die on the way if they do not have sufficient 

stored body fat to complete the trip (USFWS at 

http://www.fws.gov/species/species_accounts/bio_salm.html ). Since salmonids do not eat 

during their migration to freshwater, nutrients from ocean prey are consumed during 

vitellogenesis, even if that process is not completed prior to entry into the estuary (i.e., is 

completed upon reaching natal freshwater). Since salmonids do not forage much in the estuary 
62

if at all, using it as a migratory corridor, our analysis of dietary effects from prey in the estuary 

does not include effects to adult salmonids41. 

Diet: None of the three species considered (juvenile Chinook salmon, juvenile steelhead 

trout and Delta smelt) consume Corbula (or other bivalve species that efficiently accumulate 

selenium), so their dietary exposure of selenium in the estuary will be lower than other species 

that do. Juvenile Chinook salmon consume mainly insects, amphipods, copepods, Cladocera or 

water fleas, and larger salmon also consume smaller fish; juvenile steelhead consume a variety 

of insects, and larger steelhead also consume smaller fish (USFWS, 2008). The Delta smelt, a 

small fish, consumes primarily amphipods, copepods, and cladocerans, and to a lesser extent, 

insect larvae (USFWS, 2008). 

A summary of the representative species within each general food web, their probable 

critical life stage, estimated diet mix, and federal status under the ESA is shown in Table 4-2 

Summary of Life Stages and Diet Mixes of Representative Species Most at Risk. 

 

41

 Since steelhead trout are iteroparous, there is some risk from dietary selenium when adult steelhead pass 

through the estuary on their return to the ocean after spawning. Sufficient information does not exist to quantify 

this risk; however, since adult steelhead do not appear to remain in the estuary for prolonged periods, it is unlikely 

that prey from the estuary would have a significant effect on the next cycle of vitellogenesis. 
63

Table 4-2 Summary of Life Stages and Diet Mixes of Representative Species Most at Risk 

General Food Web 

and Representative 

Species

Probable Critical Life Stage Estimated Diet Mix Federal Status

Under ESA

A. Clam-Eating Fish

White Sturgeon 

Adult Female/Reproduction; and 

Juvenile/Growth and Development

Corbula 40%;

Annelids & Crustaceans 60% (Not listed)

Juvenile Green 

Sturgeon* Juvenile/Growth and Development

Corbula 40%;

Annelids & Crustaceans 60% Threatened 

Sacramento 

Splittail**

Adult Female/Reproduction; and 

Juvenile/Growth and Development

Corbula ≤ 10%;

Insects, Crustaceans, Other 

Invertebrates ≥ 90% (Not listed)

B. Clam-Eating (Diving) Birds 

California Ridgway’s 

Rail 

Adult Female/Reproduction Corbula 20%; Other Mollusks 40%; 

Insects 30%; Plant 10%

Endangered

Greater & Lesser 

Scaup;

White-Winged, Surf, 

& Black Scoter

Adult Female/Reproduction; and 

Adult/Migration

Corbula 45%; Other Materials 5%;

Food Outside Estuary 50% (Not Listed)***

C. Insect-Eating Fish 

Chinook Salmon

Juvenile/Larval Mortality, Growth 

and Development

Insects; Amphipods; 

Copepods; Cladocera Endangered

Steelhead Trout

Juvenile/Larval Mortality, Growth 

and Development Insects 100% Threatened

Delta Smelt

Adult Female/Reproduction; and

Juvenile/Growth and Development

Amphipods; Copepods;

Cladocera; Insect larvae Threatened

* Since reproductive endpoints are more sensitive than non-reproductive endpoints, juvenile green (and white) sturgeon (critical 

life stage of juvenile growth and development) should be protected if white sturgeon (critical life stage of adult female 

reproduction) are protected.

** Since Sacramento splittail consume less Corbula (≤ 10%) than white sturgeon (40%), critical life stages in splittail should be 

protected if white sturgeon are protected.

*** Although scoter and scaup species are not listed as threatened or endangered under the Endangered Species Act (16 U.S.C. 

§1531 et seq.), they are protected under the Migratory Bird Treaty Act (16 U.S.C. §703 et seq.).

Trophic Transfer Factors: TTFs represent the bioaccumulation of selenium from one 

trophic level to the next (see Chapter 2). The food web for clam-eating birds and clam-eating 

fish in the estuary consists mostly of Corbula. Other food sources for clam-eating birds and fish 

include other mollusks, annelids, crustaceans, insects and other invertebrates (USFWS, 2008). 

For insect-eating fish, the food web consists mostly of aquatic insects and amphipods, and for 

higher trophic level fish, smaller fish within an insect-based food web (USFWS, 2008). TTF 

values for species living in the San Francisco estuary and considered in the modeling are shown 

in Table 4-3 Trophic Transfer Factors (TTFs).
64

Table 4-3 Trophic Transfer Factors (TTFs) 

Food Chain TTF Prey (Diet) Source Notes

A. Clam-Eating Fish 

Potamocorbula amurensis 

(Corbula) 17

Suspended particulate 

material (Spm) USGS, 2010 Site-Specific Value

Annelids

(Lumbriculus variegatus) 1.3 Spm USEPA, 2016 Freshwater species

Crustaceans:

 Copepod-marine 1.35 Spm

USGS, 2010;

Presser and Luoma, 2010

Crustaceans:

 Mysid-marine 1.3 Spm

USGS, 2010;

Presser and Luoma, 2010

Next Trophic Level: 

 Fish 1.1 Invertebrates

USGS, 2010;

Presser and Luoma, 2010

B. Clam-Eating Birds

Potamocorbula amurensis 

(Corbula) 17 Spm USGS, 2010 Site-Specific Value

Other bay/estuarine mollusks

(Corbicula fluminea)* 2.8 Spm

USGS, 2010;

Presser and Luoma, 2010

Insect – aquatic

(average value)** 2.8 Spm

USGS, 2010;

Presser and Luoma, 2010

Next Trophic Level: 

 Bird (egg)

1.8 Invertebrates Presser and Luoma, 2010

0.8 Invertebrates

Personal Communication,

USFWS (see text)

Site-Specific Value –

California rail

C. Insect-Eating Fish

Insect – aquatic

(average value)** 2.8 Spm

USGS, 2010;

Presser and Luoma, 2010

Crustaceans:

 Amphipod-marine 0.6 Spm

USGS, 2010;

Presser and Luoma, 2010

Crustaceans:

 Copepod-marine 1.35 Spm

USGS, 2010;

Presser and Luoma, 2010

Crustaceans:

 Cladocera

 (Daphnia magna)

1.9 Spm USGS, 2010;

Presser and Luoma, 2010

Next Trophic Level: 

 Fish 1.1 Invertebrates

USGS, 2010;

Presser and Luoma, 2010

* Other common, widespread mollusks inhabiting the Bay include the species Corbicula fluminea (see California 

Department of Water Resources at http://www.water.ca.gov/bdma/BioGuide/ ). 

 ** Mean value of TTFs for mayfly, caddisfly, crane fly, stonefly, damselfly, corixid and chironomid (Presser and Luoma, 

2010).

For clam-eating birds and clam-eating fish, USGS used two diet scenarios to illustrate 

how the model responds: an all-clam (Corbula) diet (TTF(Corbula) = 17), and a mixed diet of 50% 

Corbula and 50% amphipods (TTF(amphipod) = 0.6), using a weighted TTF of 8.8 (i.e., [0.5 x 17] + 

[0.5 x 0.6] = 8.8) (see USGS, 2010 and Chapter 2). For insect-eating fish, USGS used an all-insect 

diet (TTF(insect) = 2.8) to illustrate how the model responds (see USGS, 2010 and Chapter 2). In 

this section, we consider different diet scenarios and weighted TTF values for use in the 

Ecosystem-Scale Selenium Model for developing water quality criteria for the estuary. The TTF 
65

values we chose reflect more detailed diet mixes for the representative species of interest in 

the estuary.

Clam-eating Fish: For clam-eating fish, to model a diet of 40% Corbula (TTF(Corbula) = 17) 

and 60% annelids and crustaceans (TTF(annelids/crustaceans) = 1.3), we used a representative, 

weighted TTF of 7.6 (i.e., [0.40 x 17] + [0.60 x 1.3] = 7.6). The TTFs for annelids and crustaceans 

are taken from the published literature and are referenced in Table 4-3. 

For the next trophic level for clam-eating fish, we used a TTF(fish) of 1.1, the value that 

was used in the published model of the estuary (USGS, 2010). This is the mean value of a 

compilation of TTFs for 25 different fish species, from 0.51 to 1.8, a relatively narrow range 

(USGS, 2010; Presser and Luoma, 2010). The TTFs for fish were derived from laboratory and 

matched field datasets.

Clam-eating Birds: For California Ridgway’s rails, to calculate a diet consisting of 20% 

Corbula (TTF(Corbula) = 17), 40% other mollusks (TTF(bay mollusk) = 2.8) and 30% insects (TTF(insect) = 

2.8), we used a representative, weighted TTF of 5.4 (i.e., [0.20 x 17] + [0.40 x 2.8] + [0.30 x 2.8] = 

5.4)42. For scoter and scaup, to model a diet (for the six months a year that they live in the 

estuary) consisting of 45% Corbula and 5% other animal material from the estuary 

(TTF(misc/mollusk/insect) = 2.8), we used a representative, weighted TTF of 7.8 (i.e., [0.45 x 17] + [0.05 

x 2.8] = 7.8). The TTFs for other bay mollusks and insects are taken from published reports, and 

are referenced in Table 4-3. The TTF for other animal material of 2.8 reflects the TTFs of other 

sources of invertebrate foods in the estuary, such as insects (2.8) and other mollusks (2.8) (see 

Table 4-3).

For the next trophic level for clam-eating birds, USGS used a TTF(bird egg) of 2.6 to 

illustrate scenarios of bioaccumulation in the estuary in its report to EPA (USGS, 2010). This is 

the mean value of a range of bird egg TTFs (0.87 to 4.7) derived from matched data pairs of diet 

and bird egg tissue in the FWS analysis (USFWS, 2009), compiled from the Heinz et al. (1989) 

study on mallards (USGS, 2010). Presser and Luoma (2010) found a similar range of TTF(bird egg)

values (1.5 to 4.5), calculated from mallard data in Ohlendorf (2003). Mallards are thought to 

be one of the most sensitive avian species based on reproductive endpoints (Presser and 

Luoma, 2010). Since species-specific information is not available, and mallards are found in the 

estuary but are one of the most sensitive species, we chose a TTF(bird egg) of 1.8, a value toward 

 

42

 The small (10%) proportion of plant material consumed by rails is considered a de minimus source of selenium 

for this analysis. 
66

the lower end of the range to develop criteria. This value was also used in Presser and Luoma 

(2010) for scoters and scaups. 

Species-specific information is available for the California Ridgway’s rail, based on colocated selenium concentrations in invertebrates (yellow shore crab, ribbed mussels, mud 

snails, macoma clams and polychaete worms) and in eggs collected in the Corte Madera Marsh 

and in Wildcat Marsh (personal communication, Tom Maurer, USFWS, May, 2014). The TTF(bird 

egg) for rails in the Corte Madera Marsh is 0.7 based on a rail egg selenium concentration of 1.43 

parts per million (ppm) and an invertebrate selenium concentration of 1.84 ppm (1.43/1.84 = 

0.7). Similarly, the TTF(bird egg) for rails in Wildcat Marsh is 0.9 based on a rail egg selenium 

concentration of 1.57 ppm and an invertebrate selenium concentration of 1.71 ppm (1.57/1.71 

= 0.9). The TTFs are close; we used the mean TTF of 0.8 for modeling the California Ridgway’s 

rail in the Ecosystem-Scale Selenium Model. 

Insect-eating Fish: For the insect-eating fish food web, we used a TTF(insects) of 2.8 in our 

modeling for the estuary; it is the mean value of a compilation of TTFs of freshwater insects 

(mayfly, caddisfly, crane fly, stonefly damselfly, corixid and chironomid) derived from matched 

field datasets (USGS, 2010; Presser and Luoma, 2010). For the next trophic level, we used a 

TTF(fish) of 1.1, as discussed above. The diet of juvenile steelhead is 100% insect-based. The 

diets of juvenile Chinook salmon and delta smelt also include amphipods, copepods and 

Cladocera; the TTFs for these prey items are 0.6, 1.35 and 1.9, respectively (USGS, 2010; Presser 

and Luoma, 2010). Since the TTFs for these prey items are less than the TTF for insects (2.8), if 

juvenile steelhead are protected, then juvenile Chinook salmon and delta smelt should be 

protected. 

Table 4-4 Summary of Diet Mixes and TTFs for Representative Species Most at Risk 

shows the representative diets and TTFs for the representative species in the three food web 

categories.
67

 Table 4-4 Summary of Diet Mixes and TTFs for Representative Species Most at Risk 

Food Web /

Representative Species Representative Diet Representative TTFs

Clam-eating Fish

White Sturgeon

(Adult)*

40% Corbula

60% Annelids/Crustaceans

7.6(spm to prey)

1.1(prey to fish)

Clam-eating Birds 

California Ridgway’s rail

20% Corbula

40% Other mollusks

30% Insects

(10% Plant)

5.4(spm to prey)

0.8(prey to bird egg)

Scoter and Scaup

45% Corbula

5% Other Animal Material

(50% Food Outside Estuary)

7.8(spm to prey)

1.8(prey to bird egg)

Insect-eating Fish

Steelhead Trout

(Juvenile)**

100% Insect 2.8(spm to insect)

1.1(insect to fish)

* Analyses based on adult white sturgeon should be protective of juvenile white and green sturgeon, and 

Sacramento splittail.

** Analyses based on juvenile steelhead trout should be protective of juvenile Chinook salmon and delta smelt.

Effect Concentrations: The Clean Water Act (33 U.S.C. §1251 et seq.) requires a level of 

protection for ambient surface waters that ensures specific uses of the water will be available, 

i.e., the protection and propagation of fish, shellfish and wildlife, and recreation in and on the 

water (see CWA §101(a)(2)). For the Bay and Delta, consistent with the approach to the 

national recommended freshwater aquatic life selenium criterion (USEPA, 2016), EPA is 

choosing to base water quality criteria on an EC10 level of protection, i.e., an effect 

concentration that represents a ten percent population effect level. An EC10 value is 

appropriate given the nature of exposure and effects for this bioaccumulative chemical. Where 

concentrations of selenium in fish tissue approach an effect threshold, there is potential for 

sustained impacts on aquatic systems, relative to chemicals that are not bioaccumulative. In 

order to maintain sufficient protection, choosing a low level of effect is appropriate. The 

selenium criteria for the estuary are derived from protective (EC10) egg/ovary tissue values. 

Water column values vary more frequently over time, and derived values are based on 

extrapolation from tissue values, whereas tissue values are expected to vary more gradually. 

As discussed in Chapter 3, this proposed criteria document employs an EC10 

reproductive effect concentration value in whole body fish tissue of 8.5 mg/kg dw (USEPA, 

2016) for clam-eating fish and insect-eating fish in the Ecosystem-Scale Selenium Model to 

determine allowable dissolved and particulate water column values and prey concentration 

values. EPA is considering an EC10 value and the resulting dissolved and particulate water 
68

column and prey concentration values in developing the water quality criteria for species in the 

estuary. For clam-eating birds, we employ an EC10 bird egg value of 12.5 mg/kg dw to 

determine allowable dissolved and particulate water column values and prey concentration 

values. 

Table 4-5 Summary of Species-Specific Variables shows the species-specific values 

chosen for the San Francisco Bay and Delta using the Ecosystem-Scale Selenium Model. 

 Table 4-5 Summary of Species-Specific Variables 

Food Web /

Representative Species

Diet TTFs

Effect Concentration 

(μg/g, or mg/kg, dw)

 EC10

Clam-eating Fish:

 

White Sturgeon

40% Corbula

60% Annelids/Crustaceans

7.6(spm to prey)

1.1(prey to fish)

 8.5*

 (USEPA, 2016)

Clam-eating Birds:

California Ridgway’s rail

20% Corbula

40% Other mollusks

30% Insects

(10% Plant)

5.4(spm to prey)

0.8(prey to bird egg)

 

 12.5

 (USEPA, 2011)

Scoter and Scaup

45% Corbula

5% Other Animal Material

(50% Food Outside Estuary)

7.8(spm to prey)

1.8(prey to bird egg)

 

 12.5

 (USEPA, 2011)

Insect-eating Fish:

Steelhead Trout 100% Insect

2.8(spm to insect)

1.1(insect to fish)

 8.5*

 (USEPA, 2016)

* This is a whole body value. For modeling reproductive effects, whole body fish tissue (and bird egg tissue) values 

best represent dietary bioaccumulation; however, a corresponding EC10 muscle fish tissue concentration of 11.3 

μg/g dw may be more useful for other purposes, e.g., monitoring (USEPA, 2016; see also discussion in Chapter 1 

Introduction).
69

ii. Environment-Specific Variables

Partitioning Coefficient, Kd: For seaward modeling of clam-based food webs, sitespecific data from 1998 and 1999 for the estuary from Suisun Bay to the Golden Gate Bridge 

were used to determine Kd values for four transects (see USGS, 2010 Table 8, developed using 

data from Cutter and Cutter [2004] and Doblin et al. [2006]). Calculated Kd values ranged from 

712 to 26,912 (USGS, 2010). Because of the wide range of values, a focused approach to 

location was taken to eliminate uncertainties associated with the ocean-influenced variability, 

and a subset of Kd values for Suisun Bay and Carquinez Strait was used to narrow the ranges of 

Kd values for the seaward profiles. This provided a set of estimates that eliminated the highly 

variable end member values at the downstream ocean interface at the mouth of the Bay near 

the Golden Gate Bridge (see USGS, 2010 Table 9, developed using data from Cutter and Cutter 

[2004] and Doblin et al. [2006]). Since five oil refineries that discharge selenium are located in 

Suisun Bay and Carquinez Strait, this is considered an important area for modeling and 

regulatory oversight. This area is also habitat for species of concern including juvenile sturgeon 

as well as rails and migrating scoter and scaup.43 The Kd values for the constrained transects 

range from 712 to 7,725, and mean Kd values range from 1,180 to 5,986 (USGS, 2010). The 75th

percentile Kd values range from 1,414 to 7,089. We chose to consider the Kd values of the 

transects through Suisun Bay and Carquinez Strait for the clam-based food webs for more 

focused modeling of the interior Bay area, which is most affected by the refineries and other 

point and non-point sources, and provides a more compartmentalized representation of the 

seaward portions of the estuary.

44

For landward modeling of insect-based food webs, we used site-specific data from 2003 

and 2004 for the estuary from Rio Vista (on the Sacramento River) and Stockton (on the San 

Joaquin River) to Benicia to determine Kd values for four transects (see USGS, 2010 Table 10, 

developed using data from Lucas and Stewart [2007]). Calculated Kds range from 554 to 12,650

and mean Kds range from 2,268 to 5,855 (USGS, 2010). The 75th percentile Kd values range from 

3,212 to 8,569.

Hydrologic Variables: Water Year Type and Flow Season: Water year type and flow 

season affect Kd values. Drier years and low flow seasons, characterized by lower, slower flows 

and longer residence times, are generally associated with higher Kd values. Extreme conditions 

 

43 Selenium tissue concentrations in Corbula collected in this area were used to validate the model (USGS, 2010).

44 We note that using a narrower range of Kd values lowers the mean Kd values used in the model which generally 

produces less conservative (less stringent) results; using a wider range of Kd values increases the mean Kd values 

used in the model which generally produces more conservative (more stringent) results. Using constrained 

transects with a smaller range of Kd values reduces the uncertainty of the Kd values for the targeted area.
70

are generally found during critically dry or dry water years in a low flow season. Table 4-6,

Hydrologic Variables, summarizes water year types and seasons, data availability, and effect on 

Kd. 

Table 4-6 Hydrologic Variables 

Variable Type Data Availability Effect on Kd

1. Flow Season a. Low 

(June – Nov)

Seaward & landward 

transects.

Longer residence times →

↑ Kds & Se levels in food webs

b. High 

(Dec – May)

Seaward & landward 

transects.

Shorter residence times →

↓ Kds & Se levels in food webs

2. Water Year a. Critically Dry

(critical condition)

No data*. Longer residence times →

↑ Kds & Se levels in food webs

b. Dry

(critical condition)

No data*. Longer residence times →

↑ Kds & Se levels in food webs

c. Below Normal Landward transects

only.

Longer residence times →

↑ Kds & Se levels in food webs

d. Normal No data*.

e. Above Normal Seaward & landward 

transects.

Shorter residence times →

↓ Kds & Se levels in food webs

f. Wet Seaward transects

only.

Shorter residence times →

↓ Kds & Se levels in food webs

* This type of water year did not occur during the time in which data were collected.

Data collected during four seaward transect sampling events were used to model the 

clam-based food webs: June 1998; October 1998; April 1999; and November 1999. The June 

1998, October 1998 and April 1999 data are from wet water years, and the November 1999 

data are from an above-average water year (see USGS, 2010 Table 8, developed using data 

from Cutter and Cutter [2004] and Doblin et al. [2006]). No data from critically dry, dry, below 

normal, or normal water years are available for seaward modeling. The June 1998, October 

1998, and November 1999 data were collected during the low flow season (June to November), 

although the early June (late spring) data, with a residence time of 11 days, reflects the high 

flow season (USGS, 2010). Data during critical conditions (data from critically dry or dry water 

years during the low flow season) are not available. Limited data exist for more conservative 

conditions, i.e., normal (or dry) water year data in the low flow season. We chose to use the 

75th percentile of all available Kd values for each focused seaward transect in the modeling to 

reflect a larger range of hydrologic conditions represented in the data, given that only wet 

conditions are represented. 
71

Since data reflecting only above normal and wet years for focused seaward transects 

were available, the results may underestimate the necessary conditions to protect sensitive 

species in drier hydrologic conditions. Given that only wet conditions are represented, we 

selected a conservative Kd value. The data for the focused seaward transects are summarized 

in Table 4-7 Available Transects and Calculated Kd Values.

Data collected during four landward transect sampling events were used to model the

insect-based food webs: January 2003; April 2003; October 2003, and January 2004. The 

October 2003 and January 2004 data are from below normal water years; the October 2003 

data are from the low flow season and the January 2004 data are from the high flow season. 

The January 2003 and April 2003 data are from above normal water years in the high flow 

season. No data are available for critical conditions. Here again we chose to consider the 75th

percentile of all available Kd values for each transect in the modeling to reflect a larger range of 

conditions represented in the data, and yield a protective model output. The data for landward 

transects are summarized in Table 4-7 Available Transects and Calculated Kd Values.

 Table 4-7 Available Transects and Calculated Kd Values

Food Web /

Transect 

Type

Transect Date Residence 

Time 

(Days)

Water Year 

Type

Flow 

Season

Observed 

Dissolved 

Se (μg/L)

Mean

Observed

Particulate

Se (μg/g dw)

Mean

Kd Mean Kd 75th

percentile

Kd

Range

A. Clam-Eating Birds and Fish – Focused Approach: Suisun Bay – Carquinez Strait 

Constrained 

Seaward June 16-17, 1998 11 Wet High 0.213 0.252 1,180 1,414 712-1,647

Oct 7-8, 1998 22 Wet Low 0.135 0.462 3,435 4,498 2,202-5,212

April 13-14, 1999 16 Wet High 0.118 0.303 2,666 2,861 2,274-3,168

Nov 4-5, 1999 70

Above 

Normal Low 0.123 0.740 5,986 7,089 3,496-7,725

Mean Values 0.147 0.439 3,317 3,966 -

B. Insect-Eating Fish

Landward Jan 22, 2003 --

Above

Normal High 0.245 0.411 2,268 3,212 554-3,503

April 22-23, 2003 -- Above 

Normal

High 0.356 0.614 2,684 3,564 927-4,351

Oct 10, 2003 -- Below Normal Low 0.174 0.751 5,855 8,569 1,628-12,650

Jan 15, 2004 -- Below Normal High 0.215 0.519 2, 981 3,808 1,256-6,398

Mean Values 0.248 0.574 3,447 4,788 -
72

iii. Summary of Variables

A summary of the species-specific and environment-specific variables chosen for 

scenarios for further analysis are shown in Table 4-8 Summary of EPA Modeling Variables.

Table 4-8 Summary of EPA Modeling Variables 

Food Web;

Representative 

Species;

(Federal Status)

Effect Level 

And Value

Diet Mix and 

Trophic Transfer 

Factors

Transect Date

And Type

Water 

Year 

Type

Flow 

Season

Kd 

(Range)

Kd

(75th

percentile)

A. Clam-Eating Fish  Reproductive and Non-reproductive Effects:

White Sturgeon

(protective of 

juvenile green 

sturgeon 

[threatened] and 

Sacramento 

splittail)

EC10

8.5 μg/g dw 

whole body

fish tissue

Mixed: 

40% Corbula

60% Annelids/

Crustaceans

TTF(prey) = 7.6 

TTF(fish) = 1.1

June 1998

Focused Seaward Wet High 712 - 1,647 1,414

October 1998

Focused Seaward Wet Low 2,202 - 5,212 4,498

April 1999

Focused Seaward Wet High 2,274 - 3,186 2,861

November 1999

Focused Seaward

Above 

Normal Low 3,496 - 7,725 7,089

3,966 Mean

B. Clam-Eating Birds  Reproductive and Non-reproductive Effects:

California 

Ridgway’s Rail 

(endangered)

Scaup:

Greater and 

Lesser; and 

Scoter:-

White-winged, 

Surf, and Black

EC10

12.5 μg/g dw 

egg tissue

Rail: Mixed:

20% Corbula

40% Other mollusk

30% Insect

(10% Plant)

TTF(prey) = 5.4 

TTF(egg) = 0.8

Duck: Mixed:

45% Corbula

5% Other Material

(50% outside 

estuary)

TTF(prey) = 7.8

TTF(egg) = 1.8

June 1998

Focused Seaward

Wet High 712 - 1,647 1,414

October 1998

Focused Seaward

Wet Low 2,202 - 5,212 4,498

April 1999

Focused Seaward

Wet High 2,274 - 3,186 2,861

November 1999

Focused Seaward

Above 

Normal

Low 3,496 - 7,725 7,089

3,966 Mean

C. Insect-Eating Fish  Reproductive and Non-reproductive Effects:

Juvenile 

Steelhead Trout

(threatened)

(protective of 

juvenile Chinook 

salmon

[endangered] and

delta smelt

[threatened])

EC10

8.5 μg/g dw

whole body 

fish tissue

Insect 100%

TTF(insect) = 2.8

TTF(fish) = 1.1

January 2003

Landward

Above

Normal High 554 – 3,503 3,212

April 2003

Landward

Above

Normal High 927 – 4,351 3,564

October 2003

Landward

Below 

Normal Low 1,628 -12,650 8,569

January 2004

Landward

Below 

Normal High 1,256 - 6,398 3,808

4,788 Mean
73

b. EPA Modeling Results

Using the species and environmental variables discussed above, the model generated 

dissolved and particulate selenium concentrations for the water column. The model also 

predicted invertebrate (prey) selenium values. For mixed diet scenarios, the invertebrate 

selenium concentrations are the weighted averages of the prey (Corbula, other mollusks, 

annelids, crustaceans and insects) contributions to the species’ diet. The results of the 

modeling for clam-eating fish, clam-eating birds, and insect-eating fish, using white sturgeon, 

California Ridgway’s rails and scoter and scaup, and steelhead trout as representative species 

(respectively), are summarized in Table 4-9 Summary of Representative Scenarios and Results. 

Tables showing the results of each of the model runs are included in Appendix F. 

Dissolved Selenium: To protect clam-eating fish at an EC10 level, the predicted 

protective dissolved selenium estuarine water column concentration is between 0.143 and 

0.719 μg/L, or between approximately 0.1 and 0.7 μg/L, based on available data. Using the 

mean value of the 75th percentile Kds (3,966), the predicted protective dissolved selenium 

estuarine water column concentration is 0.256 μg/L, or approximately 0.3 μg/L. 

To protect clam-eating birds at an EC10 level, the predicted protective dissolved 

selenium estuarine water column concentration is between 0.126 and 2.046 μg/L, or between 

approximately 0.1 and 2.0 μg/L, based on available data. Using the mean value of the 75th

percentile Kds (3,966), the predicted protective dissolved selenium estuarine water column 

concentration is 0.224 μg/L for scoter and scaup45, or approximately 0.2 μg/L. 

To protect insect-eating fish at an EC10 level, the predicted protective dissolved 

selenium estuarine water column concentration is between 0.322 and 0.859 μg/L, or between 

approximately 0.3 and 0.9 μg/L, based on available data. 

Based on these analyses, the protective dissolved selenium water column concentration 

selected is 0.2 μg/L. This value should protect existing species in the estuary most of the time, 

under the environmental conditions used in the modeling. These analyses indicate that if clameating birds are protected, clam-eating fish and insect-eating fish should also be protected.

Tetra Tech, Inc. collected and analyzed more recent (2010 – 2012) ambient data for the 

estuary in a report for the Western States Petroleum Association (WSPA, 2012). Inserting the 

 

45 For the California Ridgway’s rail, using a Kd value of 3,966 results in a dissolved value of 0.730 μg/L, well above 

the protective value for clam-eating ducks. See Appendix F.
74

ambient data from the report (for Kd values) in the Ecosystem-Scale Selenium Model, we found 

that the range of protective dissolved selenium water column concentrations for clam-eating 

fish (focused seaward transects) was 0.157 to 0.283 μg/L, with a mean value of 0.209 μg/L. For 

clam-eating ducks (focused seaward transects), the range was 0.138 to 0.248 μg/L, with a mean 

value of 0.183 μg/L. These correspond well with our proposed dissolved water column criterion 

value of 0.2 μg/L. We did not include these data in our analysis to determine criteria values, 

since the data have not been peer reviewed, however, we include the results of the model runs 

in Appendix G for general comparison purposes. 

Particulate Selenium: To protect clam-eating fish at an EC10 level, the predicted 

protective particulate selenium concentration is 1.017 μg/g dw, or approximately 1 μg/g dw, 

based on available data. To protect clam-eating birds at an EC10 level, the predicted protective 

particulate selenium concentration is between 0.890 and 2.894 μg/g dw, or between 

approximately 1 and 3 μg/g dw, based on available data. The lower end of this range is 

approximately equal to the protective value for clam-eating fish. To protect insect-eating fish at 

an EC10 level, the predicted protective particulate selenium concentration is 2.760 ug/g dw, or 

approximately 3 ug/g dw, based on available data. To protect clam-eating and insect-eating 

species in the estuary, the proposed particulate selenium concentration is 1 μg/g dw. 

Clam Tissue: To protect clam-eating fish at an EC10 level, the predicted protective 

selenium dietary invertebrate concentration is 7.7 μg/g dw; the predicted protective selenium 

dietary Corbula contribution is 6.9 μg/g dw, based on available data. To protect clam-eating 

birds at an EC10 level, the predicted protective selenium dietary Corbula contribution is 9.8

μg/g dw for rails and 6.8 μg/g dw for scoter and scaup, based on available data. 

To determine the allowable Corbula tissue concentration in the estuary, the dietary 

contribution must be divided by the percent of Corbula in the species’ diet. For clam-eating fish 

(40% Corbula diet), the allowable Corbula tissue concentration is ≤ 17 μg/g dw (6.9 μg/g dw / 

0.40). For clam-eating rails (20% Corbula diet), the allowable Corbula tissue concentration is ≤ 

49 μg/g dw (9.8 μg/g dw / 0.20). For clam-eating ducks (45% Corbula diet), the allowable 

Corbula tissue concentration is ≤ 15 μg/g dw (6.8 μg/g dw / 0.45). To protect all clam-eating 

species in the estuary, the proposed Corbula tissue concentration is 15 μg/g dw. 

All proposed values have been rounded to one significant digit. The rounded values 

provide a reasonable prediction of the appropriate protective values of allowable dissolved and 

particulate water column selenium concentrations and prey tissue selenium concentrations 

that will protect clam-eating fish and birds, and insect-eating fish in the estuary. 
75

 Table 4-9 Summary of Representative Scenarios and Results

Representative 

Species

Effect

Concentration

(μg/g dw)

Representative 

Diet and TTFs

Water Year/

Flow Season

Transect Type and 

Transect Date

Kd 

75th

percentile

Predicted 

Dissolved Se 

(μg/l)

Predicted 

Particulate Se 

(μg/g dw)

Predicted Dietary 

Invertebrate Se 

(μg/g dw)

Predicted Dietary

Corbula Se Contribution

(μg/g dw)

Clam-eating Fish

Green Sturgeon 

White Sturgeon

Sacramento 

Splittail

EC10 

8.5 Whole Body

40% Corbula

60% Annelids/

Crustaceans

TTF(prey) =7.6

TTF(fish) = 1.1

Wet/ High

Focused Seaward

June 1998 1,414 0.719 1.017 7.7 6.9 

Wet/Low

Focused Seaward

October 1998 4,498 0.226 1.017 7.7 6.9

Wet/High

Focused Seaward

April 1999 2,861 0.355 1.017 7.7 6.9

Above Normal/

Low

Focused Seaward

November 1999 7,089 0.143 1.017 7.7 6.9

Range: 

1,414 – 7,089 0.143 – 0.719

-> 0.1 – 0.7 1.017

-> 1 

7.7 6.9

3,966 mean 0.256 -> 0.3

Clam-eating Birds 

California 

Ridgway’s Rail

EC10

12.5 Egg Tissue

20% Corbula

40% Other 

mollusk

30% Insect

(10% Plant) 

TTF(prey) = 5.4

TTF(egg) = 0.8

Wet/High

Focused Seaward

June 1998 1,414 2.046 2.894 15.6 9.8

Wet/Low

Focused Seaward

October 1998 4,498 0.643 2.894 15.6 9.8

Wet/High

Focused Seaward

April 1999 2,861 1.011 2.894 15.6 9.8

Above Normal/

Low

Focused Seaward

November 1999 7,089 0.408 2.894 15.6 9.8

Ducks:

Greater Scaup

Lesser Scaup

White-winged 

Scoter

Surf Scoter

Black Scoter

45% Corbula

5% Other 

Animal Material

TTF(prey) = 7.8

TTF(egg) = 1.8

Wet/High

Focused Seaward

June 1998 1,414 0.630 0.890 6.9 6.8

Wet/Low

Focused Seaward

October 1998 4,498 0.198 0.890 6.9 6.8

Wet/High

Focused Seaward

April 1999 2,861 0.311 0.890 6.9 6.8

Above Normal/

Low

Focused Seaward

November 1999 7,089 0.126 0.890 6.9 6.8

Range:

1,414 – 7,089 0.126 – 2.046

-> 0.1 – 2 0.890 – 2.894

-> 1 - 3

6.9 – 15.6 6.8 – 9.8

3,966 mean 0.224 -> 0.2 duck -> 7 - 10

Insect-eating Fish

Chinook Salmon

Steelhead Trout

Delta Smelt

EC10

8.5 Whole Body

100% Insect

TTF(insect) = 2.8

TTF(fish) = 1.1

Above Normal/

High

Landward

January 2003 3,212 0.859 2.760 7.7 N/A

Above Normal/

High

Landward

April 2003 3,564 0.774 2.760 7.7 N/A

Below Normal/

Low

Landward

October 2003 8,569 0.322 2.760 7.7 N/A

Below Normal/

High

Landward

January 2004 3,808 0.725 2.760 7.7 N/A

Range: 3,212 – 8,569

0.322 – 0.859

-> 0.3 – 0.9 

2.760

-> 3 7.7 N/A
76

C. Proposed Criteria

a. Applicable Waters; Magnitude, Duration and Frequency

Applicable Waters: The proposed criteria are intended to apply to all marine waters of 

the Bay and to all estuarine waters of the Bay and Delta, i.e., all waters of the Bay and Delta in 

which the salinity is greater than 1 part per thousand (ppt) 95% of the time. This is consistent 

with the National Toxics Rule and the California Toxics Rule.46 Since the invasive Corbula clam 

species is found in the estuary in waters of salinities between 1 and 33 ppt (Cohen, 2011), the 

most vulnerable clam-eating species should be protected. These proposed criteria are intended 

to replace the selenium aquatic life criteria promulgated in the National Toxics Rule for marine 

and estuarine “waters of the San Francisco Bay upstream to and including Suisun Bay and the 

Sacramento-San Joaquin Delta” (57 FR at 60921, and 40 CFR 131.36(d)(10)).

Criteria Media and Magnitude: EPA is proposing to apply criteria in various media for

the protection of aquatic life and aquatic-dependent wildlife. The media choices considered for 

criteria include:

1. Selenium water column concentrations (dissolved or total);

2. Selenium particulate concentrations; 

3. Selenium predator tissue concentrations (fish, and/or bird egg);

4. Selenium prey/dietary tissue concentrations (e.g., clam or Corbula)

5. Combinations of the above concentrations.

Criteria values for selenium in tissue concentrations directly reflect the biological uptake 

of selenium in the species’ diet, and depending on the type of tissue, concentrations can be 

easily monitored, e.g., clam tissue can be easily monitored while fish egg/ovary tissue is more 

difficult to obtain. Ambient water quality criteria serve two primary functions: they are used to 

designate the maximum allowable pollutant level that is protective of the designated uses of 

the waterbody and to regulate the sources of the pollutant by limiting the amount of the 

pollutant that may be discharged into the waterbody so that the designated uses are 

maintained. Discharges are in dissolved water and particulate form, whereas tissue 

concentrations are most predictive of observed biological effects because they are more closely 

 

46 The National Toxics Rule and California Toxics Rule aquatic life freshwater criteria apply to waters in which the 

salinity is equal to or less than 1 ppt 95% or more of the time; the aquatic life saltwater criteria apply to waters in 

which the salinity is equal to or greater than 10 ppt 95% of the time; and the more stringent of the freshwater or 

saltwater criteria apply to waters in which the salinity is between 1 and 10 ppt 95% of the time (40 CFR 

131.36(c)(3) and 40 CFR 131.38(c)(3), respectively).
77

tied to the endpoints of concern and do not require cross-media extrapolations. Tissue 

concentrations can present challenges when attempting to use them to regulate or limit 

sources of a pollutant into a water body. Increased pollutant levels in an ecosystem usually 

occur as a result of continued and/or elevated discharges of the pollutant from anthropogenic 

sources, and for the estuary, refinery wastewater and agriculture drainage are the largest 

contributors of selenium. It is most straightforward to establish regulatory limits for effluent 

discharge and agricultural drainage based on expectations in ambient water column 

concentrations (both dissolved and particulate). Therefore, in order to set water quality criteria 

that will be more easily implemented to limit selenium entering the estuary, the proposed 

criteria include values in fish and clam tissue, and in dissolved and particulate water column 

concentration values. The dissolved and particulate water column concentration values can be 

used to regulate selenium discharges into the estuary in order to maintain the existing 

beneficial uses.

Chapter 3 discusses appropriate EC10 tissue values for the San Francisco Bay and Delta 

ecosystem. Using site-specific data, the Ecosystem-Scale Model provides corresponding 

dissolved and particulate water column and prey tissue concentrations. Thus, the proposed 

criteria should be equally protective in different media. The proposed criteria are described in 

Table 4-11 Proposed Selenium Water Quality Criteria for the San Francisco Bay and Delta. All 

criteria are chronic values; they represent protective levels of selenium through dietary 

exposure, which reflects a long term or chronic exposure. 

Duration and Frequency: Each proposed criterion also has a specified duration and 

exceedance frequency. Both the proposed dissolved and particulate water column selenium 

criteria have durations of 30 days (approximately monthly) to reflect the seasonal changes in 

system hydrology. As discussed earlier, the partitioning between the particulate and dissolved 

phases of selenium can change with the time of year and type of water year (i.e., high vs. low 

season, and wet vs. dry year). The proposed fish tissue and clam tissue criteria durations are 

based on an instantaneous measurement, since tissue concentrations provide a point 

measurement that already reflects an integrative accumulation of selenium over time in 

response to environmental fluctuations, assuming the system represents a steady 

state/equilibrium condition. 

The proposed dissolved and particulate water column criteria values have an allowable 

exceedance frequency of no more than once in three years, which is the typical frequency for 

EPA’s recommended ambient water quality criteria for aquatic life. This frequency reflects the 
78

Agency’s intent to provide for ecological recovery from a variety of severe stresses47, including 

a periodic exceedance of a water column criterion. The proposed fish and clam tissue criteria 

values are not to be exceeded. Since tissue concentrations reflect an accumulation of selenium 

from the environment over long periods of time, if the tissue concentration was exceeded, it 

might reflect sustained high levels of selenium in the environment, and require a long period of 

time for tissue levels to return to protective levels. By prohibiting an exceedance, sustained 

adverse conditions may be avoided.

b. Acute and Intermittent Criteria

Acute Criterion: The proposed criteria are chronic values. Since dietary exposure poses 

the highest risk to wildlife, acute toxicity, or toxicity from a brief exposure of a significantly 

elevated concentration of waterborne forms of selenium, is not pertinent for regulatory 

purposes in the Bay and Delta, and we do not include an acute criterion in any medium. 

However, if a significantly elevated concentration of waterborne selenium occurs in a 

waterbody, it may introduce a load of selenium into the system from which it may be difficult 

to recover. Some high, short-term exposures of selenium could be more detrimental to the 

system than lower chronic exposures, as they may have significant long-term residual 

bioaccumulative effects, which would be similar to causing the protective chronic exposure 

level to be exceeded for longer than allowable periods of time. In order to prevent such an 

occurrence, we include a proposed intermittent criterion.

Intermittent Criterion: To address intermittent exposures that could cause an 

exceedance of the chronic fish tissue criterion or clam tissue criterion, or otherwise contribute 

to the chronic effects of selenium bioaccumulation, we are proposing an intermittent exposure 

water column criterion (see intermittent exposure criterion in Aquatic Life Ambient Water 

Quality Criterion for Selenium – Freshwater 2016; USEPA, 2016). This intermittent criterion is 

intended to limit cumulative exposure, and is derived from the chronic 30-day water column 

criterion by algebraically rearranging a representative equation based on time and 

concentration to establish a limit on an intermittent elevated concentration that occurs over a 

specified percentage of the time. Figure 1, Illustration of an Intermittent Spike Exposure, shows 

a possible sequence of exposures over a 30 day period; it illustrates a spike exposure occurring 

a certain percentage of time (e.g., 10% or 3 days) over a 30-day period, and background 

exposure occurring the remaining percentage of time (e.g., 90% or 27 days).

 

47 For a full discussion of exceedance frequency, see Water Quality Standards Handbook, Second Edition, EPA-823-

B-94-005a, August 1994, Office of Water, U.S Environmental Protection Agency.
79

 Figure 4-1. Illustration of an Intermittent Spike Exposure 

The 30-day average concentration, C30 day, is given by:

C30 day = Cintfint + Cbkgrnd(1 − fint)

where Cint is the intermittent spike concentration, fint is the fraction of any 30-day period 

during which elevated concentrations occur, and Cbkgrnd is the background concentration 

occurring during the remaining time. C30 day is not to exceed the proposed chronic criterion, 

WQC30 day, or 0.2 μg/L for the estuary. If the intent is to apply a criterion, WQCint to the 

intermittent spike concentrations, then replacing Cint with WQCint and C30-day with WQC30-day or 

0.2 μg/L in the above equation, and then solving for WQCint yields:

WQCint =

[WQC30 dayor 0.2 μg/L] − Cbkgrnd(1 − fint)

fint

The above equation expresses the intermittent exposure criterion in terms of the 30-day 

average chronic criterion, while accounting for the fraction in days of any 30-day period the 

intermittent spikes occur and for the background concentration occurring during the remaining 

time. If the concentrations of the three spikes in Figure 1 differ, or the background 

concentrations vary, then the average48 of the spike concentrations and/or the average of the 

background concentrations can be used in the equation, as appropriate. This approach is not 

 

48 A weighted average may also be used if appropriate, i.e., if spikes of largely different volumes and 

concentrations occur within the same 30-day period.
80

intended to apply to ordinary, smoothly varying concentrations, as that situation is better 

addressed by applying the chronic water criterion as a 30-day average.

Table 4-10 illustrates example values for the intermittent water criterion concentration. 

The values in the last row and the far right column demonstrate that WQCint is not an 

independent criterion but a re-expression of the 30-day average water column criterion. 

WQCint converges to WQC30-day when the background concentration is already at WQC30-day or 

when the intermittent exposure occurs throughout the 30-day period.

 Table 4-10 Representative Values of the Proposed Intermittent Water Concentration Criterion

Bkgrnd 

Conc, 

Cbkgrnd

 (μg/L)

Fraction of Time, f int

0.033

(1 day)

0.05

(1.5 days)

0.1

(3 days)

0.2

(6 days)

0.5

(15 days)

1

(30 days)

Intermittent Criterion, WQCint

0 6.00 4.00 2.00 1.00 0.40 0.20

0.08 3.64 2.48 1.28 0.68 0.32 0.20

0.10 3.03 2.10 1.10 0.60 0.30 0.20

0.15 1.52 1.15 0.65 0.40 0.25 0.20

0.20 0.20 0.20 0.20 0.20 0.20 0.20

The value of fint, the intermittent exposure fraction of the month, should not be 

assigned a value less than one day (i.e., fint < 0.033), to ensure that the monthly water column 

value will be met. An extremely high peak or concentrated discharge (greater than 

approximately 160 μg/L) in one hour (i.e., fint < 0.0013) could exceed water concentration 

thresholds that have been shown to be toxic in 2-day or 4-day toxicity tests (compiled in USEPA, 

2004), and would require zero discharge for the entire remaining averaging period of 

approximately 30 days in order to meet the 30-day average water column value. Consequently, 

the intermittent fraction of the month should not be assigned a value less than 0.033 

(corresponding to one day), and a discharge greater than approximately 6 μg/L should not 

occur for longer than one day during any 30-day period, assuming a background concentration 

of 0 μg/L.
81

Table 4-11 Proposed Selenium Water Quality Criteria for the San Francisco Bay and Delta

Media 

Type

Tissue Water Column1

Criteria

Fish Whole 

Body Or 

Muscle

Clam 

Dissolved 

Chronic Intermittent Exposure2

Particulate

Chronic

Magnitude 8.5 μg/g dw

whole body

or 

11.3 μg/g dw 

muscle 

15 μg/g dw 0.2 μg/L WQCint =

0.2 μg/L − Cbkgrnd(1 − f int)

f int

1 μg/g dw

Duration Instantaneous 

measurement

Instantaneous 

measurement

30 days Number of days/month 

with an elevated 

concentration

30 days

Frequency Not to be 

exceeded

Not to be 

exceeded

Not more than 

once in three 

years 

Not more than once in 

three years 

Not more than 

once in three 

years 

1 Water column values are based on dissolved total selenium (includes all oxidation states, i.e., selenite, selenate, organic 

selenium and any other forms) in water.

2 Where Cbkgrnd is the average background selenium concentration in μg/L, and fint is the fraction of any 30-day period 

during which elevated selenium concentrations occur, with fint assigned a value ≥ 0.033 (corresponding to one day).

Note 1: The criteria apply to all waters of the San Francisco Bay and Delta in which the salinity is greater than 1 part per

thousand 95% or more of the time. 

Note 2: A translator of 1 shall be used to determine total recoverable selenium values from dissolved selenium criteria 

values for use in deriving water quality-based effluent limitations for point sources. 

These proposed criteria values are specific to the San Francisco Bay and Delta estuary, 

and the low chronic water column value is due to the presence of the abundant and invasive 

species, Potamocorbula amurensis or Corbula. Corbula very efficiently accumulates selenium 

(Stewart et al., 2004), and therefore has an unusually high TTF compared to most other mollusk 

species for which TTFs have been derived. Given the site-specific nature of Corbula

distribution, this TTF is only applicable in the San Francisco Bay and Delta estuary, unless (and 

until) other locations are observed with Corbula invasions.

Form of Permit Limits: Although proposed water column criteria values are expressed 

in dissolved selenium concentrations, water quality-based permit limits, in most instances, are 

required to be in total recoverable values (40 CFR §122.45(c)). For most metals, criteria are in 

the dissolved form because the dissolved fraction provides a better representation of the 
82

biologically active portion of the metal than does the total or total recoverable fraction49

(USEPA, 1996). When water quality criteria are in the dissolved form, a translator can be used 

to determine a total recoverable permit limit. The translator is the fraction of the total 

recoverable metal in the downstream water that is dissolved (USEPA, 1996). However, for 

selenium, both the dissolved and particulate fractions are bioavailable to the aquatic biota. 

Thus, EPA proposes a translator of 1 in the proposed criteria table, Table 4-11 (see Note 2), an 

appropriate assumption for the Bay and Delta. 

D. Summary 

The proposed site-specific criteria for the San Francisco Bay and Delta include tissue, 

and dissolved and particulate water column values, which should be comparably protective 

based on the detailed modeling of the estuary using the Ecosystem-Scale Selenium Model. The 

dissolved and particulate water column criteria are intended to facilitate implementation from 

different sources of selenium to the estuary. In addition, the total amount of selenium entering 

the estuary is more appropriately regulated by limiting both dissolved and particulate selenium 

loads. Clam tissue criteria are designed to ensure the protection of higher trophic level species. 

For each of the proposed criteria values, a duration and frequency is specified.

 

49 Total selenium in an unfiltered water column sample is the sum of the dissolved fraction and the particulate 

fraction of selenium in the sample. The dissolved fraction is operationally defined as that which passes through a 

0.45 μm filter (USGS Water Resources Glossaries, Water Resources Data – Definition of Terms at: 

http://water.usgs.gov/glossaries.html). Total recoverable is the amount of a constituent that is in solution after a 

water-suspended sediment sample has been “digested by a method (usually using a dilute acid solution) that 

results in dissolution of only readily soluble substances” (USGS Water Resources Glossaries, Water Resources Data 

– Definition of Terms at: http://water.usgs.gov/glossaries.html). Since digestion does not always result in 

complete dissolution of particulate matter, the total recoverable amount of the constituent is usually less than the 

total amount of the constituent present in the sample.
83

REFERENCES 

Adams, W.J., J.E. Toll, K.V. Brix, L.M. Tear, and D.K. DeForest. 2000. Site-specific Approach for 

Setting Water Quality Criteria for Selenium: Differences Between Lotic and Lentic Systems. In 

Proceedings Mine Reclamation Symposium: Selenium Session, Williams Lake, British Columbia, 

Canada. June 21-22. pp. 231-240.

Adams, W.J., K.V. Brix, M. Edwards, L.M. Tear, D.K. Deforest, and A. Fairbrother. 2003. Analysis 

of field and laboratory data to derive selenium toxicity thresholds for birds. Environmental

Toxicology and Chemistry 22:2020-2029. 

Battelle Memorial Institute. 2008. San Francisco Bay Subtidal Habitat Goals Project: Economic 

Valuation of San Francisco Bay Natural Resource Services, Final Report, Submitted to: National 

Oceanic and Atmospheric Administration, San Francisco, California. Portland, Oregon.

Beckon, William N., Cary Parkins, Alexey Maximovich, and Angela V. Beckon. 2008. A General 

Approach to Modeling Biphasic Relationships. Environmental Science and Technology 42:1308-

1314.

Brain, P. and R. Cousens. 1989. An equation to describe dose responses where there is 

stimulation of growth at low doses. Weed Research 29:93-96.

Brodsky, A., S. Zueg, N. Kogut, A.R. Stewart, Z. Jackson, J. Merz. 2014. White sturgeon diet 

response to invasive species-mediated changes in a benthic prey assemblage. Poster 

presentation. California-Nevada Chapter of the American Fisheries Society, 48th Annual 

Conference, March 27 – 29, 2014. Sacramento, California.

California Department of Fish and Game. 2001. California’s Living Marine Resources: A Status 

Report. Agriculture and Natural Resources Communication Services, University of California. 

Richmond, California. At: http://www.dfg.ca.gov/marine/status/status2001.asp.

California Department of Fish and Game. 2002. California Department of Fish and Game 

Comments to NMFS Regarding Green Sturgeon Listing. Sacramento, California. 

California Department of Water Resources. 2004. Matrix of Life History and Habitat 

Requirements for Feather River Fish Species SP-F3.2 Task 2, Splittail; Oroville Facilities 

Relicensing, FERC Project No. 2100. Sacramento, California.

Central Valley Regional Water Quality Control Board, State of California. 2010. Sacramento-San 

Joaquin Delta Estuary TMDL for Methylmercury, Staff Report. Rancho Cordova, California.

Carlton, James T., Janet K. Thompson, Laurence E. Schemel, and Frederic H. Nichols. 1990. 

Remarkable invasion of the San Francisco Bay (California, USA) by the Asian clam 

Potamocorbula amurensis. Marine Ecology Progress Series 66:81-94.
84

Central Valley Regional Water Quality Control Board, State of California. 2010. Sacramento-San 

Joaquin Delta Estuary TMDL for Methylmercury Staff Report. Rancho Cordova, California. At:

http://www.waterboards.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/delt

a_hg/april_2010_hg_tmdl_hearing/apr2010_tmdl_staffrpt_final.pdf.

Central Valley Regional Water Quality Control Board, State of California. 2011. The Water 

Quality Control Plan (Basin Plan) for the California Regional Water Quality Control Board Central 

Valley Region, Fourth Edition, The Sacramento River Basin and the San Joaquin River Basin. 

Rancho Cordova, California. At: 

http://www.waterboards.ca.gov/centralcoast/publications_forms/publications/basin_plan/ind

ex.shtml.

Chapman, P.M., W.J. Adams, M.L. Brooks, C.G. Delos, S.N. Luoma, W.A. Maher, H.M. Ohlendorf, 

T.S. Presser, and D.P. Shaw. 2009. Ecological assessment of selenium in the aquatic 

environment: Summary of a SETAC Pellston Workshop. Pensacola, Florida.

Chesser, R. Terry, Richard C. Banks, Carla Cicero, Jon L. Dunn, Andrew W. Kratter, Irby J. 

Lovette, Adolfo G. Navarro-Siguenza, Pamela C. Rasmussen, J. V. Remsen, Jr., James D. Rising, 

Douglas F. Stotz, and Kevin Winker. 2014. Fifty-Fifth Supplement to the American 

Ornithologists’ Union Check-list of North American Birds. The Auk: October 2014, 131:4, CSiCSxv. At: http://www.bioone.org/doi/full/10.1642/AUK-14-124.1.

Cohen, Andrew N. 2011. The Exotics Guide: Non-native Marine Species of the North American 

Pacific Coast. Center for Research on Aquatic Bioinvasions, Richmond, California, and the San 

Francisco Estuary Institute, Oakland, CA. Revised September 2011. At: 

http://www.exoticsguide.org.

Cutter, G.A. and L.S. Cutter. 2004. Selenium biogeochemistry in the San Francisco Bay estuary: 

changes in water column behavior. Estuarine, Coastal, and Shelf Science 61:3:463-476. 

De La Cruz, S.E., J.Y. Takekawa, A. Miles, J.M. Eadie, E.C. Palm, and M.T. Wilson. 2008. The 

Influence of Winter Habitat Use and Diet on Selenium Risks for Surf Scoters (Melanitta 

perspicillata) in the San Francisco Bay Estuary [abs.]. State of the San Francisco Estuary 

Conference. Oakland, CA. The San Francisco Estuary Project. 1 p.

De La Cruz, S.E.W., J.Y. Takekawa, M.T. Wilson, D.R. Nysewander, J.R. Evenson, D. Esler, W.S. 

Boyd and D.H. Ward. 2009. Surf Scoter Spring Migration Routes and Chronology: A Synthesis of 

Pacific Coast Studies. Canadian Journal of Zoology 87:1069-1086. 

De La Cruz, S.E. 2010. Habitat, diet, and contaminant relationships of surf scoters wintering in 

San Francisco Bay: implications for conservation in urban estuaries, PhD dissertation, University 

of California, Davis. Davis, California. 
85

De La Cruz, S.E.W., J.M. Eadie, A.K. Miles, J. Yee, K.A. Spragens, E.C. Palm and J.Y. Takekawa. 

2014. Resource selection and space use by sea ducks during the non-breeding season: 

Implications for habitat conservation planning in urbanized estuaries. Biological Conservation

169:64-78. 

De Riu, Nicola, Jan-Won Lee, Susie S.Y. Huang, Giuseppe Moniello, and Silas S.O. Hung. 2014. 

Effect of Dietary selenomethionine of growth, performance, tissue burden, and histopathology 

in green and white sturgeon. Aquatic Toxicology 148:65-73.

DeVink, Jean-Michael A., Robert G. Clark, Stuart M. Slattery and Tony M. Scheuhammer. 2008. 

Effects of Dietary Selenium on Reproduction and Body Mass of Captive Lesser Scaup. 

Environmental Toxicology and Chemistry 27:2:471-477.

Doblin, M.A., S.B. Baines, L.S. Cutter, and G.A. Cutter. 2006. Sources and biogeochemical cycling 

of particulate selenium in the San Francisco Bay estuary. Estuarine, Coastal, and Shelf Science

67:4:681-694. 

Doroshov, S.I., G.P. Moberg, and J.P. VanEenennaam. 1997. Observations on the reproductive 

cycle of cultured white sturgeon, Acipenser transmontanus. Environmental Biology of Fishes

48:265-278. 

Eastern Research Group, Inc. 2012. External Peer Review of the Evaluation of the Toxicity of 

Selenium to White and Green Sturgeon, Contract No.: EP-C-07-059, Work Assignment 4-18, 

submitted to USEPA Region 9. San Francisco, California.

Eisler, R. 1985. Selenium hazards to fish, wildlife, and invertebrates: a synoptic review. U.S. Fish 

and Wildlife Service Biological Report 85(1.5). Laurel, Maryland.

Feyrer F., B. Herbold, S.A. Matern, and P.B. Moyle. 2003. Dietary shifts in a stressed fish 

assemblage: consequences of a bivalve invasion in the San Francisco Estuary. Environmental 

Biology of Fishes 67:277-288.

Great Lakes Environmental Center. 2014. Examination of the Relationship of Selenium 

Concentrations and Mallard Egg Hatchability in Field-Collected Eggs. A Summary of U.S. Fish 

and Wildlife Service (2011) Region 8 Document: “Toxic Thresholds of Selenium in Mallard Eggs: 

Data Report.” Prepared for USEPA under HECD Contract: EP-C-09-001.

Hamilton, S.J., K.J. Buhl, N.L. Faerber, R.H. R.H. Weidmyer, and F.A. Bullard. 1990. Toxicity of 

organic selenium in the diet to Chinook salmon. Environmental Toxicology and Chemistry 9:347-

358.

Heinz, G.H., D.J. Hoffman, A.J. Krynitsky, and D.M.G. Weller. 1987. Reproduction in mallards fed 

selenium. Environmental Toxicology and Chemistry 6:423-433. 
86

Heinz, G.H., D.J. Hoffman, and L.G. Gold. 1989. Impaired Reproduction of Mallards Fed an 

Organic Form of Selenium. Journal of Wildlife Management 53:418-428. 

Heinz, G.H., and D.J. Hoffman. 1996. Comparison of the effects of seleno-L-methionine, selenoDL-methionine, and selenized yeast on reproduction of mallards. Environmental Pollution

91:169-175. 

Heinz, G.H. and D.J. Hoffman. 1998. Methylmercury chloride and selenomethionine interactions 

on health and reproduction in mallards. Environmental Toxicology and Chemistry 17:139-145. 

Heublin, Joseph C., John T. Kelly, Carlos E. Crocker, A. Peter Klimley, and Steve T. Lindley. 2009. 

Migration of green sturgeon, Acipenser medirostris, in the Sacramento River. Environmental 

Biology of Fishes 84:245-258. 

Hilton, J.W., P.V. Hodson, and S.J. Slinger. 1980. The Requirement and Toxicity of Selenium in 

Rainbow Trout (Salmo Gairdneri). Journal of Nutrition 110:2527-2535.

Hoffman, D.J. 2002. Role of selenium toxicity and oxidative stress in aquatic birds. Aquatic 

Toxicology 57:11-26.

Interagency Ecological Program for the San Francisco Estuary. 2011. Status and Trends of San 

Francisco Estuary White Sturgeon. 24:1 Spring 2011 Newsletter. Sacramento, California. 

Israel, Joshua A., and A. Pete Klimley. 2008. Sacramento-San Joaquin Delta Regional Ecosystem 

Restoration Implementation Plan, Life History Conceptual Model, North American Green 

Sturgeon (Acipenser medirostris). University of California, Davis. Davis, California.

Jackson, Z.J., and J.P. Van Eenennaam. 2013. 2012 San Joaquin River sturgeon spawning survey, 

Final Annual Report. Stockton Fish and Wildlife Office, Anadromous Fish Restoration Program, 

U.S. Fish and Wildlife Service. Lodi, California. 

Janz, David M., David K. Deforest, Marjorie L. Brooks, Peter M. Chapman, Guy Gilron, Dale Hoff, 

William A. Hopkins, Dennis O. McIntyre, Christopher A. Mebane, Vincent P. Palace, Joseph P. 

Skorupa, and Mark Wayland. 2010. Selenium Toxicity to Aquatic Organisms. In Ecological 

Assessment of Selenium in the Aquatic Environment pp. 133-231. Pensacola, Florida.

Kaufman, R.C., A.G. Houck, and J.J. Cech. 2008. Effects of dietary selenium and methylmercury 

on green and white sturgeon bioenergetics in response to changed environmental conditions. 

5

th Biennial CALFED Science Conference. Global Perspectives and Regional Results: Science 

Management in the Bay-Delta System. Sacramento, California. 

Kogut, N. 2008. Overbite Clams Corbula amurensis Defecated Alive by White Sturgeon 

Acipenser transmontanus. California Fish and Game 94(3):143-149. 
87

Leidy, R.A., G.S. Becker, and B.N. Harvey. 2005. Historical distribution and current status of 

steelhead/rainbow trout (Oncorhynchus mykiss) in streams of the San Francisco Estuary, 

California. Center for Ecosystem Management and Restoration. Oakland, California. At: 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentVersionID=19943

Lemly, A. Dennis. 1997. Environmental Implications of Excessive Selenium. Biomedical and 

Environmental Sciences 10:415-435. 

Linares-Casenave, J., J.P. Van Eenennaam, S.I. Doroshov, and D. Kueltz. 2010. The yolk sac 

larvae of white (Acipenser transmountanus) and green (A. medirostris) sturgeon are highly 

sensitive to selenium and temperature stresses. Poster, Department of Animal Science, 

University of California, Davis, California. Poster presentation: 6

th Biennial Bay Delta Science 

Conference, September 27-29. Sacramento, California.

Linville, R.G. 2006. Effects of excess selenium on the health and reproduction of white sturgeon 

(Acipenser transmountanus); Implications for San Francisco Bay-Delta, PhD dissertation, 

University of California, Davis. Davis, California. 232 pp. 

Lovvorn, James R., Susan E.W. De La Cruz, John Y. Takekawa, Laura E. Shaskey and Samantha E. 

Richman. 2013. Niche overlap, threshold food densities, and limits to prey depletion for a diving 

duck assemblage in an estuarine bay. Marine Ecology Progress Series 476:251-268. 

Lucas, L. and A.R. Stewart. 2007. Transport, transformation, and effects of selenium and carbon 

in the Delta of the Sacramento-San Joaquin Rivers: Implications for ecosystem restoration. 

CALSFED Ecosystem Restoration Program, Agreement No. 4600001955, Project No. ERP-01-C07. 

515 pp. At: 

http://wwwrcamnl.wr.usgs.gov/Selenium/Library_articles/san_luis_articles/Lucas_Stewart_Del

ta_ERP-01-C07.pdf.

Luoma, S.N., C. Johns, N.S. Fisher, N.A. Steinberg, R.S. Oremland, and J.R. Reinfelder. 1992. 

Determination of selenium bioavailability to a benthic bivalve from particulate and solute 

pathways. Environmental Science and Technology 26:3:485-491. 

McKechnie, R.J., and R.B. Fenner. 1971. Food habits of white sturgeon, Acipenser 

transmontanus, in San Pablo and Suisun Bays, California. California Fish and Game 57:209-212. 

Moyle, P.B. 2002. Inland Fishes of California. University of California Press. Berkeley and Los 

Angeles, California. 

Moyle, P.B., R.D. Baxter, T. Sommer, T.C. Foin, S.A. Matern. 2004. Biology and population 

dynamics of Sacramento splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: a 

review. San Francisco Estuary and Watershed Science 2:2: Article 3. 
88

Nagpal, N.K., and K. Howell. 2001. Water Protection Branch, Water, Lands and Air Protection. 

Water Quality Guidelines for Selenium. Victoria, British Columbia, Canada. At: 

http://www.env.gov.bc.ca/wat/wq/BCguidelines/selenium/ .

Nakamoto, Rodney J., Tom T. Kisanuki, and Greg H. Goldsmith for U.S. Fish and Wildlife Service. 

1995. Age and Growth of Klamath Green Sturgeon (Acipenser medirostris). Yreka, California.

National Marine Fisheries Service. 2012. Public Review Draft South-Central California Coast 

Steelhead Recovery Plan. Southwest Region, Protected Resources Division. Long Beach, 

California. 

Ogle, R.S., and A.W. Knight. 1989. Effects of elevated foodborne selenium on growth and 

reproduction of the fathead minnow (Pimephales promelas). Archives of Environmental 

Contamination and Toxicology 18:795-803.

Ohlendorf, H.M., D.J. Hoffman, M.K. Saiki, and T.W. Aldrich. 1986a. Embryonic mortality and 

abnormalities of aquatic birds: Apparent impacts of selenium from irrigation drainwater. 

Science of the Total Environment 52:49-63. 

Ohlendorf, H.M., R.L. Hothem, C.M. Bunck, T.W. Aldrich, and J.F. Moore. 1986b. Relationships 

between selenium concentrations and avian reproduction. Transactions of the North American

Wildlife and Natural Resources Conference 51:330-342. 

Ohlendorf, H.M., R.W. Lowe, P.R. Kelly, and T.E. Harvey. 1986c. Selenium and heavy metals in 

San Francisco Bay diving ducks. Journal of Wildlife Management 50:64-71.

Ohlendorf, H.M. 2003. Ecotoxicology of selenium. In: Handbook of Ecotoxicology. D.J. Hoffman, 

B.A. Rattner, G.A. Burton, Jr. and J. Cairns, Jr. (eds). Lewis Publishers, Boca Raton, Florida. pp. 

466-500.

Ohlendorf, H.M. 2007. Threshold Values for Selenium in Great Salt Lake: Selections by the 

Science Panel. Submitted to Great Salt Lakes Science Panel. February 28. 

Ohlendorf, H.M., and G.H. Heinz. 2011. Selenium in Birds. In: Environmental Contaminants in 

Biota: Interpreting Tissue Concentrations, 2

nd ed. W.N. Beyer and J.P. Meador (eds). CRC Press. 

Boca Raton, Florida. pp. 669-701.

Palace, V.P., J.E. Spallholz, J. Holm, K. Wautier, R.E. Evans, C.L. Baron. 2004. Metabolism of

selenomethionine by rainbow trout (Oncorhynchus mykiss) embryos can generate oxidative 

stress. Ecotoxicology and Environmental Safety 58: 17-21. 

Peterson, Mark S., Natalie J. Musselman, Jay Francis, Geoffrey Haborn, and Karen Dierolf. 1993. 

Lack of Salinity Selection by Freshwater and Brackish Populations of Juvenile Bluegill, Lepomis 

Macrochirus Rafinesque. Wetlands 13:3:194-199.
89

Presser, T.S., and S.N. Luoma. 2010. A Methodology for Ecosystem-Scale Modeling of Selenium. 

Integrated Environmental Assessment and Management 6:4:685-710 (plus Supporting 

Information).

Richman, S.E., and J.R. Lovvorn. 2004. Relative foraging value to lesser scaup ducks of native 

and exotic clams from San Francisco Bay. Ecological Applications 14:1217-1231. 

San Francisco Regional Water Quality Control Board, State of California. 2013. San Francisco Bay 

Basin (Region 2) Water Quality Control Plan (Basin Plan). Oakland, California. At: 

http://www.waterboards.ca.gov/sanfranciscobay/basin_planning.shtml. 

Schroeter, Robert E. and Peter B. Moyle. 2006. Alien Fishes. In: The Ecology of Marine Fishes: 

California and Adjacent Waters. Larry G. Allen, Daniel J. Pondella II, and Michael H. Horn (eds).

University of California Press. Berkeley and Los Angeles, California. 

Silvestre, F., J. Linares-Casenave, S.I. Doroshov, and D. Kultz. 2010. A proteomic analysis of 

green and white sturgeon larvae exposed to heat stress and selenium. Science of the Total 

Environment 408(16):3176-3188.

Simmons, Denina B.D., and Dirk Wallschlager. 2004. A Critical Review of the Biogeochemistry 

and Ecotoxicology of Selenium in Lotic and Lentic Environments. Environmental Toxicology and 

Chemistry 24:6:1331-1343. 

Skorupa, J. 2008. Great Salt Lake Selenium Standard, Written Recommendations to the Steering 

Committee. 

Stanley, Jr., T.R., J.W. Spann, G.J. Smith, and R. Roscoe. 1994. Main and interactive effects of 

arsenic and selenium on mallard reproduction and duckling growth and survival. Archives of

Environmental Contamination and Toxicology 26:444-451. 

Stanley, Jr., T.R., G.J. Smith, D.J. Hoffman, G.H. Heinz, and R. Roscoe. 1996. Effects of boron and 

selenium on mallard reproduction and duckling growth and survival. Environmental Toxicology

and Chemistry 15:1124-1132. 

State Water Resources Control Board, State of California. 2006. Water Quality Control Plan for 

the San Francisco Bay/Sacramento-San Joaquin Delta Estuary. Sacramento, California. At: 

http://www.swrcb.ca.gov/waterrights/water_issues/programs/bay_delta/wq_control_plans/20

06wqcp/index.shtml.

Stephan, C.E. 1987. Manual of Instructions for Preparing Aquatic Life Water Quality Criteria 

Documents. U.S. Environmental Protection Agency, Environmental Research Laboratory. 

Duluth, Minnesota.
90

Stewart, A. Robin, Samuel N. Luoma, Christian E. Schlekat, and Kathryn A. Hieb. 2004. Food 

Web Pathway Determines How Selenium Affects Ecosystems: A San Francisco Bay Case Study. 

Environmental Science and Technology 38:4519-4526.

Stewart, A., M. Grosell, D. Buchwalter, N. Fisher, S. Luoma, T. Mathews, P. Orr, and W. Wang. 

2010. Bioaccumulation and trophic transfer of selenium. In: Ecological Assessment of Selenium 

in the Aquatic Environment. P.M. Chapman, W.J. Adams, M.L. Brooks, C.G. Delos, S.N. Luoma,

W.A. Maher, H.M. Ohlendorf, T.S. Presser, and D.P. Shaw (eds). SETAC Press. Pensacola, Florida.

pp. 93-139.

Strange, J. 2013. Factors influencing the behavior and duration of residence of adult Chinook 

salmon in a stratified estuary. Enviromental Biology of Fishes 96:225-243. 

Stuber, R.J., G. Gebhart, and O.E. Maughan. 1982. Habitat suitability index models: Bluegill. 

U.S.D.I. Fish and Wildlife Service. FWS/OBS-82/10.8. Washington, D.C. At:

http://www.nwrc.usgs.gov/wdb/pub/hsi/hsi-008.pdf.

Tashjain, D.H., S.J. Teh, A. Sogomoyan, and S.S.O. Huang. 2006. Bioaccumulation and chronic 

toxicity of dietary L-selenoethionine in juvenile white sturgeon (Acipenser transmontanus). 

Aquatic Toxicology 79:401-409.

Teh, S.J., X. Deng, D.F. Deng, F.C. Teh, S.S.O. Hung, T.W. Fan, J. Lui, and R.M. Higasi. 2004. 

Chronic effects of dietary selenium on juvenile Sacramento splittail (Pogonichthys 

macrolepidotus). Environmental. Science and Technology 38:6085-6593.

Tetra Tech, Inc. on behalf of the Western States Petroleum Association for the San Francisco 

Regional Water Quality Control Board. 2008. Technical Memorandum 3: North San Francisco 

Bay Selenium Toxicological Assessment. Lafayette, California. 

Thompson, Janet K. and Francis Parchaso. 2010. Corbula amurensis Conceptual Model. USGS 

Priority Ecosystem Science and Toxic Substances Hydrology Program. 

Urquhart, K. and K. Regalado. 1991. Selenium Verification Study 1988 – 1990 Report 91-2-WQ. 

California Department of Fish and Game for the State Water Resources Control Board, State of 

California. 

U.S. Environmental Protection Agency, Office of Research and Development. 1985. Guidelines 

for Deriving Numerical National Water Quality Criteria for the Protection of Aquatic Organisms 

and their Uses. PB85-227049. Duluth, Minnesota, Narragansett, Rhode Island, Corvallis, 

Oregon. 

U.S. Environmental Protection Agency, Office of Water. 1987. Ambient Water Quality Criteria 

for Selenium – 1987. EPA-440/5-87-008. Washington, D.C. 
91

U.S. Environmental Protection Agency, Office of Water. 1994. Water Quality Standards 

Handbook, Second Edition. EPA-823-B-94-005a. Washington, D.C. 

U.S. Environmental Protection Agency, Office of Water. 1996. The Metals Translator: Guidance 

for Calculating A Total Recoverable Permit Limit From a Dissolved Criterion. EPA-823-B-96-007. 

Washington, D.C.

U.S. Environmental Protection Agency, Office of Environmental Information. 2002. Guidelines 

for Ensuring and Maximizing the Quality, Objectivity, Utility, and Integrity, of Information 

Disseminated by the Environmental Protection Agency. Washington, D.C.

U.S. Environmental Protection Agency, Region 8. 2011a. EPA Action on the Gilbert Bay Selenium 

Criterion and Footnote (14), and Enclosure. Denver, Colorado.

U.S. Environmental Protection Agency. 2011b. Unabridged Advance Notice of Proposed 

Rulemaking for Water Quality Challenges in the San Francisco Bay/Sacramento-San Joaquin 

Delta Estuary. San Francisco, California. (See also 76 FR 9709).

U.S. Environmental Protection Agency, Office of Water, EPA 822-R-16-006. 2016. Aquatic Life 

Ambient Water Quality Criteria for Selenium – Freshwater 2015. Washington, D.C.

U.S. Fish and Wildlife Service by William N. Beckon and Thomas C. Maurer. 2008. Species at Risk 

from Selenium Exposure in the San Francisco Estuary; Final Report to the Environmental 

Protection Agency. Sacramento, California. 

U.S. Fish and Wildlife Service by William Beckon. 2009. Selenium effect levels for selected 

representative/surrogate species. Sacramento, California.

U.S. Fish and Wildlife Service by K.M. Aceituno and T.C. Maurer. 2011. Toxic Thresholds of 

Selenium in Mallard Eggs: Data Report. 

U.S. Fish and Wildlife Service by William Beckon. 2012. Evaluation of the Toxicity of Selenium to 

White and Green Sturgeon. Sacramento, California.

U.S. Geological Survey by S.N. Luoma and T.S. Presser. 2000. Forecasting Selenium Discharges 

to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain 

Extension, USGS Open-File Report 00-416. At: http://pubs.usgs.gov/of/2000/ofr00-416/.

U.S. Geological Survey by T.S. Presser and S.N. Luoma. 2006. Forecasting Selenium Discharges 

to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain 

Extension. Professional Paper 1646. At http://pubs.usgs.gov/pp/p1646/.
92

U.S. Geological Survey by Theresa S. Presser and Samuel N. Luoma. 2010. Ecosystem-Scale 

Selenium Modeling in Support of Fish and Wildlife Criteria Development for the San Francisco 

Bay-Delta Estuary, California, Administrative Report. Menlo Park, California.

U.S. Geological Survey. 2012. Streamflow of 2011 – Water Year Summary. Reston, Virginia. At:

http://pubs.usgs.gov/fs/2012/3085/fs2012-3085.pdf.

Wallus, R. and T.P. Simon. 2008. Reproductive Biology and Early Life History of Fishes in the 

Ohio River Drainage, Elassomatidae and Cenrtrarchidae, Volume 6. CRC Press. Boca Raton, 

Florida. 

Wang, Johnson C.S. 1986. Fishes of the Sacramento-San Joaquin Estuary and Adjacent Waters,

California, A Guide to Early Life Histories. Interagency Ecological Program Technical Report #9. 

National Environmental Sciences, Inc. Clayton, California. Republished December 2010. U.S. 

Department of the Interior Bureau of Reclamation Mid-Pacific Region. Byron, California. At: 

http://www.usbr.gov/pmts/tech_services/tracy_research/tracyreports/Tech%20Report%209r.p

df.

Western States Petroleum Association by Tetra Tech, Inc. 2012. North San Francisco Bay 

Selenium Characterization Study, Final Report. Lafayette, California. 

Zeug, Steven C., Anne Brodsky, Nina Kogut, A. Robin Stewart, and Joseph E. Merz. 2014. Ancient 

fish and recent invaders: white sturgeon (Acipenser transmontanus) diet response to invasive 

species-mediated changes in benthic prey assemblage. Marine Ecology Progress Series 514:163-

174.