TECHNICAL MEMORANDUM 2: 

NORTH SAN FRANCISCO BAY SELENIUM DATA 

SUMMARY AND SOURCE ANALYSIS

July 2008 

Prepared for: 

Regional Water Quality Control Board 

San Francisco Bay Region 

1515 Clay Street 

Oakland, CA 94612 

Prepared by: 

Tetra Tech, Inc. 

3746 Mt. Diablo Blvd., Suite 300 

Lafayette, CA 94549 

North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. i 

ABBREVIATIONS

BASMAA Bay Area Stormwater Management Agencies Association 

cfs cubic feet per second 

mgd million gallon per day 

NDOI Net Delta Outflow Index 

NSFB North San Francisco Bay 

psu Practical Salinity Unit 

RMP Regional Monitoring Program 

SFEI San Francisco Estuary Institute 

SSC Suspended Sediment Concentration 

SWAMP Surface Water Ambient Monitoring Program 

SFBRWQCB San Francisco Bay Regional Water Quality Control Board 

TMDL Total Maximum Daily Load 

TSM Total Suspended (Particulate) Material 

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TABLE OF CONTENTS

Abbreviations ................................................................................................................... i

1. Introduction ...........................................................................................................1-1

2. Selenium Concentrations in Bay Water and Bottom Sediments ...........................2-1

2.1. Goals of Data Summary...............................................................................2-1

2.2. Data Description...........................................................................................2-1

2.3. What is the distribution of selenium in the water column?............................2-3

2.4. What are the long term trends of selenium concentrations in water?...........2-6

2.5. What is the relative mix of dissolved and particulate selenium in the 

water column?............................................................................................2-10

2.6. How does selenium correlate with salinity and freshwater flows?..............2-11

2.7. What was the impact of refinery selenium load reductions in 1998?..........2-19

2.8. How does selenium correlate with suspended sediments and 

chlorophyll-a?.............................................................................................2-21

2.9. What is the distribution of selenium in sediments?.....................................2-30

3. Source Characterization........................................................................................3-1

3.1. Overview of Previous Source Estimates ......................................................3-1

3.2. Direct Atmospheric Deposition.....................................................................3-2

3.3. Urban and Non-urban Stormwater Runoff from Local Tributaries ................3-3

3.4. Inputs from San Joaquin and Sacramento Rivers via the Delta .................3-19

3.5. Municipal and Industrial Wastewater Dischargers......................................3-43

3.6. Petroleum Refineries..................................................................................3-50

3.7. Internal Sources - Sediment Erosion..........................................................3-56

3.8. Loads from the South Bay..........................................................................3-57

3.9. Comparison of Selenium Concentrations and Loads from Different 

Sources......................................................................................................3-58

3.10.Low Flow vs. High Flow Concentrations ....................................................3-61

4. Summary...............................................................................................................4-1

5. Key Findings and Implications for Model Development.........................................5-1

6. References............................................................................................................6-1

Appendices ..................................................................................................................A-1

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LIST OF FIGURES

Figure 1-1 The San Francisco Bay estuary, Delta and Sacramento and San Joaquin 

Rivers. ................................................................................................................1-3

Figure 2-1 Locations of RMP long-term monitoring sites and sampling by Cutter and 

Cutter (2004) during November 1999.................................................................2-3

Figure 2-2 Total selenium concentrations at long-term monitoring sites for the period of 

1993-2005. .........................................................................................................2-6

Figure 2-3 Dissolved selenium concentrations as a function of time in stations near 

Mallard Island and in Suisun Bay .......................................................................2-7

Figure 2-4 Dissolved selenium concentrations as a function of time in the San Pablo 

and Central Bay..................................................................................................2-8

Figure 2-5 Total selenium concentrations as a function of time in stations near Mallard 

Island and in Suisun Bay....................................................................................2-9

Figure 2-6 Total selenium concentrations as a function of time in the San Pablo and 

Central Bay.......................................................................................................2-10

Figure 2-7 Correlation between dissolved and total selenium concentrations for 

long-term monitoring sites. ...............................................................................2-11

Figure 2-8 Dissolved selenium concentrations along salinity gradient during low and 

high flow sampling periods by RMP and Cutter and Cutter (2004) before 

1999. ................................................................................................................2-12

Figure 2-9 Dissolved selenium concentrations as a function of salinity during low and 

high flow sampling periods by RMP and Cutter and Cutter (2004) from 

1999 onwards...................................................................................................2-13

Figure 2-10 Spatial distribution of dissolved selenium and salinity during a sampling 

event in a dry period of a dry year (August 2001) by the RMP.........................2-14

Figure 2-11 Spatial distribution of dissolved selenium and salinity during a sampling 

event in a wet period (February 2001) by the RMP..........................................2-15

Figure 2-12 Transects of dissolved selenium, selenite, selenate, and organic selenide 

under high flow sampling periods.....................................................................2-17

Figure 2-13 Transects of dissolved selenium, selenite, selenate and organic selenide 

under low flow sampling periods. .....................................................................2-18

Figure 2-14 Dissolved selenium concentrations under low and high flow before and 

after July 1998..................................................................................................2-20

Figure 2-15 Speciation of dissolved selenium in Bay water column during different 

time periods......................................................................................................2-21

Figure 2-16 Transects of TSM, chlorophyll-a, particulate selenium and selenium in 

particulate material under high flow..................................................................2-23

Figure 2-17 Transects of TSM, chlorophyll-a, particulate selenium and selenium in 

particulate material under low flow ...................................................................2-24
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Figure 2-18 Transects of total particulate selenium, particulate elemental selenium, 

particulate adsorbed selenite and selenate, and particulate organic 

selenium during high flow.................................................................................2-26

Figure 2-19 Transects of total particulate selenium, particulate elemental selenium, 

particulate adsorbed selenite and selenate, and particulate organic 

selenium during low flow ..................................................................................2-27

Figure 2-20 Correlation between particulate selenium and TSM under low and high 

flow ...................................................................................................................2-28

Figure 2-21 Concentrations of TSM, Chl a, and particulate selenium and selenium 

content in particulates for a low flow sampling event of Oct. 1998...................2-29

Figure 2-22 Mean selenium concentrations in sediments for the period of 1993-2005. ......2-31

Figure 2-23 Selenium concentrations in sediments with data from RMP random 

sampling sites and data collected by G. Cutter’s research group ....................2-31

Figure 2-24 Relationship between selenium concentrations in sediments and sediment 

characteristics at long-term sites......................................................................2-32

Figure 2-25 Relationship between selenium concentrations in sediments and sediment 

characteristics at random sampling sites..........................................................2-33

Figure 2-26 Selenium concentrations in sediments as a function of time in stations near 

Mallard Island and in Suisun Bay. ....................................................................2-34

Figure 2-27 Selenium concentrations in sediments as a function of time in San Pablo 

and Central Bay................................................................................................2-35

Figure 3-1 Total selenium concentrations in the wet (a), spring (b) and dry (c) seasons 

in local tributaries of the North Bay, sampled in the SWAMP program. .............3-6

Figure 3-2 Total selenium concentrations in tributaries of NSFB sampled during 

1990–1996 and 2000–2003 ...............................................................................3-7

Figure 3-3 Hydrological areas surrounding NSFB ...............................................................3-8

Figure 3-4 Estimated long-term average monthly selenium loadings at gaging stations 

of local tributaries. ............................................................................................3-12

Figure 3-5 Comparison of dry and wet season selenium loadings for tributaries in the 

North Bay. ........................................................................................................3-13

Figure 3-6 Dry and wet season selenium loadings by water year at Napa River near 

Napa.................................................................................................................3-15

Figure 3-7 Flow from Sacramento River, San Joaquin River, compared to Delta 

exports and outflow to Delta for a dry year and a wet year .............................3-20

Figure 3-8 Daily Delta outflow for water years 1992-2006.................................................3-23

Figure 3-9 Estimated wet and dry season total selenium loadings from Delta to the 

Bay by water year.............................................................................................3-23

Figure 3-10 Relationship between total selenium concentrations and flow at Mallard 

Island................................................................................................................3-24

Figure 3-11 Dissolved selenium concentrations in Sacramento River at Freeport and 

San Joaquin River at Vernalis during 1984-1988 and 1998-2000....................3-26
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Figure 3-12 Dissolved selenium concentrations at Sacramento River at Freeport and 

San Joaquin River at Vernalis during 1998-2000.............................................3-27

Figure 3-13 Relationship between dissolved selenium concentrations and daily flow for 

Sacramento River at Freeport and San Joaquin River at Vernalis for the 

period of 1998-2000 .........................................................................................3-28

Figure 3-14 Dry and wet season dissolved selenium loadings at Sacramento River at 

Freeport and San Joaquin River at Vernalis for 1991-2007. ............................3-30

Figure 3-15 Dissolved selenium concentrations sampled by Cutter and Cutter (2004) at 

San Joaquin River at Vernalis compared to total selenium concentrations 

observed in SWAMP study...............................................................................3-31

Figure 3-16 A subset of dissolved selenium concentrations sampled by Cutter and 

Cutter (2004) compared to total selenium concentrations from SWAMP.........3-31

Figure 3-17 Total selenium concentrations along main stem of San Joaquin River at 

Crows Landing, at Patterson, and at Vernalis .................................................3-32

Figure 3-18 Relationship between total selenium and flow at San Joaquin River at 

Vernalis ............................................................................................................3-33

Figure 3-19 Dry and wet season total selenium loadings at San Joaquin River at 

Vernalis, estimated from concentrations from SWAMP study..........................3-33

Figure 3-20 Comparison of selenium loadings at San Joaquin River at Vernalis 

estimated from Cutter and Cutter (2004) data and data from SWAMP study. .3-34

Figure 3-21 Dissolved selenium concentrations at various locations of the Delta and 

North Bay in October 1998 and November 1999 sampling..............................3-35

Figure 3-22 Estimated selenium loadings from the Delta to the bay as a result of inputs 

from Sacramento River at Freeport and San Joaquin River at Vernalis,..........3-36

Figure 3-23 Long-term percentage contribution of flows at the Banks Pumping Plant........3-37

Figure 3-24 Estimated selenium loadings through the aqueducts and contributions from 

the Sacramento River and the San Joaquin River. ..........................................3-41

Figure 3-25 Estimated selenium loadings from the Delta to the Bay as the difference 

between loads from the Rivers and export through aqueducts, as well as 

contributions attributed to the Sacramento River and the San Joaquin 

Rivers individually.............................................................................................3-42

Figure 3-26 Estimated selenium concentrations in the aqueducts using flow weighted 

method compared to observed concentrations in Delta Mendota Canal 

near Tracy Headworks .....................................................................................3-43

Figure 3-27 POTW discharge locations in and around San Francisco Bay.........................3-45

Figure 3-28 Daily effluent average flow at five largest dischargers in North Bay.................3-47

Figure 3-29 Effluent maximum concentrations for the five largest dischargers in the 

North Bay. ........................................................................................................3-48

Figure 3-30 Estimated daily total selenium loadings from EBMUD. ....................................3-50

Figure 3-31 Effluent daily maximum selenium concentrations for the refineries in the 

North Bay. ........................................................................................................3-52
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Figure 3-32 Daily average effluent flow rate from the refineries. .........................................3-53

Figure 3-33 Concentrations and flow for the refineries in the North Bay .............................3-54

Figure 3-34 Dry and wet season selenium loadings from refineries for the years of 

1999-2007. .......................................................................................................3-55
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LIST OF TABLES

Table 2-1 RMP long-term sampling locations in the North Bay..........................................2-2

Table 2-2 Summary of dissolved selenium concentrations in the water column for the 

period 1993-2005 for the North Bay ...................................................................2-4

Table 2-3 Summary of total selenium concentrations in the water column for the period of 

1993-2005 for the North Bay ..............................................................................2-5

Table 2-4 Speciation of dissolved selenium in Bay water.................................................2-19

Table 2-5 Summary of particulate concentrations during low and high flow periods........2-25

Table 3-1 Total and dissolved selenium concentrations observed at the SWAMP sites 

during wet, spring and dry seasons....................................................................3-5

Table 3-2 Runoff and selenium loadings from local watersheds to the North Bay .............3-9

Table 3-3 Major USGS gaging stations in North Bay watersheds....................................3-10

Table 3-4 Long-term average monthly flow at USGS gaging stations in North Bay 

watersheds for the record period......................................................................3-11

Table 3-5 Estimated long-term average monthly total selenium loadings to the gaging 

stations. ............................................................................................................3-14

Table 3-6 Estimated annual total selenium loadings for the hydrological areas in the 

North Bay. ........................................................................................................3-15

Table 3-7 Summary of drainage areas and land use for each hydrologic area of 

NSFB ...............................................................................................................3-17

Table 3-8 Land use specific runoff coefficient and mean selenium concentrations..........3-17

Table 3-9 Estimated total selenium loadings by land use from hydrological areas 

draining NSFB by land uses.............................................................................3-18

Table 3-10 Estimated total and dissolved selenium loadings from the Delta .....................3-24

Table 3-11 Summary statistics of daily maximum effluent concentrations at the 

municipal dischargers.......................................................................................3-46

Table 3-12 Estimated total selenium loadings from POTWs in the North Bay ...................3-49

Table 3-13 Estimated selenium loadings from industrial wastewater dischargers in the 

North Bay .........................................................................................................3-50

Table 3-14 Summary statistics of daily maximum effluent concentrations at the 

refineries...........................................................................................................3-51

Table 3-15 Estimated total selenium loadings from petroleum refineries in the North 

Bay ...................................................................................................................3-51

Table 3-16 Estimated selenium mass associated with dredge material disposal ..............3-57

Table 3-17 Representative selenium concentration in different sources............................3-58

Table 3-18 Relative importance of loadings from different sources....................................3-59

Table 3-19 Summary of dry and wet season selenium loading from major sources ..........3-60

Table 3-20 Comparison of alternative total selenium loadings estimates to North San 

Francisco Bay...................................................................................................3-61
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Table 3-21 Estimated selenium concentrations under different flow conditions.................3-62

Table A-1 Parameters and inputs of one-box model.......................................................... A-1

Table A-2 Summary of dissolved selenium concentrations in water for the period of 

1993-2005 for the whole Bay ............................................................................ A-2

Table A-3 Summary of total selenium concentrations in water for the period of 

1993-2005 for the whole Bay ............................................................................ A-3

Table A-4 Summary of selenium concentrations in sediments for the period of 

1993-2005 for the whole Bay ............................................................................ A-4

Table A-5 Detailed Information on Selenium from POTWs in North San Francisco Bay... A-5
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1. INTRODUCTION

North San Francisco Bay (NSFB) including Suisun Bay, Carquinez Strait, San Pablo Bay 

and Central Bay, shown in Figure 1-1, is listed as being impaired for selenium under section 

303(d) of the Clean Water Act. This listing was based, in part, on elevated concentrations in 

white sturgeon and diving ducks in the 1980s and is more than a decade old. There is an 

ongoing effort by the San Francisco Bay Regional Water Board to prepare a TMDL for 

selenium in North San Francisco Bay with the most up-to-date information. This technical 

memorandum has been prepared in support of the TMDL development effort. The purpose 

of this memorandum is two-fold: provide a summary of relevant water and sediment 

selenium data in the North Bay and to develop a quantitative estimate of the sources of 

selenium to the waters of the North Bay. In addition to this document, two other technical 

memorandums are under preparation. The first of these assesses the scientific literature to 

develop recommendations for selenium toxicological endpoints in the North Bay, and the 

second presents a conceptual model of selenium behavior in the North Bay, with an 

emphasis on describing the biogeochemical processes relating selenium sources to 

concentrations in biological tissues. Information in these memorandums will support the 

development of a mechanistic model of selenium in NSFB linking sources to endpoints of 

interest in the TMDL. 

There has been a long history of research on selenium sources, transport, and biological 

uptake in San Francisco Bay, the Delta, and in the Central Valley (e.g., Cutter, 1989; Cutter 

and San Diego-McGlone, 1990; Cutter and Cutter, 2004; Presser and Luoma, 2006; Meseck 

and Cutter, 2006). Starting in the mid-1980’s, selenium concentrations have been monitored 

in the bay across the salinity gradient and in different seasons reflecting variations in 

freshwater flows. Major sources of selenium to the Bay-Delta identified in these previous 

studies include: 

! San Joaquin River that receives discharge from agricultural drainage from the 

western San Joaquin Valley 

! Selenium discharged from the effluents of North Bay refineries. 

! Sacramento River, which is the dominant freshwater inflow to the Bay-Delta during 

the wet season. 

This memorandum contains a summary of data and findings from past work, including an 

updated estimate of the selenium load contributions from various point and non-point 

sources. Over the past two decades, there have been major declines in refinery loads due to 

improved wastewater treatment installed in 1998; there is some evidence that San Joaquin 

River concentrations were lower in the late 1990s and beyond than in the 1980s, although 

this is not clear cut. 

The data summary (Section 2) provides an overview of water and sediment data collected in 

and upstream of NSFB over the past two decades. Data on selenium in biota are discussed in 

the memo on toxicological endpoints (TM-3). The water and sediment data are presented in 

maps and plots to provide a visual summary and to identify major processes occurring in the 

North Bay. There are many ways to represent this large and complex data set. The broad 

objective of the data summary was to provide a reader with the spatial and temporal extent 
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of the data collected to date, and to evaluate whether existing data could be used to address 

questions of interest to the TMDL. A more detailed evaluation of the data and underlying 

processes will be presented in the Conceptual Model (TM-4). These data will also serve as 

the basis for model calibration to be performed in the next step of the TMDL development. 

The majority of the data collected in the bay is focused on total selenium. Speciation, 

particularly the concentrations of selenate, selenite, and particulate selenium, determines 

how efficiently selenium enters higher aquatic food web (Presser and Luoma, 2006). To the 

extent available, speciation data on selenium are also described. 

The goal of the source analysis (Section 3) was to use data on concentrations and flow 

volumes of each of the identified sources in NSFB, and to take a fresh look at estimating the 

relative magnitudes of the key point and non-point sources of selenium. The source 

estimates differ from previous work in the use of more recent data and the examination of a 

wider range of potential sources. Sources considered include: atmospheric deposition, urban 

and non-urban runoff, Delta inflows and the relative contributions of the Sacramento and 

San Joaquin Rivers, municipal wastewater effluents, petroleum refinery effluents, and inputs 

from the existing reservoir of selenium in the sediments of the North Bay. Accurate 

quantification of sources is a key input to selenium fate and transport modeling proposed for 

the bay. In the event that the TMDL finds that most recent data are consistent with selenium 

impairment in the North Bay, the source analysis is a means to identify the loads that need to 

be decreased to meet targets in the bay. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

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Figure 1-1 The San Francisco Bay estuary, Delta and Sacramento and San Joaquin Rivers. 

The cross-hatched area shows the area of interest for the North San Francisco 

Bay Selenium TMDL. The Sacramento River at Freeport and the San Joaquin 

River at Vernalis are the principal freshwater inflows into the Delta. A significant 

portion of the freshwater inflows are exported out of the Delta through the four 

pumping plants shown. 

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2. SELENIUM CONCENTRATIONS IN BAY WATER AND BOTTOM SEDIMENTS

2.1. GOALS OF DATA SUMMARY

A key objective of the data summary is to evaluate whether the following questions of 

relevance to the selenium TMDL in the NSFB can be addressed through the existing 

database: 

! What is the distribution of selenium in the water column? 

! What are the long term trends of selenium concentrations in water? 

! What is the relative mix of dissolved and particulate selenium in the water column? 

! How does selenium correlate with salinity and freshwater flows? 

! What was the effect of refinery selenium load reduction in 1998? 

! How does selenium correlate with suspended sediments and chlorophyll-a? 

! What is the distribution of selenium in sediments? 

In this section, the data sources used in this evaluation are first described, and plots and 

maps of the data are used to address each of the questions above. 

2.2. DATA DESCRIPTION

Selenium concentrations in the bay water column and bottom sediments have been collected 

by different entities since the 1980s. The major sources of data for selenium in the North 

Bay are: 1) data collected by the Regional Monitoring Program (RMP) since 1993; and 2) 

data collected by Dr. Greg Cutter’s research group at Old Dominion University1. The RMP 

is a joint effort among San Francisco Estuary Institute (SFEI), the Regional Board, and local 

dischargers. All data collected by the Cutter research group from the mid-1980s onwards 

was made available to us electronically for the preparation of this and subsequent technical 

memorandums. \

 

The RMP was initiated in 1993 to sample contaminant concentrations in water, sediment 

and bivalves. Fifteen monitoring sites were located in the North Bay (out of 26 sites in the 

whole bay; Figure 2-1; Table 2-1). Samples were collected at a frequency of 2-3 times a year 

during high flow, intermediate flow and low flow periods. Starting in 2002, EPA’s 

Generalized Random Tessellation Stratified (GRTS) sample design approach was utilized to 

monitor contaminants (SEFI, 2006). Thereafter, most of the long-term sites were 

discontinued except for five locations noted in Table 2-1. Since 2002, each year 12 

randomly selected sites in the North Bay have been sampled for selenium in the water and 

24 random sites have been sampled for selenium in sediments. Water samples were 

collected 1-2 feet below surface. Water samples were analyzed for total and dissolved (0.45 

μm filtered) concentrations, with a detection limit of 0.02 μg/L. Sediment samples were 

 

1

 Funded by the U.S. Bureau of Reclamation, CALFED (Grant 01WRPA0077), California Department of Water 

Resources, and National Science Foundation, Environmental Geochemistry and Biogeochemistry Initiative (Grant: 

OCE-9707946). 
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analyzed for dry weight concentrations with detection limit of 0.01 mg/kg. Sediment 

samples were taken from the top 5 cm of the sediment surface. 

Dr. Cutter’s research group used a different sampling design to sample dissolved and 

particulate selenium concentrations along the estuarine transect from the Golden Gate to the 

Sacramento (Rio Vista) and San Joaquin River (USGS Station 757), during 1980s and again 

during 1997-1999 (Cutter and Cutter, 2004; Doblin et al. 2006). Samples were taken along 

the salinity gradient at approximately equal salinity intervals and were analyzed for 

dissolved selenium and selenium species (selenate, selenite, and organic dissolved selenide) 

at detection limits of 1.6 ng/L. Because salinity varied according to the sampling year, the 

spatial locations varied slightly for individual sampling events. Locations for a sampling 

event during November 1999 are shown in Figure 2-1 along side RMP sampling stations. 

Samples were also analyzed for particulate selenium and its speciation (elemental selenium, 

selenite and selenate). Sampling depth is at 1-2 m below surface. The detection limit for 

particulate selenium was 0.4 ng/L. For the sediments, Dr. Cutter’s research group sampled 

sediment cores at 23 locations in the Bay-Delta (Meseck, 2002). Sediment core profiles were 

taken from depths ranging from 5 cm to 20 cm at different locations. The cores were 

analyzed for total selenium, elemental selenium and selenite and selenate. Dr. Cutter’s 

research group is the only one that has reported selenium speciation in the bay. 

Table 2-1 

RMP long-term sampling locations in the North Bay. 

Site Code Site Name Sample Matrix Period of data 

BC10* Central Bay/Yerba Buena Island Water, sediment, bivalve 1993-2005 

BC21 Central Bay/Horseshoe Bay Sediment, bivalve 1993-2001 

BC30 Central Bay/Richardson Bay Water, sediment 1993-2001 

BC41 Central Bay/Point Isabel Water, sediment 1993-2001 

BC60 Central Bay/Red Rock Water, sediment, bivalve 1993-2001 

BD15 San Pablo Bay/Petaluma River Water, sediment, bivalve 1993-2001 

BD20 San Pablo Bay Water, sediment, bivalve 1993-2001 

BD30* San Pablo Bay/Pinole Point Water, sediment, bivalve 1993-2005 

BD40 San Pablo Bay/Davis Point Water, sediment, bivalve 1993-2001 

BD50 San Pablo Bay/Napa River Water, sediment, bivalve 1993-2001 

BF10 Suisun Bay/Pacheco Creek Water, sediment 1993-2001 

BF20* Suisun Bay/Grizzly Bay Water, sediment, bivalve 1993-2005 

BF40 Suisun Bay/Honker Bay Water, sediment 1993-2001 

BG20* Delta/Sacramento River Water, sediment, bivalve 1993-2005 

BG30* Delta/San Joaquin River Water, sediment, bivalve 1993-2005 

*Sampling continued at these locations after 2002 
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Figure 2-1 Locations of RMP long-term monitoring sites and sampling by Cutter and Cutter 

(2004) during November 1999. 

2.3. WHAT IS THE DISTRIBUTION OF SELENIUM IN THE WATER COLUMN? 

Selenium concentrations observed in the North Bay water column are generally low and 

mostly in the dissolved form. Over the period of 1993-2005, mean dissolved and total 

selenium concentrations averaged at each station were between 0.12-0.18 μg/L and 0.13-

0.24 μg/L in the North Bay (Table 2-2 and Table 2-3). Particulate selenium (calculated as 

the difference between total and dissolved selenium) accounts for approximately 10% of the 

total. During the most recent sampling over 1999-2005, i.e., following improved wastewater 

control in the oil refineries in 1998 (Presser and Luoma, 2006), mean dissolved and total 

selenium concentrations pooled across all the long-term monitoring sites in North Bay were 

0.10 μg/L (0.03-0.24 !g/L, n = 105 ) and 0.13 μg/L (0.04-0.45 !g/L, n = 100). In 

comparison, mean dissolved and total selenium concentrations for the period of 1993-1999 

at these pooled long-term sites were 0.17 μg/L (range: 0.03-0.44 !g/L, n = 258) and 0.20 

!g/L (0.02-0.5 !g/L, n = 230). 

Spatially, total selenium concentrations are marginally higher in the mid-estuarine regions of 

Suisun and San Pablo Bays compared to the freshwater and marine portions (Figure 2-2). 

Total selenium concentrations in the Central Bay are lower, most likely due to ocean 

exchange and dilution. A few locations near the confluence of local tributaries (e.g., 

Petaluma and Napa River) show higher total selenium concentrations relative to the rest of 

the bay (Figure 2-2). The trends are most apparent when median values are considered. 
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Table 2-2 

Summary of dissolved selenium concentrations in the water column for the period 1993-2005 for 

the North Bay (data source: RMP). 

Site Code Site Name 

Mean 

(μg/L) 

S.D. 

(μg/L) 

Median 

(μg/L) Count 

BC10 Yerba Buena Island 0.14 0.08 0.11 27 

BC20 Horseshoe Bay 0.14 0.10 0.10 23 

BC30 Richardson Bay 0.14 0.10 0.13 23 

BC41 Point Isabel 0.14 0.09 0.10 24 

BC60 Red Rock 0.15 0.10 0.12 20 

BD15 Petaluma River 0.18 0.07 0.17 21 

BD20 San Pablo Bay 0.15 0.06 0.14 24 

BD30 Pinole Point 0.16 0.06 0.15 24 

BD40 Davis Point 0.17 0.06 0.16 25 

BD50 Napa River 0.16 0.06 0.16 24 

BF10 Pacheco Creek 0.17 0.08 0.15 24 

BF20 Grizzly Bay 0.14 0.06 0.13 25 

BF40 Honker Bay 0.12 0.05 0.11 22 

BG20 Sacramento River (near Mallard 

Island) 

0.13 0.09 0.12 29 

BG30 San Joaquin River(near Mallard 

Island) 

0.16 0.09 0.14 28 

S.D. - Standard deviation 
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Table 2-3 

Summary of total selenium concentrations in the water column for the period of 1993-2005 for the 

North Bay (data source: RMP). 

Site Code Site Name 

Mean 

(μg/L) 

S.D. 

(μg/L) 

Median 

(μg/L) Count 

BC10 Yerba Buena Island 0.16 0.09 0.12 23 

BC20 Horseshoe Bay 0.17 0.12 0.11 19 

BC30 Richardson Bay 0.13 0.08 0.11 22 

BC41 Point Isabel 0.14 0.07 0.12 20 

BC60 Red Rock 0.18 0.08 0.15 16 

BD15 Petaluma River 0.24 0.09 0.25 19 

BD20 San Pablo Bay 0.18 0.07 0.17 23 

BD30 Pinole Point 0.18 0.08 0.17 23 

BD40 Davis Point 0.21 0.08 0.18 23 

BD50 Napa River 0.20 0.05 0.19 22 

BF10 Pacheco Creek 0.19 0.07 0.19 22 

BF20 Grizzly Bay 0.17 0.07 0.17 23 

BF40 Honker Bay 0.16 0.05 0.15 22 

BG20 Sacramento River (near Mallard 

Island) 

0.15 0.08 0.13 27 

BG30 San Joaquin River (near Mallard 

Island) 

0.18 0.09 0.16 26 

S.D.- Standard deviation 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-6 Tetra Tech, Inc. 

Total Selenium

BC10 Yerba Buena Island (23)

BC20 Golden Gate (19)

BC30 Richardson Bay (22)

BC41 Point Isabel (20)

BC60 Red Rock (16)

BD15 Petaluma River (19)

BD20 San Pablo Bay (23)

BD30 Pinole Point (23)

BD40 Davis Point (23)

BD50 Napa River (22)

BF10 Pacheco Creek (22)

BF20 Grizzly Bay (23)

BF40 Honker Bay (22)

BG20 Sacra. R. nr. Mallard Island (27)

BG30 San Joa. R. nr. Mallard Island (26)

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

Outlier

90th percentile

75th percentile

Median

25the percentile

10th percentile

Outlier

Figure 2-2 Total selenium concentrations at long-term monitoring sites for the period of 

1993-2005. Values in parentheses are numbers of samples (data source: RMP). 

Data from random sampling during 2002-2005 also indicated relatively low dissolved and 

total selenium concentrations, below 0.15 μg/L, with a whole North Bay average of 0.12 

μg/L. Total selenium concentrations are higher in the upper estuary (Suisun Bay) than the 

San Pablo and Central Bays. 

2.4. WHAT ARE THE LONG TERM TRENDS OF SELENIUM CONCENTRATIONS IN WATER? 

Over the long-term, dissolved and total selenium concentrations show large temporal (both 

inter-annual and seasonal) variations (Figure 2-3 to Figure 2-6). For most stations in the 

North Bay, a weak negative correlation with time is noted, beginning in 1993. In most 

instances, the data show a general negative slope with time, and not an abrupt change in 

1998 when refinery loads and concentrations were decreased. The temporal patterns in 

dissolved selenium closely resemble those in the total selenium. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-7 

Suisun Bay 

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

BF10 - Pacheco Creek

BF20 - Grizzly Bay

BF40 - Honker Bay

Delta

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

BG20 - Sacramento River (near Mallard Island)

BG30 - San Joaquin River (near Mallard Island)

Figure 2-3 Dissolved selenium concentrations as a function of time in stations near Mallard 

Island and in Suisun Bay (data source: RMP). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-8 Tetra Tech, Inc. 

Central Bay 

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

BC10 - Yerba Buena Island

BC20 - Golden Gate

BC30 - Richardson Bay

BC41 - Point Isabel

BC60 - Red Rock

San Pablo Bay 

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

BD15 - Petaluma River

BD20 - San Pablo Bay

BD30 - Pinole Point

BD40 - Davis Point

BD50 - Napa River

Figure 2-4 Dissolved selenium concentrations as a function of time in the San Pablo and 

Central Bay (data source: RMP). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-9 

Suisun Bay

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

BF10 - Pacheco Creek

BF20 - Grizzly Bay

BF40 - Honker Bay

Delta

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

BG20 - Sacramento River (near Mallard Island)

BG30 - San Joaquin River (near Mallard Island)

Figure 2-5 Total selenium concentrations as a function of time in stations near Mallard 

Island and in Suisun Bay (data source: RMP). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-10 Tetra Tech, Inc. 

Central Bay 

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

BC10 - Yerba Buena Island

BC20 - Golden Gate

BC30 - Richardson Bay

BC41 - Point Isabel

BC60 - Red Rock

San Pablo Bay 

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/L

0.0

0.1

0.2

0.3

0.4

0.5

BD15 - Petaluma River

BD20 - San Pablo Bay

BD30 - Pinole Point

BD40 - Davis Point

BD50 - Napa River

Figure 2-6 Total selenium concentrations as a function of time in the San Pablo and Central 

Bay (data source: RMP). 

2.5. WHAT IS THE RELATIVE MIX OF DISSOLVED AND PARTICULATE SELENIUM IN THE WATER 

COLUMN? 

Pooling all the data from the RMP monitoring indicates a close correlation between 

dissolved and total selenium (Figure 2-7), with the dissolved fraction representing more than 

two-thirds of the total selenium. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-11 

Total Selenium ("g/L)

0.0 0.1 0.2 0.3 0.4 0.5

Dissolved Selenium (

"g/L)

0.0

0.1

0.2

0.3

0.4

0.5

R2 = 0.696

[Dis. Se] = 0.011 + 0.764 * [Tot. Se]

Figure 2-7 Correlation between dissolved and total selenium concentrations for long-term 

monitoring sites (data source: RMP). 

2.6. HOW DOES SELENIUM CORRELATE WITH SALINITY AND FRESHWATER FLOWS? 

Freshwater inflows from the Delta and from local tributaries, which are strongly seasonal, 

influence salinity and selenium concentrations in the bay. Measured dissolved selenium 

concentrations by RMP long-term monitoring were plotted as a function of salinity for the 

period before July 1998 and after July 1998, and for low flow and high flow periods (Figure 

2-8 and Figure 2-9). The July 1998 cutoff represented periods before and after refinery load 

reductions. Transect sample data from Cutter and Cutter (2004) were also included for 

comparison. During low flow periods, dissolved selenium concentrations are low at salinity 

0 psu, and increase in the middle of estuary (salinity 5-20 psu), and then decrease again with 

increase of salinity (> 25 psu). During high flow periods, selenium concentrations were 

generally higher at low salinity and decreased with increase of salinity or remain relatively 

constant (e.g. Feb 1999, Feb 2000). The observed patterns in the RMP data set agree well 

with the patterns observed by Cutter and Cutter (2004). Similar patterns for both low and 

high flow were observed for sampling dates after July 1998: during low flows, a midestuarine peak is more evident while concentrations were relatively constant during high 

flow (Figure 2-9). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-12 Tetra Tech, Inc. 

Low Flow

Salinity

0 5 10 15 20 25 30 35

Dissolved Se (

"g/L)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

Sep 93 (RMP)

Aug 95 (RMP)

Jul 96 (RMP)

Jul 97 (RMP)

Jul 98 (RMP)

Sep 86 (Cutter) 

Nov 97 (Cutter) 

Oct 98 (Cutter) 

High Flow

Salinity

0 5 10 15 20 25 30 35

Dissolved Se (

"g/L)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

May 93 (RMP) 

Apr 95 (RMP) 

Apr 96 (RMP) 

Apr 97 (RMP) 

Apr 98 (RMP) 

Apr 86 (Cutter) 

Jun 98 (Cutter) 

Figure 2-8 Dissolved selenium concentrations along salinity gradient during low and high 

flow sampling periods by RMP and Cutter and Cutter (2004) before 19992

. 

 

2

 Low flow and high flow for the RMP data set were defined based on sampling months: July-November (low flow), 

January-June (high flow). Low flow and high flow definition for the Cutter data set were the classification reported 

in Doblin et al. (2006): NDOI < 1.5 x 1010l/d (low flow), NDOI > 8.5 x 1010l/d (high flow) with October 1998 

defined as low flow for simplification. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-13 

Low Flow

Salinity

0 5 10 15 20 25 30 35

Dissolved Se (

"g/L)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

Jul 99 (RMP) 

Jul 00 (RMP) 

Aug 01 (RMP) 

Nov 99 (Cutter) 

Oct 98 (Cutter)

High Flow

Salinity

0 5 10 15 20 25 30 35

Dissolved Se (

"g/L)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

Feb 99 (RMP) 

Apr 99 (RMP) 

Feb 00 (RMP) 

Feb 01 (RMP) 

Apr 99 (Cutter) 

Figure 2-9 Dissolved selenium concentrations as a function of salinity during low and high 

flow sampling periods by RMP and Cutter and Cutter (2004) from 1999 onwards. 

Selenium concentrations during the low flow period of a dry year (August 2001) indicated 

elevated concentrations in the Suisun Bay relative to the head of the estuary (Figure 2-10), 

suggesting local inputs of selenium. Maximum concentrations were observed in Suisun Bay 

near the Carquinez Strait. Concentrations in the San Pablo Bay remain relatively high 

compared to the head of estuary. Concentrations in Central Bay are lower. Salinity showed 

an increasing pattern from the head of estuary to the Golden Gate: from 0 to 10 psu in 

Suisun Bay, 25 psu in San Pablo Bay and above 30 psu in Central Bay. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-14 Tetra Tech, Inc. 

During a wet period of the same year (February 2001), dissolved selenium concentrations 

were similar among the head of the estuary, Suisun Bay and San Pablo Bay stations (Figure 

2-11). Lower concentrations were observed in the Central Bay. As expected, salinity during 

high flow is lower in Suisun and San Pablo Bay compared to the low flow period of the 

same year (August 2001). 

Figure 2-10 Spatial distribution of dissolved selenium and salinity during a sampling event in 

a dry period of a dry year (August 2001) by the RMP. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-15 

Figure 2-11 Spatial distribution of dissolved selenium and salinity during a sampling event in 

a wet period (February 2001) by the RMP. 

During high flow periods, dissolved selenium concentrations along several salinity transects 

sampled by Cutter and Cutter (2004) suggested either a dilution pattern by seawater or were 

relatively constant throughout the bay (Figure 2-12). Dissolved selenium concentrations in 

April 1986 and June 1998 decreased with increase of salinity with some removal along 

salinity gradient, possibly due to phytoplankton uptake. Dissolved selenium concentrations 

were lower in April 1999 compared to April 1986 and June 1998. With the implementation 

of improved waste water treatment in the refineries in 1998, the most significant change in 

water column selenium was with respect to selenite (Cutter and Cutter, 2004). For both 

April 1986 and June 1998, selenite concentrations indicated an increase in the mid-estuary. 

In contrast, selenite concentrations for April 1999 remained low throughout the Bay (Figure 

2-12). Selenate concentrations exhibited more conservative mixing behavior. Selenate 

concentrations in April 1999 were lower than in April 1986 and June 1998. Organic selenide 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-16 Tetra Tech, Inc. 

concentrations showed some variability along the salinity transect although concentrations 

for the three high flow periods are similar. 

Dissolved selenium concentrations during low flow sampling events indicated elevated 

concentrations in the mid-estuary (salinity 5-25 psu; Figure 2-13). Concentrations for 

October 1998 and November 1999 are generally lower than September 1986. However, total 

dissolved selenium concentrations are still slightly elevated in the mid-estuary. The most 

significant change is the observed decrease in selenite concentrations (Figure 2-13; Cutter 

and Cutter, 2004). Selenite concentrations for November 1999 are significantly lower than 

September 1986 and remain relatively constant throughout the Bay. Selenate concentrations 

were generally similar between the 1986 transect and October 1998 and November 1999 

transects. Selenate concentrations show slightly elevated concentrations between salinity 10-

20 psu. Organic selenide shows variable concentrations along the salinity transects. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-17 Total dissolved Se(

"g/L)

0.05

0.10

0.15

0.20

0.25

0.30

0.35

Apr 86

Jun 98

Apr 99

Selenite (

"g/L)

0.00

0.02

0.04

0.06

Selenate (

"g/L)

0.00

0.05

0.10

0.15

0.20

Salinity

0 5 10 15 20 25 30

Organic Selenide (

"g/L)

0.00

0.05

0.10

0.15

0.20

Figure 2-12 Transects of dissolved selenium, selenite, selenate, and organic selenide under 

high flow sampling periods (April 1986, June 1998, and April 1999; from Cutter 

and Cutter, 2004). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-18 Tetra Tech, Inc. Total dissolved Se(

"g/L)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

Sep 86

Oct 98

Nov 99

Selenite (

"g/L)

0.00

0.02

0.04

0.06

0.08

0.10

0.12

Selenate (

"g/L)

0.00

0.02

0.04

0.06

0.08

0.10

0.12

Salinity

0 5 10 15 20 25 30 35

Organic Selenide (

"g/L)

0.00

0.02

0.04

0.06

0.08

0.10

0.12

Figure 2-13 Transects of dissolved selenium, selenite, selenate and organic selenide under 

low flow sampling periods (September 1986, October 1998, and November 1999; 

from Cutter and Cutter, 2004). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-19 

2.7. WHAT WAS THE IMPACT OF REFINERY SELENIUM LOAD REDUCTIONS IN 1998? 

Cutter and Cutter (2004) sampled the effluents of five refineries in the North Bay for three 

time periods during 1999-2000. Average dissolved selenium concentrations in the effluents 

of the refineries was 16.4 μg/L, a 66% decrease from average concentrations of 45.8 μg/L 

during 1987-1988 (Cutter and Cutter, 2004). The resulting decreases in selenium 

concentrations in the bay water are both evident for the low flow and high flow period 

(Figure 2-14). 

Speciation of refinery effluent also changed dramatically after improved wastewater 

treatment. Average selenite concentrations at the five refineries changed from 28.2 !g/L 

(4.3 – 59.0 !g/L) from 1987 to 2.3 !g/L (0.3-5.0 !g/L) during the 1999-2000 (Cutter and 

Cutter, 2004). 

Dissolved selenium speciation in the bay water column is dominated by selenate, followed 

by organic selenide and selenite (Table 2-4). Selenite averages 15% of total dissolved 

selenium in a low flow sampling event in November 1999, compared with 22% during a 

high flow sampling event in April 1999. Selenate was 64% and 56% of total dissolved 

selenium for November 1999 and April 1999, respectively. The changes in wastewater 

treatment at the refineries resulted in changes in speciation in the bay water column, most 

noticeably during low flow (Figure 2-15). 

Table 2-4 

Speciation of dissolved selenium in Bay water (Cutter and Cutter, 2004) 

Selenite Selenate Organic selenide 

Total 

dissolved 

!g/L 

% of 

total μg/L 

% of 

total !g/L 

% of 

total !g/L 

Apr 99 (high 

flow) 

0.026 ± 

0.006 

22% 0.067 ± 

0.010 

56% 0.026 ± 

0.017 

22% 0.119 ± 0.024 

Nov 99 

(low flow) 

0.016 ± 

0.002 

15% 0.067 ± 

0.012 

64% 0.022 ± 

0.013 

21% 0.105 ± 0.019 

Apr 86 (high 

flow) 

0.031 ± 

0.010 

19% 0.099 ± 

0.094 

59% 0.035 ± 

0.055 

21% 0.167 ± 0.062 

Nov 86 

(low flow) 

0.057 ± 

0.029 

35% 0.058 ± 

0.023 

36% 0.047 ± 

0.024 

29% 0.162 ± 0.063 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-20 Tetra Tech, Inc. 

Low Flow

Salinity

0 5 10 15 20 25 30 35

Dissolved Se (

"g/L)

0.0

0.1

0.2

0.3

0.4

0.5

RMP (pre 07/98)

Cutter (pre 07/98)

RMP (post 07/98)

Cutter (post 07/98)

High Flow

Salinity

0 5 10 15 20 25 30 35

Dissolved Se (

"g/L)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

RMP (pre 07/98) 

Cutter (pre 07/98)

RMP (post 07/98)

Cutter (post 07/98)

Figure 2-14 Dissolved selenium concentrations under low and high flow before and after July 

1998 (data: RMP and Cutter and Cutter, 2004). The July 1998 cutoff date 

represents samples before and after improved wastewater treatment at the North 

Bay refineries. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-21 

April 1999 

(Dissolved Se: 0.12 "g/L)

Selenate

56%

Organic 

selenide

22%

Selenite

22%

November 1999 

(Dissolved Se: 0.11 "g/L)

Selenite

15% Organic 

selenide

21%

Selenate

64%

November 1986 

(Dissolved Se: 0.16 "g/L)

Selenate

36%

Organic 

selenide

29%

Selenite

35%

April 1986 

(Dissolved Se: 0.17 "g/L)

Selenate

60%

Organic 

selenide

21%

Selenite

19%

Figure 2-15 Speciation of dissolved selenium in Bay water column during different time 

periods (Data: Cutter and Cutter, 2004). 

2.8. HOW DOES SELENIUM CORRELATE WITH SUSPENDED SEDIMENTS AND CHLOROPHYLL-A? 

Doblin et al. (2006) reported the variation of total suspended particulate material (TSM),3

and selenium on particles in San Francisco Bay. Particulate selenium content, including 

speciation, was measured directly using material collected on 0.4 μm filters. Particulate 

selenium was reported as mass of selenium per unit volume of water or as mass of selenium 

per unit mass of particles. The latter measure normalizes for the effect of changing TSM in 

water samples at different locations and times. 

Particulate selenium concentrations along the salinity gradient generally track the pattern in 

TSM, and decrease along the salinity gradient during high flow (Figure 2-16). Chlorophyll-a 

concentrations show some occasional elevated values for the April 1986 transect. Selenium 

concentrations in particulate material are generally lower during high flow than low flow 

(Doblin et al., 2006), however, values as high as 1.6 !g/g were measured in the bay. 

 

3

 TSM: total suspended particulate material, was determined by directly filtering 2l of water (out of 5l of sample 

water collected) through 142mm diameter, 0.4 !m polycarbonate membranes that were pre-weighted. The filters 

were dried at 40 oC and weighed for TSM concentration (Doblin et al. 2006). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-22 Tetra Tech, Inc. 

During low flow, TSM concentrations also decrease slightly with an increase in salinity 

(Figure 2-17). TSM concentrations show occasional increases in the middle of estuary, 

possibly due to resuspension. Particulate selenium concentrations track the patterns in TSM 

(Doblin et al. 2006), most evidently for the September 1986 and November 1999 transects. 

Selenium concentrations in particulate material exceed values measured during high flow 

and also show some increase with increase of salinity (up to 2.2 !g/g). For the October 1998 

and November 1999 transects, chlorophyll-a concentrations are relatively constant 

throughout the bay with some increases in the Central Bay. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-23 TSM (mg/L)

0

10

20

30

40

50

60

70

80

Chlorophyll-a ("g/L)

0

2

4

6

8

10

12

14

16

Apr 86

June 98

Apr 99 

Particulate Se ("g/L)

0.000

0.005

0.010

0.015

0.020

0.025

Salinity

0 5 10 15 20 25 30

Se in particulate material ("g/g)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

Figure 2-16 Transects of TSM, chlorophyll-a, particulate selenium and selenium in particulate 

material under high flow (April 1986, June 1998 and April 1999; Doblin et al. 2006). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-24 Tetra Tech, Inc. TSM (mg/L)

0

10

20

30

40

50

60

70

Sep 86

Oct 98

Nov 99

Chlorophyll-a ("g/L)

0

1

2

3

4

5

6

7

8

Particulate Se ("g/L)

0.005

0.010

0.015

0.020

0.025

0.030

0.035

Salinity

0 5 10 15 20 25 30 35

Se in particulate material ("g/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 2-17 Transects of TSM, chlorophyll-a, particulate selenium and selenium in particulate 

material under low flow (September 1986, October 1998, and November 1999; 

Doblin et al. 2006). 

Particulate selenium concentrations, expressed as μg/l, vary less over time than TSM (Table 

2-5), although selenium content in suspended particles differs between low flow and high 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-25 

flow conditions. Low flow periods were found to have higher selenium content in suspended 

particles, most likely due to longer residence time and accumulation by phytoplankton and 

bacteria (Doblin et al. 2006). Selenium:Carbon ratios are higher during low flow. Selenium 

species on particulate material are dominated by organic selenide (45 ± 27%), followed by 

elemental selenium (35 ± 28%), and adsorbed selenite and selenate (20 ± 10%). The 

percentage of organic selenide is roughly similar during low and high flow periods. 

Speciation of particulate selenium along the five sampling transects are shown in Figure 

2-18 and Figure 2-19. 

Table 2-5 

Summary of particulate concentrations during low and high flow periods (Doblin et al. 2006). 

Low Flow High flow 

Oct. 1998 Nov. 1999 Nov. 1997 June 1998 April 1999 

TSM (mg/L) 19.1 ± 10.4 19.4 ± 8.8 13.1 ± 5.8 30.2 ± 22.0 31.2 ± 20.0 

Particulate Se (!g/L) 0.010 ± 0.002 0.013 ± 0.004 0.010 ± 0.003 0.010 ± 0.005 0.015 ± 0.006 

Se content in 

particulate (!g/g) 

0.70 ± 0.41 0.73 ± 0.25 0.87 ± 0.30 0.49 ± 0.31 -- 

Se: C ratio (X 10-6) 4.7 ± 3.1 5.9 ± 2.7 6.5 ± 2.5 4.1 ± 2.0 3.0 ± 1.0 

Particulate selenium concentrations are correlated with TSM (Figure 2-20). Particulate 

concentrations along the salinity gradient follow the pattern of TSM, which exhibit a linear 

decline along the salinity gradient due to mixing (Figure 2-21). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-26 Tetra Tech, Inc. Particulate Se* ("g/L)

0.000

0.004

0.008

0.012

0.016

0.020

0.024

0.028

June 98

Apr 99

Elemental Se ("g/L)

0.000

0.004

0.008

0.012

0.016

0.020

0.024

Selenite and selenate ("g/L)

0.000

0.004

0.008

0.012

Salinity

0 5 10 15 20 25 30

Organic Se ("g/L)

0.000

0.004

0.008

0.012

0.016

0.020

*include all adsorbed selenite and selenate, elemental and organic selenium 

Figure 2-18 Transects of total particulate selenium, particulate elemental selenium, 

particulate adsorbed selenite and selenate, and particulate organic selenium 

during high flow (June 1998 and April 1999; Doblin et al. 2006). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-27 Particulate Se* ("g/L)

0.004

0.008

0.012

0.016

0.020

0.024

Nov 97

Oct 98 

Nov 99

Elemental Se ("g/L)

0.000

0.004

0.008

0.012

0.016

Selenite and selenate ("g/L)

0.000

0.004

0.008

0.012

0.016

Salinity

0 5 10 15 20 25 30 35

Organic Se ("g/L)

0.000

0.004

0.008

0.012

0.016

*include all adsorbed selenite and selenate, elemental and organic selenium 

Figure 2-19 Transects of total particulate selenium, particulate elemental selenium, 

particulate adsorbed selenite and selenate, and particulate organic selenium 

during low flow (November 1997, October 1998 and November 1999; Doblin et al. 

2006). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-28 Tetra Tech, Inc. 

TSM (mg/L)

0 10 20 30 40 50 60 70

Particulate Se (

"g/L)

0.000

0.005

0.010

0.015

0.020

0.025

0.030

0.035

Low Flow

High Flow

Low Flow: Part. [Se] ("g/L) = 

3.76x10-4 TSM (mg/L) + 5.56 x 10-3

High Flow: Part. [Se] ("g/L) = 

2.13 x10-4 TSM (mg/L) + 4.44 x 10-3

R2=0.68

R2

=0.57

Figure 2-20 Correlation between particulate selenium and TSM under low and high flow (Data 

Source: G. Cutter, personal communication) 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-29 TSM (mg/L)

0

10

20

30

40

50

Chl a (

"g/L)

0.8

1.2

1.6

2.0

2.4

2.8

3.2

Particulate Se (

"g/L)

0.004

0.008

0.012

0.016

Salinity

0 5 10 15 20 25 30

Se in particulate material (

"g/g)

0.0

0.5

1.0

1.5

2.0

2.5

TSM = -0.80*Salinity + 29.68

r 2 =0.55

Figure 2-21 Concentrations of TSM, Chl a, and particulate selenium and selenium content in 

particulates for a low flow sampling event of Oct. 1998 (Doblin et al. 2006). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-30 Tetra Tech, Inc. 

2.9. WHAT IS THE DISTRIBUTION OF SELENIUM IN SEDIMENTS? 

Average selenium concentrations in bottom sediments of the North Bay show spatial 

variations at the RMP long-term monitoring sites although the total range of concentrations 

is not large (Figure 2-22). Sediment selenium concentrations are somewhat lower for the 

San Joaquin and Sacramento River stations near Mallard Island and the Central Bay stations 

(below 0.3 μg/g), whereas bottom sediments at sites in Grizzly Bay, San Pablo Bay and 

Napa River exhibit slightly elevated selenium concentrations (> 0.4 μg/g). 

Sediment concentrations from RMP random sampling indicate somewhat larger spatial 

variation than the long-term sites because these are single point concentrations and not 

averages. The majority of the sediment samples have concentrations between 0.2 – 0.3 μg/g, 

while concentrations as high as 1.7 μg/g were also observed (Figure 2-23). The average for 

the whole North Bay is 0.25 μg/g. Generally, the sediment selenium concentrations 

observed are well below the ecological guideline of 1.5 μg/g established by SFBWQCB 

(1992). Selenium concentrations in seston however can reach 1.5 !g/g occasionally, as 

observed by Doblin et al. (2006). 

Selenium concentrations in the bottom sediments are correlated to sediment grain size and 

organic carbon content. Sediment selenium concentrations were found to be highly related to 

percent fines < 0.00625 mm and percent total organic carbon (TOC) (R2

 = 0.78 and R2 = 

0.56; Figure 2-24; pooling all the data from long-term sites). Relationships between 

sediment selenium and percent fines and TOC are weaker for the random monitoring sites 

(Figure 2-25), however clear positive relationships are still observed. As illustrated in Figure 

2-24, sites with low sediment selenium concentrations correspond to low percent fines in the 

sediments and vice versa. Meseck (2002) observed a similar strong relationship between 

sediment selenium and organic carbon concentrations (R2 = 0.85). 

Average selenium concentrations for sediment cores, 5-15 cm deep, collected by G. Cutter’s 

research group range between 0.22-0.41 μg/g in the North Bay. Selenium in sediment cores 

is found to be dominated by elemental selenium (Meseck, 2002). Elemental selenium 

accounts for a median of 45% of the total selenium in the sediments across the sites, with 

selenite and selenate accounting for a median of 17%. The difference between total, 

elemental and selenite and selenate is the organic selenium. Selenium concentrations are 

generally uniform in the sediment cores, although some variations along the depth were 

observed (Cutter, unpublished data). 

Long term data from the RMP indicated that despite sediment selenium concentrations 

showing inter-annual or seasonal variations, concentrations are generally stable at the 

monitoring sites except in early 1990s (Figure 2-26 and Figure 2-27). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-31 

Figure 2-22 Mean selenium concentrations in sediments for the period of 1993-2005 (data 

source: RMP). 

Figure 2-23 Selenium concentrations in sediments with data from RMP random sampling 

sites (circles) and data collected by G. Cutter’s research group (squares). 

Numbers shown are individual values from the sampling. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-32 Tetra Tech, Inc. 

Fines < 0.0625 mm (%)

0 20 40 60 80 100

Se in Sediments (

"g/g)

0.0

0.1

0.2

0.3

0.4

0.5

0.6

R2 = 0.778

[Se] = 0.0537+ 0.0028 * % Fines

TOC (%)

0.0 0.5 1.0 1.5 2.0 2.5

Se in Sediments (

"g/g)

0.0

0.1

0.2

0.3

0.4

0.5

0.6

R2 = 0.564

[Se] = 0.0678+ 0.1561 * % TOC

Figure 2-24 Relationship between selenium concentrations in sediments and sediment 

characteristics at long-term sites (data source: RMP). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-33 

Fines < 0.0625 mm (%)

0 20 40 60 80 100

Se in Sediments (

"g/g)

0.0

0.1

0.2

0.3

0.4

0.5

0.6

TOC (%)

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0

Se in Sediments (

"g/g)

0.0

0.1

0.2

0.3

0.4

0.5

R2 = 0.385

[Se] = 0.0346+ 0.0028 * % Fines

R2 = 0.387

[Se] = 0.0253+ 0.1783 * % TOC

Figure 2-25 Relationship between selenium concentrations in sediments and sediment 

characteristics at random sampling sites (data source: RMP). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

2-34 Tetra Tech, Inc. 

Suisun Bay 

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/g

0.0

0.1

0.2

0.3

0.4

0.5

BF10 - Pacheco Creek

BF21 - Grizzly Bay

BF40 - Honker Bay

Delta

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/g

0.0

0.1

0.2

0.3

0.4

0.5

BG20 - Sacramento River (near Mallard Island)

BG30 - San Joaquin River (near Mallard Island)

Figure 2-26 Selenium concentrations in sediments as a function of time in stations near 

Mallard Island and in Suisun Bay (data source: RMP). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 2-35 

Central Bay 

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/g

0.0

0.2

0.4

0.6

0.8

1.0

BC11 -Yerba Buena Island

BC21 - Horseshoe Bay

BC31 - Richardson Bay

BC41-Point Isabel

BC60 - Red Rock

San Pablo Bay

1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 

"g/g

0.0

0.5

1.0

1.5

2.0

2.5

BD15 - Petaluma River

BD22 - San Pablo Bay

BD31 - Pinole Point

BD41 - Davis Point

BD50 - Napa River

Figure 2-27 Selenium concentrations in sediments as a function of time in San Pablo and 

Central Bay (data source: RMP). 

North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-1 

3. SOURCE CHARACTERIZATION

The goal of the source characterization is to quantify the various point and non-point sources 

that contribute selenium to North San Francisco Bay. The sources evaluated and their key 

features are listed below. 

! Atmospheric deposition – includes both dry and wet deposition to the bay water 

surface, and is usually considered as a small selenium source 

! Urban and non-urban runoff from local tributaries – includes both agricultural and 

urban stormwater runoff, and may be a significant source of selenium during the wet 

season 

! Delta inflow – which consists of flow from both the San Joaquin and Sacramento 

Rivers, is the major source of selenium to the bay 

! Municipal wastewater effluents – which generally have low concentrations of 

selenium 

! Petroleum refineries – which were the major sources of selenium (in the form of 

selenite) in the 1980’s and have decreased dramatically since 1999 because of 

improved wastewater treatment 

! Input from bay sediment – net sediment erosion, resuspension, diffusion, and 

dredging activities can be potential internal sources of selenium to the bay water 

column 

The magnitudes of the selenium loads associated with these sources are discussed in the 

subsequent sections. The dry season is a critical period for selenium bioaccumulation due to 

longer residence time, while wet season has larger flow volumes and can potentially 

contribute larger loads of selenium to the Bay. Therefore, for source categories with 

available flow information, both dry and wet season loads were calculated and compared. 

The relative contribution of loads may vary significantly between the dry and wet seasons. 

3.1. OVERVIEW OF PREVIOUS SOURCE ESTIMATES

Presser and Luoma (2006) estimated annual selenium loads from San Joaquin River at 

Vernalis to be 1,614 – 7,819 kg/yr with an average of 4,440 kg/yr for the years of 1986-

1998. Selenium loads from five agricultural sub-areas of western San Joaquin Valley were 

also estimated under different discharging scenarios by Presser and Luoma (2006). 

Of special relevance to any long-term evaluation of selenium trends in NSFB is the 

reduction of loads from refineries that occurred because of major improvements in 

wastewater treatment in the late 1990s. Selenium loadings from oil refineries ranged 

between 928-2,116 kg/yr during 1987 and 1988 (Cutter and San Diego-McGlone, 1990) and 

1,415-3,400 kg/yr during 1986-1992 (SFBRWQCB, 1993). Refinery discharge declined 

after July 1998 and selenium loads from five refineries were estimated to be 506 kg/yr in 

1999 (Presser and Luoma, 2006). 

Loads from the Sacramento River were calculated using an average concentration of 0.04 

!g/L as a conservative estimate and were estimated to be 247 kg/yr during a critically dry 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-2 Tetra Tech, Inc. 

year, 494 kg/yr for dry to critically dry year, 839 kg/yr for a median year and 1579 for a wet 

year (Presser and Luoma, 2006). 

Abu-Saba and Ogle (2005) developed a conceptual model for selenium in the bay and 

estimated various sources including: 

! Riverine fluxes via the Delta 

! North Bay refinery effluent discharges 

! Municipal wastewater, local tributaries, and urban runoff 

Loading rates from the Delta were estimated by multiplying net freshwater discharge from 

the Delta and a “river end member concentration” estimated by flow weighting 

concentrations at the Sacramento and San Joaquin Rivers, measured by Cutter and Cutter 

(2004). Estimated loading rates from the Delta by Abu-Saba and Ogle (2005) for the period 

of November 1997-November 1999 were 282-9,570 kg/yr for dissolved selenium, and 47-

686 kg/yr for particulate selenium. Oil refinery effluent discharge loading was calculated 

from effluent flow rates and selenium concentrations reported by Cutter and Cutter (2004) 

and ranged between 204-552 kg/yr. Urban and non-urban runoff and municipal wastewater 

loadings were estimated by some simple calculations (Abu-Saba and Ogle, 2005). Average 

annual runoff volume (both urban and non-urban) for the Bay Area is about 900 Mm3

(McKee et al., 2002) and annual discharge volume from wastewater is at a similar volume of 

866 Mm3 (Grovhoug et al., 2004). Selenium concentration in local runoff and municipal 

wastewater effluents were thought to range from 0.1-1 !g/L, therefore Abu-Saba and Ogle 

(2005) estimated loadings from each of these sources to range between 90-900 kg/yr with 

uncertainty. 

Cutter and Cutter (2004), based on data for five sampling events in 1997, 1998, and 1999, 

estimated riverine inputs from the Delta into the bay and inputs from refineries to the bay. 

Riverine inputs of dissolved selenium ranged between 773–26,195 g/day, with selenite 

inputs ranging between 110-2,446 g/day, selenate ranging between 497 – 17,121 g/day, and 

organic selenide ranging between 55 – 6,486 g/day. Refinery loadings were estimated to 

range between 1,515-6,328 g/day with selenite ranging between 379-2,414 g/day, selenate 

between 970-2,107 g/day and organic selenide ranging between 174-1,854 g/day. These data 

are described in daily load terms, as in the original work; the analysis below uses this 

information to compute annual loads. Because of the variability in daily flows and loads, the 

daily loads cannot be converted to annual loads simply by multiplying by 365. The 

computation needs assumptions or data on daily flows, as described for the loads 

calculations performed in the current study. 

Subsequent sections present load estimates for all significant non-point and point-sources. 

These analyses build on previous work and include consideration of the most recent data, 

especially for point sources, tributaries, and the Delta. 

3.2. DIRECT ATMOSPHERIC DEPOSITION

Atmospheric deposition of selenium occurs both as dry and wet forms. Selenium is emitted 

to the atmosphere naturally as volatile dimethyl selenide, or as selenium dioxide and 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-3 

elemental selenium from fossil fuel combustion (Cutter and Church, 1986). Deposition of 

selenium is part of a global cycle as gaseous selenium bound to particulate materials can be 

transported over long distances (EPA, 2002). Selenium in wet deposition consists of 

selenate, selenite, and elemental selenium. Rainwater samples from coastal California 

indicated that selenite is the major species in wet deposition for the region (Cutter, 1978). 

Dry deposition of selenium is mainly associated with fine particles (< 1 μm; Duce et al. 

1976; Sweet et al. 1998) and gaseous forms. 

Dry and wet deposition of selenium has not been measured in the San Francisco Bay and 

estimates were made using data from other studies. Atmospheric deposition of selenium is 

believed to represent only a small input to the water surface and the watershed in other 

studies (EPA, 2002). Reported concentrations of selenium in precipitation are 0.1 - 0.4 μg/L 

in urban areas (Mosher and Duce, 1989). Concentrations in precipitation measured in the 

Chesapeake Bay atmospheric deposition study are in the range of 0.07- 0.17 μg/L (EPA, 

1996). To estimate the significance of wet deposition, a simple calculation was done by 

extrapolating concentrations in the literature to the North Bay. Given an approximate annual 

rainfall of 450 mm/yr (McKee et al. 2003) and a water surface of 434 km2

 in the North Bay, 

direct wet deposition of selenium is in the range of 13.7 – 78.1 kg/yr (assuming selenium 

concentrations of 0.07-0.4 μg/L). Wet deposition of selenium is relatively bioavailable as 

selenite is the major species. 

Dry deposition was calculated from air-phase concentrations of selenium. Reported 

concentrations in the air exhibit a large variation from 0.3 to 2.4 ng/m3

. Concentrations 

measured in the Chesapeake Bay range from 1.4 – 1.8 ng/m3 (EPA, 1996). Different 

deposition velocity values have been used to estimate dry deposition fluxes for the Great 

Lakes (0.1 cm/s, Sweet et al. 1998) and the Chesapeake Bay (0.26 cm/s low, 0.72 cm/s high, 

EPA, 1996). Selenium in the air is mostly associated with fine particles; therefore a lower 

deposition velocity is expected. Based on a concentration range of 0.3 – 2.4 ng/m3

 and 

deposition velocities of 0.1 cm/s and 0.26 cm/s, estimated dry deposition is in the range of 

4.1 – 85.4 kg/yr. 

Due to the lack of site-specific measurements of selenium deposition in the bay, the simple 

extrapolations from other sites are associated with large uncertainties. Nonetheless, these 

estimates provide a reference for comparison with other sources discussed below. 

3.3. URBAN AND NON-URBAN STORMWATER RUNOFF FROM LOCAL TRIBUTARIES

Local tributaries, that is, streams that discharge directly into the North Bay and not into the 

Delta and/or the Sacramento and San Joaquin Rivers, can contribute elevated pollutant 

loadings due to the presence of urban and agricultural lands in their watersheds. Although 

local tributaries are only responsible for about 4% of the runoff to the bay, they were found 

to have a much higher sediment export rate than the Central Valley (~100 t/km2

 vs. ~14 

t/km2; McKee et al. 2003). With respect to selenium, relatively high selenium concentrations 

have been measured in tributaries around the Bay area, both in the wet and dry seasons. 

Total recoverable selenium concentrations observed in several watersheds in the South Bay 

during 2005-2006 ranged between 0.22–1.7 μg/L (median 0.38 μg/L) for the dry season and 

0.56-9 μg/L (median 3.6 μg/L) for the wet season (EOA, 2006). Selenium concentrations 

observed in five tributaries of the North Bay in the Surface Water Ambient Monitoring 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-4 Tetra Tech, Inc. 

Program (SWAMP) study in 2001-2002 suggested high concentrations of 0.18-3.39 μg/L 

(median 0.94 μg/L) during the dry season and 0.39- 3.14 μg/L (median 0.90 μg/L) during 

the wet season (SFBRWQCB, 2007a). Total selenium concentrations as high as 1.7 μg/L 

and 4 μg/L during wet and dry seasons of 2003-2004 were observed in the Petaluma River 

(SFBRWQCB, 2007b). Selenium observed in the tributaries is mostly in the dissolved form. 

Little information is available on the speciation or bioavailability of selenium from local 

tributaries. 

3.3.1 Review of Selenium Concentration Data in Tributaries 

Selenium concentrations in local tributaries monitored for the SWAMP4 study by the San 

Francisco Bay Regional Water Quality Control Board during 2001-2004 are listed in Table 

3-1. SWAMP monitoring programs targeted both clean and polluted areas of the watershed. 

Therefore, many sampling sites are located in urban or agricultural areas. For each 

watershed, a number of stations along the tributaries were monitored with 2-4 stations 

measured for selenium. Among the watersheds monitored, Wildcat Creek/San Pablo Creek 

and Suisun Creek were sampled during 2001-2002. Kirker Creek, Mt. Diablo Creek and 

Petaluma River were sampled during 2003-2004. Three sampling events based on 

hydrological conditions were targeted for each monitoring year including wet (January to 

March), spring (April to May) and dry (June to October). Samples were analyzed for both 

total and dissolved selenium with a minimum detection limit (MDL) of 0.1 !g/L 

(SFBRWQCB, 2007b). 

Relatively high total selenium concentrations were found for all seasons (Figure 3-1). The 

highest total selenium concentration was observed at an urban influenced site during the dry 

season (8.1 !g/L at KIR115-Kirker Creek Apartments). Average total selenium 

concentrations for the most downstream sites of all the North Bay watersheds are 1.57 !g/L 

for wet season, 1.03 !g/L for spring season and 1.95 !g/L for dry season (Table 3-1). The 

downstream sites were considered to be more representative of the watershed condition by 

integrating all the land uses and therefore only downstream sites were used in the 

calculations of loads to the bay. Note that the 8.1 !g/L value did not factor in the average 

because it was not the most downstream value on Kirker Creek. Due to the limited number 

of samples, for some sampling events, higher dissolved than total selenium concentrations 

were reported. For the purpose of the load calculations, estimates were made using total 

selenium concentrations. 

The Bay Area Stormwater Management Agencies Association (BASMAA) has also sampled 

selenium concentrations from some local tributaries around the North Bay during 1988-1995 

(BASMAA, 1996). The sampling sites for the North Bay are mostly located in the Alameda 

County with two sites located in the Contra Costa County. Selenium concentrations reported 

by BASMAA are lower than values reported in subsequent SWAMP studies (Figure 3-2). 

Variable detection limits are noted for the BASMAA dataset, with higher detection limit (at 

0.2 !g/L) and higher percentage of non-detects in early period of the study (1988-1992). 

Lower detection limits (generally below 0.05 !g/L) were used for latter period of the study 

and most of the samples were above detection limits. Measured concentrations seem to vary 

 

4

 Surface Water Ambient Monitoring Program, a statewide program to assess water quality conditions in surface 

water bodies. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-5 

with detection limits. Land uses for watersheds surrounding the sampling locations include 

open forests, industrial, residential and commercial. Median concentrations are 0.40 !g/L 

during dry weather (n = 7) and 0.33 !g/L for storm event sampling (n = 28). By land use, 

median concentrations are 0.29 !g/L, 0.35 !g/L and 0.30 !g/L for residential, open and 

industrial sites. For some of the BASMAA sampling sties, monitoring was continued for 

multiple years. 

Table 3-1 

Total and dissolved selenium concentrations observed at the SWAMP sites during wet, spring and 

dry seasons. Data for the most downstream location on each stream are shown. Data are 

individual values. 

Creek Site Season Year 

Total 

!g/L 

Dissolved 

!g/L 

Wet 2003-2004 1.26 1.21 

Spring 2003-2004 1.30 1.00 

Kirker Creek KIR020 

Dry 2003-2004 2.50 2.00 

Mt. Diablo Creek MTD010 Wet 2003-2004 2.00 2.00 

Spring 2003-2004 0.40 0.30 

PET010 Wet 2003-2004 1.30 1.40 

Spring 2003-2004 0.20 0.50 

Wet 2003-2004 1.70 1.80 

Spring 2003-2004 1.30 1.50 

Petaluma River 

PET310 

Dry 2003-2004 4.00 3.90 

San Pablo Creek 206SPA020 Spring 2001-2002 2.74 2.57 

Dry 2001-2002 1.60 1.53 

Suisun Creek 207SUI010 Spring 2001-2002 0.90 1.04 

Dry 2001-2002 0.32 0.17 

Wildcat Creek 206WIL020 Spring 2001-2002 0.39 1.41 

Dry 2001-2002 1.33 1.11 

Wet 1.57 1.60 

Spring 1.03 1.19 

Average 

Dry 1.95 1.74 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-6 Tetra Tech, Inc. 

(a) 

(b) 

(c) 

Figure 3-1 Total selenium concentrations in the wet (a), spring (b) and dry (c) seasons in 

local tributaries of the North Bay, sampled in the SWAMP program. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-7 

Three methods were used to estimate selenium loads from local tributaries based on two 

different methods of estimating runoff from local watersheds and selenium concentration 

data from SWAMP and BASMAA study. 

Date

1/1/90 1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04

Total selenium (

"g/L)

0.01

0.1

1

10

100

BASMMA

BASMMA (Below DL)

SWAMP 

Detection Limit

Figure 3-2 Total selenium concentrations in tributaries of NSFB sampled during 1990–1996 

and 2000–2003 (Source: BASMAA, 1996; SWAMP data from SFBRWQCB, 

2007a, b). 

3.3.2 Method 1: Modeled Estimates of Runoff in Tributaries and Using SWAMP 

Concentrations 

Total annual runoff from local watersheds has been computed using a simple model by 

Davis et al. (2000). The predicted runoff compared reasonably well to the limited observed 

data (r2 = 0.62-0.89). We used the Davis et al. (2000) runoff estimates and concentrations 

measured in the SWAMP study to estimate loadings from each of the watersheds 

surrounding the North Bay (Table 3-2). A map of these local watersheds (hydrological 

areas) is shown in Figure 3-3. The average annual loadings of total selenium from local 

tributaries to the North Bay were estimated to be 913.9 kg/yr, with the Napa River and 

Fairfield watersheds being the largest sources. Higher selenium loads from these watersheds 

are most likely due to larger watershed areas and high annual runoff. 

Runoff in the Bay area shows large year-to-year variation. Therefore, loadings from local 

tributaries are expected to vary greatly with climate conditions. Watersheds in the Bay area 

show inter-annual variation with coefficient of variation (CV) ranging from 0.65 to 1.01 

(McKee et al. 2002). The 10th and 90th percentiles of rainfall in the Bay area for the record 

period of 1961-1990 were summarized previously in Davis et al. (2000). Assuming constant 

runoff concentrations under different climate conditions, 10th and 90th percentiles of the 

selenium loadings were calculated to be 522.8 kg/yr and 1367.2 kg/yr, respectively. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

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Figure 3-3 Hydrological areas surrounding NSFB. Source: San Francisco Estuary Institute 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

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Table 3-2 

Runoff and selenium loadings from local watersheds to the North Bay 

Hydrologic 

Area 

Total Annual 

Runoff (Mm3

/yr)1 

SWAMP 

Sampling 

Station 

Mean total selenium 

concentrations (μg/L)2 Total selenium 

loadings (kg/yr) 

San Rafael 56 1.57 87.6 

Berkeley 25 1.57 39.1 

San FranciscoBayside 8.8 1.57 13.8 

Novato 47 1.57 73.6 

Petaluma River 60 Petaluma River 1.5 90 

Sonoma Creek 68 1.57 106.4 

Napa River 180 1.57 281.7 

Pinole 35 Wildcat, San 

Pablo 

1.57 54.8 

Fairfield 129 Suisun Creek 0.9 116.1 

Concord3 106 Mt. Diablo Creek 0.4 42.4 

Concord4 6.7 Kirker Creek 1.26 8.4 

Total 721.5 913.9 

1Davis et al. (2000) 

2SFBRWQCB (2007a, b), 1.57 μg/L is the wet season mean concentration for all the most downstream sites in the North Bay 

watersheds sampled (n = 4). 

3Subunits of the Concord hydrologic area (ID: 220731, 220732, and 220733) 

4A subunit of the Concord hydrologic area (ID: 220734) 

3.3.3 Method 2: Measured Flow in Selected Tributaries and Using SWAMP 

Concentrations 

The second method is based on USGS flow data in the Bay area to estimate selenium 

loading from local tributaries. Daily flow records from several USGS gaging stations for 

some major North Bay tributaries are available for different periods (Table 3-3 and Table 

3-4). Long-term average monthly flow at these stations suggested that the majority of the 

flow is discharged during the wet season (defined as Oct 1st to Apr 30th). Flow during the 

dry season (defined as May 1st to September 30th) comprises only a very small portion of the 

wet season flow (0.2 – 3.5%) except Walnut Creek (13.1%) and Pinole Creek (5.8%). Many 

of the stations have relatively short flow records and contain values prior to 1990. Flow 

records at these stations may not fully reflect the current hydrologic regime of the 

watershed. 

The long-term average monthly flow and the seasonal concentrations measured by the 

SWAMP study were used to estimate long-term average selenium loadings at these gaging 

stations for each month. Loadings were estimated by multiplying flow and concentrations of 

the same river. For tributaries without observed selenium concentrations, the overall average 

concentration for all the North Bay downstream sites was used. The estimated loadings are 

shown in Figure 3-4. Following the pattern in flow volumes, total selenium is mainly 

delivered to the bay in wet season. Dry season loadings average 0.2 – 3.0% of wet season 

loadings for 6 of the 8 stations (Table 3-5). An annual areal loading was also estimated for 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-10 Tetra Tech, Inc. 

each of the tributary, based on total annual selenium loading and the drainage area. The 

estimated areal loadings were used to scale up loading estimates of the entire hydrological 

area (e.g. Novato Creek at Novato was scaled up for the whole Novato hydrological area). 

For hydrological areas without data (e.g., San Rafael), areal loading from a nearby 

watershed was used. 

Estimated total selenium loadings for the North Bay area by hydrological area are 

summarized in Table 3-6 and Figure 3-5. Total selenium loadings from local tributaries 

using the method above were estimated to be 1,511 kg/yr, higher than the estimates from 

Method 1. A large portion of the loadings were estimated to originate from Napa and 

Sonoma hydrological areas. Due to the lack of selenium concentrations for these two areas 

in the SWAMP dataset, an overall mean concentration of the whole North Bay tributaries 

were used and therefore the estimates are subject to large uncertainty. Flow records for the 

Napa and Sonoma rivers also suggested higher runoff from these two areas compared to the 

rest of the North Bay (337 and 422 mm/yr for Napa and Sonoma, compared to ~200 mm/yr 

for the other tributaries), contributing to the high estimated selenium loadings. 

Table 3-3 

Major USGS gaging stations in North Bay watersheds (Source: USGS) 

Station Name 

Station 

Number Latitude Longitude 

Drainage 

Area 

(mi2) Flow Period 

Novato Creek at Novato 11459500 38 06’28’’ 122 34’44’’ 17.6 1946-current 

San Antonia Creek Nr 

Petaluma 

11459300 38 10’57’’ 122 36’55’’ 28.9 1975-1981 

Petaluma River at Petaluma 11459000 38 15’40’’ 122 39’35’’ 30.9 1948-1963 

Sonoma Creek at Agua 

Caliente 

11458500 38 19’24’’ 122 29’36’’ 58.4 1955-current 

Napa River nr. Napa 11458000 38 22’06’’ 122 18’08’’ 218 1929-current 

Wildcat Creek at Richmond 11181400 37 57’41’’ 122 21’33’’ 8.69 1964-1975 

Walnut Creek at Concord 11183600 37 56’43’’ 122 02’55’’ 85.2 1968-1992 

Pinole Creek at Pinole 11182100 37 58'21'' 122 14'43'' 10 1938-1977 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-11 

Table 3-4 

Long-term average monthly flow (in cfs) at USGS gaging stations in North Bay watersheds for the 

record period (Source: http://waterdata.usgs.gov/nwis) 

USGS114

59500 

(Novato 

Creek at 

Novato) 

USGS114

59300 

(San 

Antonia 

Creek nr. 

Petaluma) 

USGS1145

9000 

(Petaluma 

River at 

Petaluma) 

USGS11

458500 

(Sonoma 

Creek at 

Agua 

Caliente) 

USGS11

458000 

(Napa 

River nr. 

Napa) 

USGS1118

1400 

(Wildcat 

Creek at 

Richmond) 

USGS1118

3600 

(Walnut 

Creek at 

Concord) 

USGS11

182100 

(Pinole 

Creek at 

Pinole) 

Jan 46.79 82.47 58.75 244.85 695.67 22.06 112.55 11.97 

Feb 46.56 70.48 64.11 216.32 710.04 11.78 132.28 11.23 

Mar 26.92 30.69 28.38 124.3 486.98 10.09 108.15 7.94 

Apr 10.50 5.35 14.00 70.74 198.32 6.20 52.33 5.44 

May 1.65 0.72 0.49 16.44 59.26 0.89 19.13 1.23 

Jun 0.82 0.17 0.03 5.12 18.46 0.61 12.32 0.59 

Jul 0.66 0 0 1.81 5.72 0.27 9.52 0.29 

Aug 0 0 0 0.98 2.51 0.01 8.27 0.16 

Sep 0 0 0 0.77 1.95 0.03 8.77 0.13 

Oct 0.69 0.01 0.96 6.28 10.26 1.01 14.33 0.53 

Nov 3.01 0.63 2.24 24.26 68.85 4.06 32.47 0.53 

Dec 16.81 13.84 37.69 159.32 335.17 7.73 52.05 3.81 

Dry 

season 

(cfs) 

3.9 0.9 0.5 25.1 87.9 1.8 58.0 2.4 

Wet 

season 

(cfs) 

151.3 203.5 206.1 846.1 2505.3 62.9 504.2 41.5 

Dry as wet 

% 

2.59 0.45 0.25 2.97 3.51 2.88 11.51 5.79 

Runoff 

(mm/yr) 

249.8 200.3 189.4 422.5 336.9 211.0 186.9 124.2 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-12 Tetra Tech, Inc. 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Loading (kg) 0

1

2

3

4

5

6

USGS11459500 (Novato Creek at Novato) 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Loading (kg)

0

2

4

6

8

10

USGS11459300 (San Antonio Creek nr. Petaluma)

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Loading (kg)

0

2

4

6

8

10

USGS11459000 (Petaluma River at Petaluma) 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Loading (kg)

0

5

10

15

20

25

30

USGS11458500 (Sonoma Creek at Agua Caliente) 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Loading (kg)

0

20

40

60

80

100

USGS11456000 (Napa River nr. Napa) 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Loading (kg) 0.0

0.5

1.0

1.5

2.0

2.5

3.0

USGS11181400 (Wildcat Creek at Richmond) 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Loading (kg)

0

2

4

6

8

10

12

14

16

USGS11183600 (Walnut Creek at Concord) 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Loading (kg) 0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

USGS11182100 (Pinole Creek at Pinole) 

Figure 3-4 Estimated long-term average monthly selenium loadings at gaging stations of 

local tributaries. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-13 Novato Creek at Novato San Antonio Creek nr. Petaluma Petaluma River at Petaluma Sonoma Creek at Agua Cal. Napa River nr. Napa Wildcat Creek at Richmond Walnut Creek at Concord Pinole Creek at Pinole Loading (kg)

0

50

100

150

200

250

300

350

Dry season

Wet season

Figure 3-5 Comparison of dry and wet season selenium loadings for tributaries in the 

North Bay. 

Seasonal selenium concentrations from the SWAMP data set were also used in conjunction 

with the daily flow at Napa River near Napa to estimate daily selenium loadings for 1991-

2007. The estimated daily loadings were accumulated to estimate seasonal loading for all the 

years. As a result of variations in hydrological conditions, total selenium loading in Napa 

River near Napa vary largely across the years (Figure 3-6). Total selenium loadings can be 

greater than 700 kg/yr during wet year (1995) versus less than 100 kg/yr during a dry year 

(1994). The dry and wet year notation was based on the classification system for San 

Joaquin and Sacramento River by the Department of Water Resources 

(http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST). Wet and above normal years are 

classified as wet years. Dry, below normal and critically dry years are classified as dry 

years. Dry season is defined as May 1st to September 30th. The wet season is defined as 

October 1st to April 30th. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-14 Tetra Tech, Inc. 

Table 3-5 

Estimated long-term average monthly total selenium loadings (kg/month) to the gaging stations. 

USGS114

59500 

(Novato 

Creek at 

Novato) 

USGS114

59300 

(San 

Antonia 

Creek nr. 

Petaluma) 

USGS114

59000 

(Petaluma 

River at 

Petaluma) 

USGS114

58500 

(Sonoma 

Creek at 

Agua 

Caliente) 

USGS114

58000 

(Napa 

River nr. 

Napa) 

USGS11181

400 

(Wildcat 

Creek at 

Richmond) 

USGS1118

3600 

(Walnut 

Creek at 

Concord) 

USGS11

182100 

(Pinole 

Creek at 

Pinole) 

Jan 5.37 7.87 7.33 28.13 79.92 2.53 12.93 1.38 

Feb 5.35 6.73 8.00 24.85 81.57 1.35 15.20 1.29 

Mar 3.09 2.93 3.54 14.28 55.94 1.16 12.42 0.91 

Apr 0.80 0.08 1.34 5.36 15.04 0.18 3.97 0.09 

May 0.13 0.01 0.05 1.25 4.49 0.03 1.45 0.41 

Jun 0.12 0.02 0.01 0.73 2.64 0.06 1.76 0.08 

Jul 0.09 0.00 0.00 0.26 0.82 0.03 1.36 0.04 

Aug 0.07 0.00 0.00 0.14 0.36 0.00 1.18 0.02 

Sep 0.04 0.00 0.00 0.11 0.28 0.00 1.26 0.02 

Oct 0.10 0.00 0.28 0.90 1.47 0.10 2.05 0.08 

Nov 0.35 0.06 0.28 2.79 7.91 0.47 3.73 0.06 

Dec 1.93 1.32 4.70 18.30 38.50 0.89 5.98 0.44 

Annual 

total 

(kg/yr) 

17.4 19.0 25.5 97.1 288.9 6.8 63.3 4.8 

Areal 

loading 

(kg/mi2) 

0.99 0.66 0.83 1.66 1.33 0.78 0.74 0.48 

Dry 

season 

(kg) 

0.45 0.04 0.06 2.49 8.59 0.12 7.01 0.26 

Wet 

season 

(kg) 

16.99 18.99 25.47 94.61 280.35 6.68 56.28 4.56 

Dry as 

wet % 

2.65 0.21 0.22 2.63 3.06 1.73 12.46 5.71 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-15 

Table 3-6 

Estimated annual total selenium loadings for the hydrological areas in the North Bay. 

Hydrological Areas 

Drainage Area 

(Mm2) Area (mi2) 

Loadings 

(kg/yr) Dry (kg) Wet (kg) 

Novato 183.98 71.03 70.4 1.8 68.6 

San Rafael 157.66 60.87 60.3 1.6 58.8 

San Francisco Bayside 28.76 11.11 11.0 0.3 10.7 

Berkeley 87.59 33.82 26.4 0.4 26.0 

Pinole 152.43 58.85 28.4 1.5 26.9 

Concord 648.27 250.30 185.9 20.6 165.3 

Fairfield 877.89 338.96 251.8 27.9 223.9 

Napa 937.89 362.12 480.0 14.3 465.7 

Sonoma 429.77 165.93 275.9 7.1 268.6 

Petaluma 377.64 145.81 120.5 0.3 120.2 

Total 1510.6 75.8 1434.8 

Total Selenium Loading in Napa River nr. Napa

1991 (dry)1992 (dry)

1993 (wet)

1994 (dry)

1995 (wet)1996 (wet)1997 (wet)1998 (wet)1999 (wet)2000 (wet)

2001 (dry)2002 (dry)

2003 (wet)

2004 (dry)

2005 (wet)2006 (wet)

2007 (dry)

Loading (kg)

0

100

200

300

400

500

600

700

800

Dry Season

Wet Season

Average load 

method 3

Figure 3-6 Dry and wet season selenium loadings by water year at Napa River near Napa. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-16 Tetra Tech, Inc. 

3.3.4 Method 3: Modeled Estimates of Runoff with BASMAA and SWAMP concentrations 

for Calculating Land Use-Specific Loads 

To estimate stormwater loads of selenium from urban areas, a previously published 

approach was used (Davis et al., 2000). This approach has been used in estimating urban 

loads of PCBs in the San Francisco Bay PCB TMDL (KLI, 2002; SFBRWQCB, 2007c). 

Loads are estimated from five broad categories of land use (agricultural, open space, 

industrial, commercial and residential) based on estimated runoff from each land use type 

and land-use specific concentrations. Urban lands are defined as a group and include 

industrial, commercial and residential lands. 

Land uses for each hydrological area were previously determined by Davis et al. (2000; 

Table 3-7). Best estimates of runoff coefficient for each land use type were also derived by 

Davis et al. (2000; Table 3-7). KLI (2002) sampled stormwater concentrations of PCBs and 

Hg in the Bay area, however selenium was not sampled in this effort. For selenium, land use 

specific concentrations were derived from BASMAA (1996) and SWAMP study 

(SFBRWQCB 2007a, b). BASMAA (1996) sampling stations include sites that are mostly 

residential and sites that are more dominated by forests/open area. Therefore, overall mean 

concentrations for sites with dominant land use of residential, open, and industrial were 

calculated. Concentrations for agricultural land use were assumed to be the same as open 

area. When concentrations were reported as below detection limits, half of the detection 

limit was used. Mean selenium concentrations from the BASMAA study are similar across 

land uses (Table 3-8). Stations from the SWAMP study are generally located in the urban 

areas, with Suisun Creek stations located in agriculture-dominated areas. Therefore values 

from Suisun Creek were used to derive concentrations for the agricultural areas. Due to the 

differences in concentrations reported in two programs, values from BASMAA were used as 

lower bound of concentrations from local tributaries, while SWAMP data were used as an 

upper bound (Table 3-8). Overall, Method 3 results in a somewhat lower estimate of loads 

than the prior two methods, with loads ranging from 354.3 to 838.7 kg/yr. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-17 

Table 3-7 

Summary of drainage areas and land use for each hydrologic area of NSFB 

(Davis et al. 2000; KLI, 2002) 

Hydrological areas 

(HA) 

Drainage Area 

(Mm2

) 

Residential 

(%) 

Commercial 

(%) 

Industrial 

(%) 

Agricultural 

(%) 

Open 

(%) Rainfall 

Berkeley 87.59 57 16 18 0 9 21 

Concord 

Concord (220731) 283.96 25 10 7 9 49 17 

Concord (220732) 212.54 44 4 1 1 50 21 

Concord (220733) 121.72 39 6 7 0 47 21 

Concord (220734) 30.05 46 9 26 6 12 17 

Fairfield 

Fairfield (220721) 226.20 12 1 5 12 70 25 

Fairfield (220722) 131.69 0 0 0 13 86 29 

Fairfield 

(220723/26) 

410.25 8 6 2 48 36 21 

Fairfield 

(220724/25) 

109.76 0 0 0 1 99 19 

Napa River 937.89 10 3 1 24 62 31 

Novato 183.98 23 7 1 13 56 33 

Petaluma River 377.64 14 1 2 35 48 27 

Pinole 152.43 33 5 12 0 49 23 

San Francisco 

Bayside 

28.76 58 39 2 0 1 21 

San Rafael 157.66 50 8 1 0 41 39 

Sonoma Creek 429.77 8 1 1 36 54 29 

Table 3-8 

Land use specific runoff coefficient and mean selenium concentrations 

Residential Commercial Industrial Agricultural Open Source 

Runoff coefficient (best 

estimate) 

0.35 0.9 0.9 0.1 0.25 Davis et al. 

(2000) 

Selenium concentration (low 

end) μg1-1 0.36 0.58 0.58 0.50 0.50 BASMAA 

(1996) 

Selenium concentration (high 

end) μg1-1 1.55 1.55 1.55 0.85 0.85 SWAMP 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-18 Tetra Tech, Inc. 

Table 3-9 

Estimated total selenium loadings (kg/yr) by land use from hydrological areas draining NSFB by 

land uses 

Hydrological 

area 

Residential Commercial Industrial Agricultural Open Total (kg/yr) 

Berkeley 14.4 10.4 11.7 0.0 0.9 37.5 

Concord 60.7 30.5 24.6 1.1 31.6 148.5 

Fairfield 18.8 20.3 16.1 11.5 67.0 133.8 

Napa River 40.1 30.9 10.3 15.1 97.3 193.6 

Novato 19.2 15.1 2.2 1.7 18.4 56.5 

Petaluma River 19.7 3.6 7.2 7.7 26.4 64.6 

Pinole 15.9 6.2 14.9 0.0 9.3 46.3 

San Francisco 

Bayside 4.8 8.3 0.4 0.0 0.0 13.6 

San Rafael 42.4 17.4 2.2 0.0 13.6 75.6 

Sonoma Creek 13.7 4.4 4.4 9.7 36.3 68.6 

Total (kg/yr)-

SWAMP 

249.8 147.2 94.1 46.8 300.8 838.7 

Lower bound 

estimates (kg/yr) - 

BASMAA 

58.4 54.8 35.0 27.7 178.4 354.3 

Urban loads1

(kg/yr) 

 491.1 (148.2 

lower bound) 

1

Urban loads are the sum of residential, commercial, and industrial land uses. 

Estimated stormwater runoff from urban areas surrounding the NSFB is 316.8 Mm3/yr, 

about 44% of the total runoff. Estimated loads from urban areas based on the SWAMP 

concentrations are at 491.1 kg/yr, about 58.6% of loads from all land use types. Because a 

lower concentration in the agricultural areas compared to other urban land uses was used 

(0.85 !g/L versus 1.55 !g/L), estimated total selenium loads from all land uses are slightly 

lower than load estimates in Method 1. Also note for Napa River watershed, because a large 

portion of the land uses is agricultural, using a lower selenium concentration for agricultural 

area resulted in lower estimates of selenium loads for the whole hydrological area (193.6 

kg/yr versus 281.7 kg/yr in method 1). Estimated loads from urban areas based on the 

BASMAA concentrations are at 148.2 kg/yr, about 43% of loads from all land use areas. 

3.3.5 Tributary Load Summary 

Three, somewhat overlapping methods were used to compute tributary loads. Using the 

SWAMP selenium data from the tributaries, loads were computed using flow from different 

sources: modeled annual flows from a recent study (Davis et al., 2000) and measured flows 

from USGS gage stations. The modeled flows were used because of the limited availability 

of measured flow data. Loads from urban and non-urban areas were also estimated based on 

modeled runoff and land use specific concentrations derived from BASMAA and SWAMP 

concentration data. Loads from urban areas generally account for 43% or 59% of total loads 

from tributaries, depending on the concentrations used. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-19 

Driven in large part by relatively high concentrations in the tributaries in both the wet and 

dry seasons, the average annual loads from the tributaries can be up to 1,511 kg/year 

depending on the methods used for the load estimation. Much of this load (greater than 

95%) is delivered to the bay in the wet months, consistent with the timing of flows, as 

shown in the calculation using the USGS gage data. The largest single sources of loads are 

the Napa River, Sonoma Creek, and the Concord hydrological area. Note that selenium is a 

naturally occurring trace element, and is found even in runoff from open areas. A 

significant portion of these loadings is associated with natural sources. 

On average, the tributary concentration data are generally higher than Sacramento River 

concentrations, which are more typical of a low background in the region. Although the 

high average concentrations are not driven by one or two measurements, it is nonetheless 

clear that the load estimates above are based on a limited amount of data. Furthermore, the 

SWAMP and BASMAA concentrations differ: lower mean concentrations were observed in 

BASMAA dataset. However, the range of concentrations (0.06 – 0.90 !g/L after 1/1/1992) 

indicates that higher concentrations than 0.1 !g/L were not uncommon in local tributaries. 

Given the underlying data limitations and uncertainty in flows, and the year-to-year 

variability, estimated loads from tributaries can be as low as 354 kg/yr using BASMAA 

concentrations and modeled runoff, 834 or 914 kg/yr based on SWAMP concentrations and 

modeled runoff, and 1511 kg/yr based on SWAMP concentrations and measured flow. For 

the purpose of this analysis, we go forward with the relatively wide range of 354-834 kg/yr, 

with about half originating in urban runoff. 

Particulate selenium loads from local tributaries were estimated based on previous estimates 

of total suspended sediment (TSS) loads for different hydrological areas in the Bay Area by 

Davis et al. (2000). Estimates of TSS loads by Davis et al. (2000) were based on SIMPLE 

model estimates of runoff multiplied by available TSS concentrations. Data on particulate 

selenium concentrations are limited from local tributaries. Therefore selenium 

concentrations in particulates measured for the Sacramento River (0. 62 ± 0.21 !g/g; n =5) 

by Doblin et al. (2006) were used in the calculation. TSS loads estimated by Davis et al. 

(2000) are 1.91x108

 kg/yr for the North Bay watersheds. With a particulate selenium 

concentration of 0.62 !g/g, estimated particulate selenium loads from local tributaries are 

118.2 kg/yr. 

3.4. INPUTS FROM SAN JOAQUIN AND SACRAMENTO RIVERS VIA THE DELTA

Although selenium inputs from the Central Valley via the Delta are expected to be a 

significant source to the North Bay, accurately estimating these loads is difficult due to the 

role of the Delta and tidal influences from the bay. Loads upstream of the Delta can be 

estimated from measurements at Freeport (on the Sacramento River) and at Vernalis (on the 

San Joaquin River) (Figure 3-7). Inflow originating from the San Joaquin River has high 

selenium concentrations due to inputs from agricultural drainage (0.68 ± 0.20μg/L dissolved 

selenium) and the Sacramento River has much lower selenium concentrations (0.07 ± 0.02 

μg/L) (Cutter and Cutter, 2004). However, flows in the San Joaquin River at Vernalis are 

usually much smaller: 10 to 15 percent of inflow from Sacramento River at Freeport (Figure 

3-7). Therefore, on an annual basis loads from both rivers to the Delta are significant. 

However, selenium processes in the Delta are not well characterized. Besides the normal 

processes of settling and mixing, a large portion of the water in the Delta is also exported for 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-20 Tetra Tech, Inc. 

agricultural and urban uses in other parts of California. The relative contribution of the 

Sacramento and San Joaquin Rivers to the overall export from the Delta to the North Bay 

changes with tidal cycles and season. The contribution from the San Joaquin River can 

potentially increase during drier months of September to November (Figure 3-7 and Presser 

and Luoma, 2006). In this section, available flow and concentration data are used to make 

the best possible estimates of the selenium load contributions of the Delta and the two major 

rivers to the North Bay. 

10/1/04 12/1/04 2/1/05 4/1/05 6/1/05 8/1/05 10/1/05 

Flow (cfs)

0

2e+4

4e+4

6e+4

8e+4

1e+5

Sacramento + 

Yolo Bypass

San Joaquin River

Exports

Delta Outflow 

10/1/05 12/1/05 2/1/06 4/1/06 6/1/06 8/1/06 10/1/06 

Flow (cfs)

0

1e+5

2e+5

3e+5

4e+5

5e+5

Sacramento + 

Yolo Bypass

San Joaquin River

Exports

Delta Outflow 

Figure 3-7 Flow from Sacramento River, San Joaquin River, compared to Delta exports 

(diversions of Central Valley Project, State Water Project, Contra Costa Water 

District Diversions and North Bay Aqueduct) and outflow to Delta for a dry year 

(water year 2004) and a wet year (water year 2005) (Data source: IEP). 

Selenium data have been collected as part of the RMP just above Mallard Island at the BG20 

(Sacramento River) and BG30 (San Joaquin River) stations. Observed total selenium 

concentrations at these stations (0.15 and 0.18 μg/L, respectively) are more representative of 

Delta concentrations than of the individual rivers. The concentrations are higher than in the 

Sacramento River at Freeport (0.07 μg/l, noted above), and substantially lower than in the 

San Joaquin River at Vernalis (0.68 μg/l), indicating mixing between the two sources, and 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-21 

possibly tidal influences from the bay during low flow periods. Concentrations observed at 

BG20 and BG30 also correlate well (R2 = 0.59) possibly due to mixing of common sources. 

In a separate study, selenium concentrations were found to decrease by 60-80% during 

transport from the San Joaquin River at Vernalis into the estuary at Antioch (Cutter 

unpublished data; Meseck and Cutter, 2006). 

Different methods have been used in previous studies to calculate riverine inputs of various 

pollutants through the Delta to the Bay. Davis et al. (2000) used average concentrations at 

two RMP monitoring stations in the Delta (BG20 and BG30) to estimate loads of different 

pollutants from Central Valley to the Bay. Leatherbarrow et al. (2005a) and McKee et al. 

(2006) used continuous monitoring data of SSC at Mallard Island to estimate loads of 

sediments, mercury and organics to the Bay. With respect to selenium, Presser and Luoma 

(2006) estimated loads from the two rivers (Sacramento River at Freeport and San Joaquin 

River at Vernalis) separately to estimate selenium inputs to the Bay. Cutter and Cutter 

(2004) and Abu-Saba and Ogle (2005) used the approach of flow weighting concentrations 

from the two rivers to calculate a riverine concentration and multiplied this by the net Delta 

outflow to estimate loads from the Delta to the bay. Meseck (2002) applied a “Delta removal 

constant” to the riverine loads to take into account the possible selenium sink in the Delta in 

her modeling analysis. 

Here we used three different approaches to estimate the selenium loadings from Central 

Valley via Delta to the bay based on the available data. The first approach is the simple 

approach similar to Davis et al. (2000), which uses average concentration of two RMP 

stations in the Delta and multiplies it by the net Delta outflow. The second approach uses 

selenium loadings from the Sacramento and the San Joaquin Rivers separately based on data 

from Cutter and Cutter (2004) and applies a “Delta removal constant” similar to Meseck 

(2002) to account for the possible selenium loss in the Delta. The third approach is 

independent of the prior two, in which the loadings from Central Valley to the bay were 

estimated as the difference between inputs from the two rivers minus the export through 

aqueducts. The third method can be used to estimate the relative selenium load contribution 

of the two rivers to the bay. 

3.4.1 Method 1. Loadings Based on the RMP data and Tidally Corrected Delta Outflows 

For the first approach, tidally corrected outflow data from the Delta were obtained from the 

Interagency Ecological Program (IEP) (http://www.iep.ca.gov/dayflow/index.html). 

Outflows from the Delta show large year-to-year variations (Figure 3-8). Concentrations 

measured at BG20 and BG30 also show year- to-year variations, and no correlation with the 

Delta outflow and no clear pattern in wet versus dry seasons were observed. 

Daily selenium loadings were estimated by multiplying daily Delta outflow with the average 

concentrations at BG20 and BG30 of the dry and wet seasons of each year. The estimated 

daily loadings were summed to compute annual loadings. Estimated annual loadings are 

highly variable (by a factor of 12) depending on the volume of outflow from the Delta 

(Table 3-10 and Figure 3-9). Water year 1998 was an exceptionally wet year. Excluding 

1998, estimated annual loadings vary by a factor 6 among the years. Loadings from the 

Delta are more significant in the wet season than the dry season (Figure 3-9). An average 

load of 3,962 kg/year from the Delta to the North Bay was estimated (1994-2006). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-22 Tetra Tech, Inc. 

There is some limited evidence that the Delta load may be higher than computed using this 

method and using BG-20 and BG-30 concentrations from the RMP. Selenium 

concentrations have been measured in the outflow from the Delta (Mallard Island) during 

the storm events of 2005 - 2006 (0.46 ± 0.13 μg/L; L. McKee, personal communication), 

and separate from the RMP data. Higher concentrations observed at Mallard Island during 

storm events suggest potential of higher loadings during these periods. Total recoverable 

selenium concentrations during storm events are a function of daily flow, suggesting a 

dilution behavior (Figure 3-10). Nonetheless, the relationship was used to estimate total 

selenium loadings during high flow. The result indicates a potential of 16-56% 

underestimate of total selenium loadings using BG20 and BG30 concentrations (e.g. 1,059 

kg/yr vs. 1,590 kg/yr for a dry year 2001 and 5,078 kg/yr vs. 21,000 kg/yr for wet year 

2006). However, the storm selenium concentration data are very limited at this point, and the 

more complete RMP data record is recommended for calculation of long term Delta loads. 

Leatherbarrow et al. (2005a) used concentrations measured at Mallard Island to estimate 

loads of PCB (polychlorinated biphenyls), PAH (polycyclic aromatic hydrocarbons), OC 

(Organochlorine) pesticides, and Hg from the Delta to the Bay. Contaminant loads were 

estimated based on relationships between contaminants and SSC, and the estimated 

sediment loads using available flow information and continuous SSC concentrations 

measured at Mallard Island. In quantifying loads of sediment from Mallard Island to the 

Bay, both the advective and dispersive loads were estimated. The relative contributions of 

the advective and dispersive load were estimated using point velocity and concentration 

measured during water year 1994 and 1996 (McKee et al. 2006). During a wet period (mean 

discharge = 2116 m3

/s), dispersive point-load averages about 11% of the advective point 

load. Due to the tidal influence at Mallard Island, dispersive loads (most commonly 

landward) can be a significant portion of total load during low flow period. Estimated 

dispersive load for a low flow period (April 15, 1994-June 4, 1994) was 49% of advective 

point load at surface and 52% at mid-depth (McKee et al. 2006). Overall the dispersive loads 

of sediment were estimated to be 0.24 Mt/yr or 20% of the total loads for the 9 year period 

of 1995-2003. There is limited applicability of this method for total selenium loadings 

because most selenium (at least two-thirds, and often more) is in the dissolved form. 

However, the sediment load estimates are used to estimate particulate loads of selenium 

from the Delta to the bay. The calculation appears at the end of this section. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-23 

1992 1994 1996 1998 2000 2002 2004 2006 2008 

Flow (cms)

0

2000

4000

6000

8000

10000

12000

14000

16000

18000

Figure 3-8 Daily Delta outflow for water years 1992-2006 (Data source: IEP) 1994 (dry) 1995 (wet) 1996 (wet) 1997 (wet) 1998 (wet) 1999 (wet) 2000 (wet) 2001 (dry) 2002 (dry) 2003 (wet) 2004 (dry) 2005 (wet) 2006 (wet) Total Selenium Loading (kg/yr)

0

2000

4000

6000

8000

10000

12000

14000

Dry Season

Wet Season

Figure 3-9 Estimated wet and dry season total selenium loadings from Delta to the Bay by 

water year. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-24 Tetra Tech, Inc. 

Table 3-10 

Estimated total and dissolved selenium loadings from the Delta 

Year 

Delta outflow 

m3

Loadings 

(total) 

kg/yr 

Loadings 

(dissolved) 

kg/yr 

1994 7.42E+09 1,831 1,647 

1995 4.11E+10 6,859 6,159 

1996 2.56E+10 4,355 2,818 

1997 4.23E+10 5,252 4,399 

1998 5.36E+10 11,752 9,736 

1999 2.78E+10 3,572 3,292 

2000 2.24E+10 2,666 1,495 

2001 8.56E+09 1,110 882 

2002 1.13E+10 1,276 814 

2003 1.73E+10 2,037 1,797 

2004 1.84E+10 1,485 2,259 

2005 1.90E+10 4,228 4,337 

2006 5.40E+10 5,078 3,970 

Average 2.68E+10 3,962 3,354 

y = 9.6971x-0.263

R2 = 0.8211

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.00E+00 1.00E+05 2.00E+05 3.00E+05 4.00E+05

Flow (cfs)

S e (ug/l)

Figure 3-10 Relationship between total selenium concentrations and flow at Mallard Island 

(Data source: L. McKee). 

3.4.2 Method 2: Loadings Based on Riverine Loads to the Delta, and Assumption of Delta 

Removal Constant 

Dissolved selenium concentrations in the Sacramento River at Freeport sampled by Cutter 

and Cutter (2004) on biweekly or monthly bases indicated relatively small changes from 

1984 to 2000 (Figure 3-11). Dissolved selenium concentrations in the Sacramento River (at 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-25 

Freeport) range between 0.01-0.13 !g/L, with an average of 0.07 ± 0.02 !g/L for the period 

of 1999-2000. Dissolved selenium concentrations in the San Joaquin River at Vernalis may 

be 10 times higher. Concentrations for the San Joaquin River at Vernalis range between 0.14 

- 4.69 !g/L for entire period of record. A significant decrease in selenium concentrations 

was observed for 1999-2000 compared to the 1980s sampling. Mean dissolved selenium 

concentration for the period of 1999-2000 is 0.68 ± 0.20 !g/L. 

Concentrations during 1999-2000 show some variations both in the Sacramento and San 

Joaquin River (Figure 3-12). For the Sacramento River, higher concentrations were observed 

for the months between April to July. For the San Joaquin River, no clear seasonal pattern 

was observed. Concentrations in relation to flow are shown in Figure 3-13. For the 

Sacramento River, no clear relationship between flow and concentrations was observed for 

the recent years, consistent with findings in Cutter and Cutter (2004). Cutter and Cutter 

(2004) reported a poor correlation between river discharge and any dissolved selenium 

forms for the Sacramento River. For San Joaquin River, a negative relationship between 

concentrations and flow was observed, possibly due to the dilution of selenium discharge by 

natural flow. 

For the Sacramento River, due to the weak relationship between dissolved selenium 

concentration and flow, monthly concentrations were used to calculate the daily loadings. 

For the San Joaquin River, the flow and concentration relationship derived was used to 

estimate daily concentrations based on flow. The daily loading was then estimated based on 

daily flow and estimated daily concentration. Daily flow for the Sacramento River at 

Freeport (USGS 11447650) and the San Joaquin River at Vernalis (USGS 11302500) were 

obtained from the USGS website (http://waterdata.usgs.gov/nwis/dv/?referred_module=sw). 

The estimated daily loadings were summed to calculate the seasonal loadings. The wet 

season was defined as Oct 1st to Apr. 30th and the dry season was defined as May 1st to Sep 

30th (Tetra Tech, 2006). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-26 Tetra Tech, Inc. 

Sacramento River at Freeport

Date

1/1/84 1/1/86 1/1/88 1/1/90 1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 

Dissolved Selenium (

"g/L)

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

San Joaquin River at Vernalis 

Date

1/1/84 1/1/86 1/1/88 1/1/90 1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 

Dissolved Selenium (

"g/L)

0

1

2

3

4

5

Figure 3-11 Dissolved selenium concentrations in Sacramento River at Freeport and San 

Joaquin River at Vernalis during 1984-1988 and 1998-2000, sampled by Cutter and 

Cutter (2004). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-27 

Sacramento River at Freeport 

(subset of data)

Date

10/1/98 2/1/99 6/1/99 10/1/99 2/1/00 6/1/00 

Dissolved Selenium ("g/L)

0.04

0.05

0.06

0.07

0.08

0.09

0.10

0.11

0.12

Date vs Se Total ug/l 

San Joaquin River at Vernalis 

(subset of data)

Date

10/1/98 2/1/99 6/1/99 10/1/99 2/1/00 6/1/00 

Dissolved Selenium ("g/L)

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

1.1

Figure 3-12 Dissolved selenium concentrations at Sacramento River at Freeport and San 

Joaquin River at Vernalis during 1998-2000, sampled by Cutter and Cutter (2004). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-28 Tetra Tech, Inc. 

Sacramento River at Freeport

y = -3E-08x + 0.0752

R2

 = 0.0012

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0 10000 20000 30000 40000 50000 60000 70000 80000

Flow (cfs)

Dissolved Se ("g/L)

San Joaquin River at Vernalis

y = 8.46x-0.3057

R2 = 0.45

0.00

0.20

0.40

0.60

0.80

1.00

1.20

0 2000 4000 6000 8000 10000 12000 14000 16000 18000

Flow (cfs)

Dissolved Se ("g/L)

Figure 3-13 Relationship between dissolved selenium concentrations and daily flow for 

Sacramento River at Freeport and San Joaquin River at Vernalis for the period of 

1998-2000 (data source: Cutter and Cutter, 2004). Note that dissolved selenium 

concentrations show no correlation with flow rate for the Sacramento River. 

The estimated annual dissolved selenium loadings range between 703 – 2,693 kg/yr for the 

Sacramento River at Freeport and 867 – 4,710 kg/yr for the San Joaquin River at Vernalis. 

Estimated dry season loadings range between 234 – 1,074 kg/yr for the Sacramento River (at 

Freeport) and 261-2,097 kg/yr for the San Joaquin River (at Vernalis). Estimated wet season 

loadings range between 417- 1,748 kg/yr for Sacramento River and 552- 3,048 kg/yr for San 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-29 

Joaquin River. On average, dry season loadings are generally lower and represent 58% and 

60% of the wet season loadings for the Sacramento River (at Freeport) and the San Joaquin 

River (at Vernalis), with only one exception (San Joaquin River in 1995). 

Estimated annual dissolved selenium loadings vary with water years (Figure 3-14). Annual 

loadings can be as high as 2,600-2,700 kg/yr during wet years for the Sacramento River (at 

Freeport) and approximately 750 – 1,000 kg/yr during dry years. Annual loadings for the 

San Joaquin River (at Vernalis) also vary with hydrological conditions. Annual loadings can 

be greater than 4,000 kg/yr during wet years and less than 1,000 kg/yr during dry years. 

Overall, average dissolved selenium loadings are higher for the San Joaquin River (at 

Vernalis) than the Sacramento River (at Freeport) (2,380 kg/yr vs. 1,634 kg/yr during 1990-

2007). 

Total selenium concentrations were also measured by the SWAMP program at San Joaquin 

River at Vernalis (Airport Way) on a weekly basis by Central Valley Water Quality Control 

Board(http://www.waterboards.ca.gov/centralvalley/water_issues/water_quality_studies/surf

ace_water_ambient_monitoring/). The observed total selenium concentrations were higher 

during the 1980s and early 1990s compared to recent years (Figure 3-15). Dissolved 

selenium concentrations for the same period measured by Cutter and Cutter (2004) agree 

relatively well with the total selenium concentrations observed in the SWAMP study but 

were slightly lower (Figure 3-16). This is to be expected as dissolved selenium usually 

accounts for 80-95% of total selenium measured. The observed decreases of selenium 

concentration at Vernalis most likely resulted from the implementation of the Grassland 

Bypass Project in 1996, which has led to a 60% decrease in selenium loads from the 

Grassland Drainage Area from pre-project conditions (www.sfei.org/grassland/reports/). 

However, the magnitudes of the decrease were more significant just below the Grassland 

Bypass Project area (at Crows Landing). With transport downstream, the change in 

concentration was smaller, likely due to inflow from other tributaries (Figure 3-17). 

Concentrations are generally lower during the wet years (1996 and 2006) and a negative 

correlation between flow and concentrations was noted (Figure 3-18). The weekly total 

selenium concentrations measured by SWAMP were extrapolated to daily concentrations for 

the week and multiplied by daily flow to estimate daily total selenium loadings for the San 

Joaquin River. Estimated daily loadings were summed up to calculate seasonal and annual 

loadings (Figure 3-19). Estimated annual loadings for total selenium based on SWAMP 

dataset are generally comparable to although slightly higher than loadings of dissolved 

selenium estimated from the Cutter and Cutter (2004) data (Figure 3-20) except for water 

years 1998 and 2006, when larger discrepancies between the two methods were observed. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-30 Tetra Tech, Inc. 

Sacramento River at Freeport

1991 (dry)1992 (dry)

1993 (wet)

1994 (dry)

1995 (wet)1996 (wet)1997 (wet)1998 (wet)1999 (wet)2000 (wet)

2001 (dry)2002 (dry)

2003 (wet)

2004 (dry)

2005 (wet)2006 (wet)

2007 (dry)

Dissolved Se loadings (Kg)

0

500

1000

1500

2000

2500

3000

Dry season

Wet season

San Joaquin River at Vernalis

1991 (dry)1992 (dry)

1993 (wet)

1994 (dry)

1995 (wet)1996 (wet)1997 (wet)1998 (wet)1999 (wet)2000 (wet)

2001 (dry)2002 (dry)2003 (dry)2004 (dry)

2005 (wet)2006 (wet)

2007 (dry)

Dissolved Se loadings (Kg)

0

1000

2000

3000

4000

5000

Dry season

Wet season

Figure 3-14 Dry and wet season dissolved selenium loadings at Sacramento River at Freeport 

and San Joaquin River at Vernalis for 1991-2007. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-31 

San Joaquin River at Vernalis 

Date

1/1/84 1/1/86 1/1/88 1/1/90 1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 1/1/08 

Selenium (

"g/L)

0.0

2.0

4.0

6.0

8.0

10.0

Total Se (SWAMP) 

Dissolved Se (Cutter and Cutter, 2004)

Figure 3-15 Dissolved selenium concentrations sampled by Cutter and Cutter (2004) at San 

Joaquin River at Vernalis compared to total selenium concentrations observed in 

SWAMP study. 

San Joaquin River at Vernalis (subset of data above)

Date

10/1/98 2/1/99 6/1/99 10/1/99 2/1/00 6/1/00 

Selenium (

"g/L)

0.0

0.5

1.0

1.5

2.0

2.5

Total Se (SWAMP) 

Dissolved Se (Cutter and Cutter, 2004)

Figure 3-16 A subset of dissolved selenium concentrations sampled by Cutter and Cutter 

(2004) compared to total selenium concentrations from SWAMP. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-32 Tetra Tech, Inc. 

San Joaquin River at Crows Landing 

1/1/84 1/1/86 1/1/88 1/1/90 1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 1/1/08 

Selenium (

"g/L)

0

2

4

6

8

10

12

14

16

18

20

22

24

San Joaquin River at Vernalis 

Date

1/1/84 1/1/86 1/1/88 1/1/90 1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 1/1/08 

Selenium (

"g/L)

0

2

4

6

8

10

12

14

16

18

20

22

24

San Joaquin River at Patterson

1/1/84 1/1/86 1/1/88 1/1/90 1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 1/1/08 

Selenium (

"g/L)

0

2

4

6

8

10

12

14

16

18

20

22

24

Figure 3-17 Total selenium concentrations along main stem of San Joaquin River at Crows 

Landing (below grassland bypass project), at Patterson, and at Vernalis (Data 

Source: Central Valley RWQCB) 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-33 

y = 17.44x-0.377

R2 = 0.27

0

0.5

1

1.5

2

2.5

3

3.5

0 10000 20000 30000 40000 50000

Flow (cfs)

Total Se ("g/L)

Figure 3-18 Relationship between total selenium and flow at San Joaquin River at Vernalis 

(Data source: Central Valley Regional Water Quality Control Board SWAMP study 

and USGS). 

San Joaquin River at Vernalis (SWAMP)

1996 (wet)1997 (wet)1998 (wet)1999 (wet)2000 (wet)

2001 (dry)2002 (dry)2003 (dry)2004 (dry)

2005 (wet)2006 (wet)

Total Se loadings (Kg)

0

2000

4000

6000

8000

Dry season

Wet season

Figure 3-19 Dry and wet season total selenium loadings at San Joaquin River at Vernalis, 

estimated from concentrations from SWAMP study. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-34 Tetra Tech, Inc. 1991 (dry) 1992 (dry) 1993 (wet) 1994 (dry) 1995 (wet) 1996 (wet) 1997 (wet) 1998 (wet) 1999 (wet) 2000 (wet) 2001 (dry) 2002 (dry) 2003 (dry) 2004 (dry) 2005 (wet) 2006 (wet) 2007 (dry) Selenium loadings (kg)

0

2000

4000

6000

8000

Dry season (SWAMP)

Wet season (SWAMP)

Dry (Cutter & Cutter (2004))

Wet (Cutter & Cutter (2004))

* SWAMP data represent total selenium and data from Cutter and Cutter (2004) 

represent dissolved selenium

Figure 3-20 Comparison of selenium loadings at San Joaquin River at Vernalis estimated 

from Cutter and Cutter (2004) data and data from SWAMP study. 

Biogeochemical processes in the Delta could potentially serve as a mechanism to remove 

high selenium concentrations originated from the San Joaquin River. As shown in Figure 

3-21, during two low flow sampling events, dissolved selenium concentrations were high in 

close proximity to the San Joaquin River and decrease through the Delta. Dissolved 

selenium concentrations at the head of estuary were much lower than the concentrations 

observed close to the river. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-35 

Figure 3-21 Dissolved selenium concentrations at various locations of the Delta and North 

Bay in October 1998 (NDOI = 4.27x1010 L/d) and November 1999 (NDOI = 1.07x1010

L/d) sampling (Cutter and Cutter, 2004). 

Meseck (2002) fitted sine wave equations to selenium data from the Sacramento and San 

Joaquin Rivers, and used the fitted functions to estimate riverine loads. Based on samples 

collected during fall 1998 and summer 2000, selenium concentrations at Vernalis are 

reduced by 60-80% after being transported through Delta into the estuary at Antioch. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-36 Tetra Tech, Inc. 

Therefore, Meseck (2002) applied a “Delta removal” constant of 60% to predict actual input 

of selenium at Antioch from the San Joaquin River. 

Using the approach described by Meseck (2002), if a removal constant of 60% was applied 

to the San Joaquin River inputs, resulting dissolved selenium loading based on estimated 

river loadings varies between 1,005- 4,578 kg/yr (Figure 3-22). The estimated loadings were 

compared to Method 1, above, for each year. The percent absolute difference between the 

two methods for each individual year ranges between 6.3-51.9% except for 1998, an 

unusually wet year. For 1998, previous method estimated a significantly higher loading of 

9,736 kg/yr compared to 4,578 kg/yr using the second approach. 

For this method, an average load of 2,493 kg/yr for 1991-2007 from Delta to the Bay was 

estimated. Average load at Sacramento River at Freeport is 1,577 kg/yr. Average load at San 

Joaquin River at Vernalis is 2,289 kg/yr. 

Loadings from Delta

1991 (dry)1992 (dry)

1993 (wet)

1994 (dry)

1995 (wet)1996 (wet)1997 (wet)1998 (wet)1999 (wet)2000 (wet)

2001 (dry)2002 (dry)

2003 (wet)

2004 (dry)

2005 (wet)2006 (wet)

2007 (dry)

Dissolved Se loadings (Kg)

0

1000

2000

3000

4000

5000

Dry season

Wet season

Figure 3-22 Estimated selenium loadings from the Delta to the bay as a result of inputs from 

Sacramento River at Freeport and San Joaquin River at Vernalis, assuming a 

“Delta Removal Constant” of 0.60. 

Both Methods 1 and 2 have limitations in estimating selenium loads from the Delta. The 

previous method based on RMP monitoring dataset at BG20 and BG30, has the potential 

issue of overestimating loads during dry season due to tidal influence. The second method, 

through applying a “Delta removal constant” cannot account for the varying impacts of 

Delta on the selenium inputs to the Bay. As discussed next, an alternative is to consider 

outflow data from the Delta through aqueducts, and the estimated selenium concentrations in 

these outflows, to evaluate the net loads delivered to bay. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-37 

3.4.3 Method 3. Calculate selenium loadings to bay by accounting for export through 

aqueducts 

Average export of water from Delta through aqueducts was 6.82 ± 0.90 × 109 m3/yr during 

1994-2006. Flow at pumping plants is mostly dominated by Sacramento River water. During 

some periods, San Joaquin River water can also dominate. Assuming equal volume mixing 

of the two rivers, the selenium concentration in pumping plants is approximately 0.4 !g/L 

(0.07 !g/L at Sacramento River at Freeport and 0.68 !g/L at San Joaquin River at Vernalis). 

Assuming a concentration range of 0.1 !g/L (low end, when Sacramento River dominates) 

to 0.4 !g/L, the export of selenium through aqueducts is likely to range between 700- 2,700 

kg/yr. For critically dry years during 1986-1998, Presser and Luoma (2006) estimated an 

aqueduct export of 1,557 kg/6 months, a value comparable to the higher end of this 

estimated range. 

A more detailed computation of the riverine contribution to exports can also be performed. 

The contribution of the Sacramento and San Joaquin Rivers or other relatively minor inflows 

to State Water Project (SWP) pumping plant at Banks was previously modeled using a 

hydrodynamic model (Delta Simulation Model, Version 2, or DSM2) by the California 

Department of Water Resources (DWR). Results from DSM2 simulations indicated that 

during dry years or in the dry season, Sacramento River is the major source of flow at Banks 

pumping plant (DWR 2004; Figure 3-23). During wet years or in wet seasons, San Joaquin 

River can contribute a large portion of the flow. Results from these DSM2 fingerprinting 

simulations were used to estimate selenium concentrations at the pumping plant based on 

concentrations from the Sacramento and San Joaquin Rivers, and selenium loads exported 

through aqueducts. 

Volume Fingerprint at Banks Pumping Plant (SWP)

0%

20%

40%

60%

80%

100%

J-90J-91J-92J-93J-94J-95J-96J-97J-98J-99J-00J-01J-02J-03J-04

Percent of Water by Source

Other Ag Central Ag East Mtz Sac SJR

Figure 3-23 Long-term percentage contribution of flows at the Banks Pumping Plant (data 

provided by DWR; Tetra Tech, 2006). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-38 Tetra Tech, Inc. 

Concentrations at pumping plants were estimated as: 

 Cexp = (Qsac * Csac + Qsjr * Csjr) / Qexp (1) 

Where Cexp is daily concentration in the aqueduct, Qsac is export flow originating from the 

Sacramento River, Csac is daily selenium concentration at the Sacramento River at Freeport 

(estimated from monthly concentrations from Cutter and Cutter, 2004), Qsjr is export flow 

originating from the San Joaquin River, Csjr is daily selenium concentration at the San 

Joaquin River (estimated previously based on relationship between flow and concentrations 

using data from Cutter and Cutter, 2004), and Qexp is total flow through the aqueducts 

(includes the Central Valley Project, State Water Project, Contra Costa Water District, and 

North Bay Aqueduct). We made the assumption that the flow composition from the two 

rivers at Banks pumping plant is the same as the other pumping plants. 

Estimated concentrations in the aqueduct were multiplied by the export flow (obtained from 

DAYFLOW) to calculate selenium loads lost from the Delta through aqueducts. The 

seasonal loads were calculated by adding the daily loads. Estimated loads exported through 

aqueducts for the years between 1993-2003 range between 883 – 1,985 kg/yr (Figure 3-24). 

Dry season loads are comparable to wet season loads, largely because aqueduct exports are 

less variable than riverine flows over the course of the year. For a few years dry season 

loads exceed wet season loads (e.g. 1995, 1998). The range of annual exported loads using 

this approach is similar to what was determined previously, i.e., 700-2,700 kg/yr. 

Contribution of loads to aqueducts from the two rivers was also estimated based on modeled 

contribution of flow from the two rivers and concentrations at each river. The results 

indicated that the San Joaquin River is the major, but not the only, source of selenium to the 

aqueducts. Estimated selenium loads from the Sacramento River are significantly lower 

ranging between 193- 486 kg/yr for 1993-2003, compared to 600-1,780 kg/yr from the San 

Joaquin River. Although the Sacramento River dominates in terms of flow in the aqueducts 

most of the time, due to higher selenium concentrations, San Joaquin River contributes more 

selenium loads to aqueducts. 

Assuming other losses are small, loads from the Delta to the bay can be estimated as the 

difference between total loads from the two rivers and the export through aqueducts. 

Estimated loads from the Delta to the bay show large variations among the years (1993-

2003; Figure 3-25). Loads for dry years are approximately 1,000 kg/yr (e.g. 1994, 2001). 

Loads in wet years can be much larger (nearly 6,000 kg/yr in 1998). Contribution of loads 

from the two rivers to the Delta outflow was estimated as the difference between loads from 

the rivers and the export through aqueducts. Estimated loads from the two rivers to the Delta 

are generally comparable. Annual selenium loads from the San Joaquin River are normally 

below 1,000 kg/yr. However during wet years larger loads can originate from the San 

Joaquin River (exceeding loads from the Sacramento River). Dry season loads from San 

Joaquin River to the Bay normally range between 200-300 kg. However for a few wet years, 

dry season loads from the San Joaquin River are approximately 1,000 kg. An average 

dissolved selenium load of 2,696 kg/yr from the Delta to the bay for 1993-2003 was 

estimated using this method. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-39 

Observed selenium concentrations at Delta-Mendota Canal near Tracy Headworks (Milepost 

3.50) obtained from U.S. Bureau of Reclamation are higher than the estimated selenium 

concentrations in the aqueducts using the flow-weighted method described above (Figure 3-

23). Note the observed concentration at Delta-Mendota Canal has a high detection limit of 

0.4 !g/L. Estimated loads in Delta-Mendota Canal near Tracy Headworks by Bureau of 

Reclamation are at 792-1279 kg/yr for water year 2002-2006. Given approximately equal 

export volume in the CVP and SWP, exported loads in aqueducts can range between 1580-

2560 kg/yr. The range of loads is at the higher end of our estimates of 700- 2700 kg/yr. 

Selenium concentration data from the State Water Project (SWP) aqueducts have been 

reported using relatively high detection limits. The SWP publishes data from monthly grab 

samples at the Banks Pumping Plant (http://wwwomwq.water.ca.gov/GrabSamplePage

/GrabSampleTables/index.cfm) with a detection limit of 0.001 mg/L or 1 !g/L, with most 

samples being below detection limits. These data were not used in the calculations. 

3.4.4 Summary of Delta load calculations 

Although loads from the Central Valley are a major source of selenium to NSFB, the 

estimation of these loads is not straightforward because of tidal influences at the edge of the 

Delta and the bay, and because of complexities caused by mixing and water export from the 

Delta. The load estimates are more difficult because of the limited data in the Delta and the 

aqueducts. 

Our approach in this section was to apply three different methods to compute loads, and to 

compare these values. Note that for the second and third methods, data was available to 

compute only the dissolved selenium loads and not the total load. 

! The first approach used average concentration of two RMP stations in the Delta and 

multiplies it by the net tidally corrected Delta outflow. This resulted in an annual 

average load estimate of 3,962 kg/yr of total selenium from the Delta to the NSFB 

(1994-2006). 

! The second approach used selenium loadings from the Sacramento and the San 

Joaquin Rivers separately based on data from Cutter and Cutter (2004) and applied a 

“Delta removal constant” similar to Meseck (2002) to account for the possible 

selenium loss in the Delta. These concentrations were reported only as dissolved 

selenium, not total selenium. This resulted in an annual average load estimate of 

2,493 kg/yr of dissolved selenium (1993-2003). 

! The third approach was independent of the prior two: the loadings from Central 

Valley to the bay were estimated as the difference between inputs from the two 

rivers minus the export through aqueducts, and assuming minimal loss processes in 

the Delta. This resulted in an annual average load estimate of 2,696 kg/yr of 

dissolved selenium (1993 to 2003). 

Given the simplifications and assumptions employed in these load calculations, and given 

that some loads are in terms of dissolved selenium, the range of annual averages is small, 

and the methods are supportive of one another. Because the data used in the analysis was 

most abundant for Method 1, and both total and dissolved data were available, and because 

the flow volumes used in load calculation are tidally corrected, it is recommended that this 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-40 Tetra Tech, Inc. 

method be used for describing Delta loads, resulting in an average Delta to bay export of 

3,962 kg/yr. 

Particulate selenium loads from the Delta to the Bay were estimated based on previously 

estimated TSS loads by Leatherbarrow et al. (2005a) or McKee et al. (2006) at Mallard 

Island. McKee et al. (2006) based on continuous monitoring data of SSC at Mallard Island 

to estimate TSS loads for water year 1995-2003. Reported TSS loads at Mallard Island vary 

greatly with water years ranging from 0.26 ± 0.08 Mt/yr (2001) to 2.6 ± 0.8 Mt/yr (1995). 

Particulate selenium concentrations average 0.62 ± 0.21 !g/g (n =5) at the Sacramento River 

and 0.66 ± 0.42 !g/g (n =5) at the San Joaquin River (Doblin et al. 2006). Therefore an 

average concentration of 0.64 !g/g was used in the calculation for all years. As a result, 

estimated particulate selenium loads from Delta range between 151 – 1,510 kg/yr for 1995-

2003 (mean: 698 kg/yr). The estimated loads are higher than those estimated by Abu-Saba 

and Ogle (2005) for November 1997 to November 1999 (47-686 kg/yr). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-41 

Export through aqueducts 1993(wet) 1994(dry) 1995(wet) 1996(wet)

1997(wet)1998(wet)1999(wet)2000(wet)

2001(dry)2002(dry)

2003(wet)

Se loading (Kg)

0

500

1000

1500

2000

2500

Dry season

Wet season

Sacramento River contribution to export 1993(wet) 1994(dry) 1995(wet) 1996(wet) 1997(wet) 1998(wet) 1999(wet)

2000(wet)

2001(dry)2002(dry)

2003(wet)

Se loading (Kg)

0

500

1000

1500

2000

2500

San Joaquin River contribution to export 1993(wet) 1994(dry) 1995(wet) 1996(wet) 1997(wet) 1998(wet) 1999(wet)

2000(wet)

2001(dry)2002(dry)2003(dry)

Se loading (Kg)

0

500

1000

1500

2000

2500

Figure 3-24 Estimated selenium loadings through the aqueducts and contributions from the 

Sacramento River and the San Joaquin River. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-42 Tetra Tech, Inc. 

Delta loads to the Bay 1993(wet) 1994(dry) 1995(wet) 1996(wet)

1997(wet)1998(wet)1999(wet)2000(wet)

2001(dry)2002(dry)

2003(wet)

Se loading (Kg)

0

1000

2000

3000

4000

5000

6000

7000

Dry season

Wet season

Bay loads from Sacramento River 1993(wet) 1994(dry) 1995(wet) 1996(wet) 1997(wet) 1998(wet)

1999(wet)2000(wet)

2001(dry)2002(dry)

2003(wet)

Se loading (Kg)

0

500

1000

1500

2000

2500

3000

3500

Bay loads from San Joaquin 

River 1993(wet)

1994(dry)

1995(wet)1996(wet)1997(wet)1998(wet)1999(wet)2000(wet)

2001(dry)2002(dry)2003(dry)

Se loading (Kg)

0

500

1000

1500

2000

2500

3000

3500

Figure 3-25 Estimated selenium loadings from the Delta to the Bay as the difference between 

loads from the Rivers and export through aqueducts, as well as contributions 

attributed to the Sacramento River and the San Joaquin Rivers individually. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-43 

Date

1/1/90 1/1/92 1/1/94 1/1/96 1/1/98 1/1/00 1/1/02 1/1/04 1/1/06 1/1/08 

Se concentration (

"g/L)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

Estimated 

Delta Mendota Canal 

Figure 3-26 Estimated selenium concentrations in the aqueducts using flow weighted method 

compared to observed concentrations in Delta Mendota Canal near Tracy 

Headworks (MP 3.50) (Open circles indicates values below detection limit of 0.4 

!g/L). 

3.5. MUNICIPAL AND INDUSTRIAL WASTEWATER DISCHARGERS

Currently there are a total of 24 Publicly Owned Treatment Works (POTWs) located in the 

North Bay (Figure 3-27). Most of these facilities receive secondary treatment although a few 

incorporate advanced treatment (i.e., City of American Canyon, Napa Sanitation District). 

Dry weather flows from these facilities range from <1 to 120 mgd. 

Flow at five largest municipal dischargers in the North Bay is shown in Figure 3-28. Flow at 

municipal discharges generally follows a seasonal pattern of higher concentration during the 

wet season, most likely due to storm water runoff. Concentrations in effluents of municipal 

dischargers generally are below 1 !g/L, with many samples below detection limit (Figure 

3-29). 

Effluent total selenium concentrations at a monthly interval are reported for these facilities. 

Total selenium concentrations in the effluents are generally near 1 μg/L (Table 3-11). 

Effluent concentrations at two facilities with the largest discharges (i.e., East Bay Municipal 

Utility District, EBMUD and Central Contra Costa Sanitation District, CCCSD) average 

0.34 ± 0.19 μg/L and 0.34 ± 0.50 μg/L. Reported concentrations compared well to the 

dissolves selenium concentrations observed by Cutter and San Diego-McGlone (1990) 

during 1987-1988 sampling (24-hour composite sample at monthly intervals; CCCSD: 0.53 

± 0.11 μg/L, EBMUD: 0.37 ± 0.10 μg/L). No relationship between flow and concentrations 

in the effluent were observed. Therefore, no flow-concentration correlation was used in the 

load estimates. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-44 Tetra Tech, Inc. 

Two methods were used in calculating daily loadings from POTWs. In the first method, the 

overall average daily maximum concentration was multiplied by overall average daily flow. 

In the second method, daily loadings were estimated based on flow and reported 

concentrations for all the available dates and an overall average of daily loadings was 

calculated. For concentrations reported as below the detection limit, concentrations were 

assumed to be half of the detection limit. Some non-detect data were reported with very high 

detection limits (e.g. 5 μg/L); in these cases data were disregarded. Estimated daily loadings 

show large temporal variations (Figure 3-30) related to the flow variability. 

Estimated annual selenium loadings from POTWs in the North Bay are 255.3-255.8 kg/yr 

(Table 3-12). More detailed information on flows and concentrations, as well as 

identification of individual ports used in load estimates is presented in Appendix A5. The 

loadings are roughly half of values previously estimated by Cutter and San Diego-McGlone 

(1990) for the entire bay (1.08 kg/day or 394 kg/yr). 

Effluents from municipal dischargers are dominated by selenate (60%), followed by selenite 

(25%) and organic and elemental selenium (15%; Cutter and San Diego-McGlone, 1990). 

The second method used for POTWs was also used to calculate loadings from the industrial 

facilities in the North Bay. Loadings from industrial facilities are minor compared to other 

sources (Table 3-13). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-45 

Figure 3-27 POTW discharge locations in and around San Francisco Bay (source: 

SFBRWQCB, Basin Plan). 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-46 Tetra Tech, Inc. 

Table 3-11 

Summary statistics of daily maximum effluent concentrations at the municipal dischargers 

Municipal dischargers Outfall 

Location 

(Fig. 3-27) 

Mean1 S.D. Min Max Count 

American Canyon (E-001-S) 1 1.16 0.59 0.2 2 32 

City of Benicia 2 0.85 0.51 <0.3 5 98 

City of Calistoga (E-001) 4 0.511 0.54 0.25 2.5 19 

City of Saint Helena (E-001)2 30 <0.5 

Central Contra Costa 5 0.34 0.50 <0.05 4 99 

Central Marin Sanitation Agency 6 0.81 0.68 0.17 6.4 99 

Delta Diablo 8 4.07 7.54 <1 37 104 

EBMUD 10 0.34 0.19 <0.2 1.6 294 

Fairfield-Suisun Sewer District 11 0.75 0.38 0 2 95 

Las Gallinas Valley SD Permit 12 0.95 0.17 0.5 0.97 15 

Marin Co. S.D. no. 5 (Paradise Cove)2 13 0.73 

Marin Co. S.D. no. 5 (Tiburon) 13 1.93 1.40 0.5 6 47 

Mount View Sanitary District 14 0.67 0.60 <0.02 5 38 

Napa Sanitation District (dry) 15 0.57 0.21 <0.5 1 13 

Napa Sanitation District (wet) 15 0.27 0.25 0 <1 26 

Novato S.D (Ignacio Dry) 

(Novato Wet) 

17 0.475 

0.833 

0.05 

0.32 

0.4 

0.4 

0.5 

1 

4 

4 

City of Petaluma 20 0.65 0.23 0.35 1.4 60 

Cities of Pinole-Hercules 21 0.91 0.66 <0.1 4 47 

Rodeo Sanitary District 21 0.80 0.61 <0.1 3 30 

Sausalito-Marin Sanitary District 26 2.46 0.91 0.5 17.5 85 

Sewerage Agency of South Marin 13 1.39 2.01 0.15 12 133 

Sonoma Valley County S.D. 28 <5.00 0.00 <5 <5 27 

US Navy Treasure Island Permit 32 0.48 0.17 <0.25 8.96 46 

Vallejo San & Flood Control District (Carquinez 

deep) 

33 0.96 0.52 <0.7 10.6 79 

West County/Richmond Permit 34 1.73 0.97 0.25 9 60 

1. For values below detection limit, half of the detection limit was used in mean calculation. 

2. Concentrations taken from permits 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-47 

Central Contra Costa

Year

98 00 02 04 06 08 

Flow (mgd)

0

20

40

60

80

100

120

140

160

EBMUD

Year

98 00 02 04 06 08 

Flow (mgd)

50

100

150

200

250

300

Fairfield - Suisun

Year

00 02 04 06 08 

Flow (mgd)

0

10

20

30

40

50

Vallejo Sanitation

Year

98 00 02 04 06 08 

Flow (mgd)

0

20

40

60

80

100

120

140

160

180

West County Agency

Year

02 03 04 05 06 07 08 

Flow (mgd)

0

20

40

60

80

100

Figure 3-28 Daily effluent average flow at five largest dischargers in North Bay. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-48 Tetra Tech, Inc. 

Central Contra Costa

Year

98 00 02 04 06 08 

Concentrations ("g/L) 0.0

0.4

0.8

1.2

1.6

2.0

2.4

3.8

4.0

EBMUD

Year

98 00 02 04 06 08 

Concentrations ("g/L) 0.0

0.4

0.8

1.2

1.6

2.0

Vallejo

Year

00 02 04 06 08 

Concentrations ("g/L)

0

1

2

3

10

11

12

Fairfield - Suisun

Year

98 00 02 04 

Concentrations ("g/L) 0.0

0.4

0.8

1.2

1.6

2.0

West County Agency

Year

02 04 06 08 

Concentrations ("g/L)

0

2

4

6

8

10

12

Figure 3-29 Effluent maximum concentrations for the five largest dischargers in the North 

Bay. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-49 

Table 3-12 

Estimated total selenium loadings from POTWs in the North Bay 

POTW Facility Name 

Outfall 

Location 

Average Flow (mgd) 

Estimated Se 

Loadings1 

(kg/yr) 

Estimated Se 

Loadings2 

(kg/yr) 

City of American Canyon (E-001 S) 

(E-003 S) 

1 0.89 

0.99 

1.42 

1.46 

1.53 

1.43 

City of Benicia 2 3.0 3.5 3.4 

City of Calistoga3 (E-001 dry) 

(E-002 wet) 

4 0.87 

0.65 

0.60 

0.46 

0.20 

City of Saint Helena E-0013 30 1.11 0.38 

Central Contra Costa S.D. 5 45.8 21.8 15.0 

Central Marin Sanitation A.G. 6 11.0 12.3 10.7 

Contra Costa Co. S.D. no. 5 (Port Costa) 7 0.02 NA NA 

Delta Diablo 8 11.46 64.5 64.1 

East Bay MUD 10 74.6 34.8 36.9 

Fairfield Suisun Sewer Dist. (E-001 A) 

(E-004) 

11 17.0 

1.44 

17.5 

1.48 

16.8 

1.68 

Las Gallinas Valley S.D. (E-001) 

(E-002) 

12 3.75 

1.44 

2.48 

0.95 

4.0 

Marin Co. S.D. no. 5 (Paradise Cove) 0.02 0.73 

Marin Co. S.D. no. 5 (Tiburon) 13 1.02 2.72 1.86 

Mount View S.D. 14 2.0 2.3 1.5 

Napa S.D. (Dry weather) 

(Wet weather) 

15 3.8 

13.98 

1.49 

2.60 

2.94 

10.34 

Novato S.D. E-001 Ignacio Dry 

E-002 Novato Wet 

17 4.01 

2.23 

2.63 

2.57 

2.90 

3.19 

City of Petaluma 20 7.6 6.88 8.3 

Cities of Pinole & Hercules 21 3.2 4.0 4.2 

Rodeo S.D. 21 0.8 0.9 0.9 

Sausalito-Marin City S.D. 26 1.6 5.5 4.9 

Sewerage Agency of South Marin 13 3.3 6.36 5.10 

Sonoma Valley County S.D. 28 4.1 -- High DL (5 μg/L) 4 

U.S. Navy Treasure Island 32 0.5 0.4 0.25 

Vallejo Sanitation & Flood Control (Carquinez 

deep) 

(Mare deep) 

33 13.2 

2.69 

17.5 

2.85 

15.66 

7.56 

West County Agency WCA (E-001 DC) 34 14.1 33.7 30.7 

Total 243.9 255.3 255.8 

1 - Estimated based on overall average concentration and average daily flow 

2 - Estimated based on flow and concentrations on all available dates 

3.- Not included in total load estimates due to distance from the Bay. 

4 - Reported concentrations below high detection limit of 5 !g/L and load not estimated. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-50 Tetra Tech, Inc. 

Table 3-13 

Estimated selenium loadings from industrial wastewater dischargers in the North Bay 

Industrial Facilities Daily loading (g/day) Annual loading (kg/yr) 

Dow Chemical 6.5 2.4 

General Chemical 4.8 1.8 

GWF (I) 1.05 0.4 

GWF (V) 0.4 0.1 

USS-Posco 31.0 11.3 

Total 43.7 16.0 

1/1/99 1/1/01 1/1/03 1/1/05 1/1/07 

Daily loading (g/day)

0

100

200

300

400

500

600

Figure 3-30 Estimated daily total selenium loadings from EBMUD. 

3.6. PETROLEUM REFINERIES

Mean selenium concentrations at the refineries range between 11.9 – 27.7 !g/L (Table 3-14). 

Concentrations show relatively large variations over time (Figure 3-31). Daily flow 

measurement at the refineries indicates some seasonal high flows, probably due to storm 

water runoff (Figure 3-32). Concentrations generally show no correlation with flow (Figure 

3-33). 

For the five petroleum refineries located in the North Bay, daily loadings were estimated 

based on the continuous daily flow data and the reported effluent daily maximum 

concentrations on a weekly basis. Mean daily maximum concentrations for the refineries 

range between 12 – 28 μg/L. No relationship between concentrations and flow were 

observed. The annual loadings were calculated by summing the daily loadings. The 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-51 

estimated total daily loading from these refineries is 1.47 kg/day or an average of 537 kg/yr 

during 1999-2007 (Table 3-15). Current loadings are significantly lower than the previous 

years (1,407 – 3,382 kg/yr in 1986 – 1992) following the improvement in waste water 

treatment practices at the refineries (Presser and Luoma, 2006). 

To calculate seasonal loads, daily loads were calculated by multiplying daily flow with 

weekly concentration extrapolated to the week and then adding up for dry and wet season. 

Wet season was defined as Oct. 1st to Apr. 30th. The dry season was defined as May 1st to 

Sep. 30th. Estimated annual selenium loadings are relatively constant throughout the years 

(Figure 3-34). Average dry season loadings are generally 62-78% of the average wet season 

loadings at four of the refineries. Average dry season loadings at Tesoro are only 35% of the 

wet season loadings. 

The effluents are dominated by selenate (56%) and organic selenide (30%), with selenite 

accounting for only 14% on average (compared to 64% in 1987-1988, Cutter and Cutter, 

2004). The speciation in refineries is similar to that in municipal wastewater effluents. 

Table 3-14 

Summary statistics of daily maximum effluent concentrations at the refineries 

Refineries Median Mean 

Standard 

deviation Min Max Count 

Chevron 11.2 12.1 5.9 2.3 48.0 308 

ConocoPhillips (at 

Rodeo) 

14.0 15.5 8.5 1.0 49.0 448 

Shell Martinez 27.0 27.7 9.4 4.0 82.0 266 

Tesoro 11.0 11.9 5.1 1.0 41.0 367 

Valero 26.1 26.6 7.4 8.0 50.0 447 

Table 3-15 

Estimated total selenium loadings from petroleum refineries in the North Bay 

Refinery 

Flow 

(mgd) 

Mean daily loading1

(kg/day) 

Mean daily loading2

(kg/day) 

Annual loading1

(kg/yr) 

Annual loading2

(kg/yr) 

Chevron 7.1 0.31 0.33 112.6 120.7 

Conoco Philips 2.3 0.16 0.16 57.9 58.0 

Shell Martinez 5.8 0.61 0.59 224.1 214.9 

Tesoro 4.1 0.19 0.19 70.2 69.3 

Valero 2.0 0.20 0.20 71.9 75.1 

Total 21.3 1.47 1.47 536.7 538 

1 – Calculated as continuous daily flow times weekly concentrations extrapolated to the rest of the week 

2 – Calculated based on daily flow and concentrations on sampling dates only 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-52 Tetra Tech, Inc. 

Chevron

Year

99 00 01 02 03 04 05 06 07 08 

"g/L

0

10

20

30

40

50

Conoco Phillips

Year

99 00 01 02 03 04 05 06 07 08 

"g/L

0

10

20

30

40

50

Shell Martinez

Year

98 99 00 01 02 03 04 05 06 07 08 

"g/L

0

20

40

60

80

100

Tesoro

Year

00 01 02 03 04 05 06 07 08 

"g/L

0

10

20

30

40

50

Valero

Year

99 00 01 02 03 04 05 06 07 08 

"g/L

0

10

20

30

40

50

Figure 3-31 Effluent daily maximum selenium concentrations for the refineries in the North 

Bay. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-53 

Chevron

98 99 00 01 02 03 04 05 06 

Flow (mgd)

0

5

10

15

20

25

30

35

Conoco Phillips

98 99 00 01 02 03 04 05 06 07 08 

Flow (mgd)

0

2

4

6

8

10

Shell Martinez

Year

98 99 00 01 02 03 04 05 06 07 08 

Flow (mgd)

0

2

4

6

8

10

Tesoro

99 00 01 02 03 04 05 06 07 08 

Flow (mgd)

0

2

4

6

8

10

12

14

16

18

Valero

98 99 00 01 02 03 04 05 06 07 08 

Flow (mgd)

0

1

2

3

4

5

Figure 3-32 Daily average effluent flow rate from the refineries. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-54 Tetra Tech, Inc. 

Valero

Flow (cfs)

0 1 2 3 4 5

Conc. ("g/L)

0

10

20

30

40

50

60

Tesoro

Flow (cfs)

0 2 4 6 8 10 12 14 16 18

Conc. ("g/L)

0

10

20

30

40

50

Shell Martinez

Flow (cfs)

2 3 4 5 6 7 8 9

Conc. ("g/L)

0

20

40

60

80

100

Chevron

Flow (cfs)

0 5 10 15 20 25 30

Conc. ("g/L)

0

10

20

30

40

50

R2=0.04

R2

=0.002

R2

=0.05

R2

=0.002

Conoco Phillips

Flow (cfs)

0 10 20 30 40 50

Conc. ("g/L)

0

2

4

6

8

10

R2=0.008

Figure 3-33 Concentrations and flow for the refineries in the North Bay. No meaningful 

correlations were found; the regression lines in the plots are to illustrate the lack 

of a relationship between flows and concentrations. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-55 

Conoco Phillips

1999 (wet)2000 (wet)

2001 (dry)

2002 (dry)

2003 (wet)

2004 (dry)

2005 (wet)2006 (wet)

2007 (dry)

Selenium loading (kg)

0

25

50

75

100

125

150

Dry Season

Wet Season

Chevron

1999 (wet)

2000 (wet)

2001 (dry)

2002 (dry)

2003 (wet)

2004 (dry)

2005 (wet)

2006 (wet)

2007 (dry)

Selenium loading (kg)

0

25

50

75

100

125

150

Dry Season

Wet Season

Shell Martinez

1999 (wet)

2000 (wet)

2001 (dry)

2002 (dry)

2003 (wet)

2004 (dry)

2005 (wet)

2006 (wet)

2007 (dry)

Selenium loading (kg)

0

50

100

150

200

250

300

Dry Season

Wet Season

Tesoro

1999 (wet)

2000 (wet)

2001 (dry)

2002 (dry)

2003 (wet)

2004 (dry)

2005 (wet)

2006 (wet)

2007 (dry)

Selenium loading (kg)

0

25

50

75

100

125

150

Dry Season

Wet Season

Valero

1999 (wet)

2000 (wet)

2001 (dry)

2002 (dry)

2003 (wet)

2004 (dry)

2005 (wet)

2006 (wet)

2007 (dry)

Selenium loading (kg)

0

25

50

75

100

125

150

Dry Season

Wet Season

Figure 3-34 Dry and wet season selenium loadings from refineries for the years of 1999-2007. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-56 Tetra Tech, Inc. 

3.7. INTERNAL SOURCES - SEDIMENT EROSION

Sediments in the North Bay represent a large reservoir of selenium (Abu-Saba and Ogle, 

2005). A review of sediment processes in the San Francisco Bay indicated an active 

sediment mixing layer of 15 cm (Leatherbarrow et al. 2005b). Given the sediment mass for 

the upper 15 cm of the whole bay (1.4 x 1011 kg; Davis (2003), cited in Abu-Saba and Ogle, 

2005) and mean selenium concentrations of 0.25μg/g, the selenium in the upper layer of 

sediments of North Bay is about 20,000 kg.5 

Selenium in bottom sediments can be mobilized to the water column through resuspension, 

erosion, diffusion and bioturbation. Resuspension rates in the San Francisco Bay were found 

to be 2 to 5 times greater than the accumulation rates, indicating sediment is resuspended 2 

to 5 times before settling (Leatherbarrow et al. 2005b). Previous studies indicated sediment 

residence time in the water column of 5 ± 3 days in San Pablo Bay. It was suggested that 

during summer low flow months, wind generated and tidal driven resuspension redistributes 

sediments to a wider area. Localized sediment erosion also occurs due to decreases in 

sediment supply from the surrounding watersheds. Net sediment erosion was found to occur 

both in the Suisun Bay and San Pablo Bay. For San Francisco Bay, the abundance of 

organisms has been found to potentially enhance mobilization of sediments to the water 

column. Diffusion of dissolved selenium from the sediment porewater to the water column 

has been found to be a small source, estimated at 18.2 kg/yr for the North Bay (Meseck, 

2002). Direct biotic uptake of particulate selenium in bottom sediments by consumer 

organisms is another pathway of selenium mobilization, but this has not been quantified for 

the source analysis. 

Selenium in sediments can also undergo a series of transformations (Meseck and Cutter, 

2006). In deeper layers of sediment, selenate and selenite can be converted to elemental 

selenium due to microbial reduction. As a result, elemental selenium comprises a large 

portion of selenium in the sediments and the presence of elemental selenium in bay water 

can be an indicator of origin from bottom sediments. Organic selenide in surface sediment 

can also be oxidized to selenite and selenate or methylated by microbes. 

Studies in San Pablo and Suisun Bay indicated that more erosion than burial is occurring in 

these two areas in the recent years (USGS 2001a, b). In Suisun Bay, net sediment erosion 

was 1-2 Mm3

/yr from 1887 to 1990 (USGS 2001a). During 1942 to 1990, Suisun Bay 

experienced a net loss of 61 Mm3 of sediment, with a net loss of 1.27 Mm3/yr at an erosion 

rate of 1.2 cm/m2

/yr. Erosion in San Pablo Bay is at a slower rate and only occurred after 

1950s. San Pablo Bay lost approximately 7 Mm3 of sediments between 1951 and 1983 at a 

rate of 0.22 Mm3/yr (USGS 2001b). This net loss of sediments can be a potential source of 

selenium from sediments to the water column. Average selenium concentration in surface 

sediment is at 0.25 μg/g. Sediment loss of Suisun and San Pablo Bay is estimated to be 

around 1,100 M kg/yr (SFBRWQCB, 2004). This results in selenium loadings due to 

sediment erosion of 275 kg/yr. 

 

5

 Assuming North and Central Bay area of 434 km2 and 214 km2, over the total area of 1133 km2 for the whole Bay 

(Tsai et al. 2001). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-57 

Loss of tidal mudflats occurs both in fringe areas of Suisun Bay and San Pablo Bay (1000 

acres in Suisun Bay during 1887 - 1990 and 125 acres/yr in San Pablo Bay). Loss of tidal 

mudflats may introduce contaminants previously deposited in these areas to the Bay 

(Marvin-DiPasquale et al., 2003). 

Sediment dredging from navigation channels and disposal in locations inside and outside the 

bay can also influence sediment selenium pool. On average, in each year 1.8 million cubic 

yards of sediments were disposed in the bay and 2.4 million cubic yards were disposed out 

of the bay. Assuming a mean concentration of 0.25 μg/g, this represents a net loss of 82.5 

kg/yr of selenium from the Bay (Table 3-16). In-bay disposal was estimated to be 248 kg Se 

/yr, while ocean disposal and upland/wetland reuse are 142.5 kg Se/yr and 225 kg Se/yr 

respectively. The dry mass of selenium was calculated assuming a particle density of 2.65 

kg/L and a 50% solid per unit mass sediment, similar to assumptions used in the recent PCB 

TMDL for San Francisco Bay (SFBRWQCB, 2007c). 

Table 3-16 

Estimated selenium mass associated with dredge material disposal (2001-2005)1 

Disposal site 

Total volume

2001-2005 

(m3) 

Average volume

(m3

/yr) 

Average annual estimated Se dry mass 

(kg/yr) 

In-bay disposal 6,800,000 1,380,000 248 

Ocean (SF-DODS) disposal 2,900,000 580,000 -142.5 

Upland/wetland reuse 6,190,000 1,220,000 -225 

Net loads -82.5 

1

Source of data for volume of dredge material is from SFBRWQCB, 2007c. 

3.8. LOADS FROM THE SOUTH BAY

Water in the South Bay and Central Bay is subject to mixing near the Bay Bridge. As a 

result, selenium loads can enter the Central Bay from South Bay or vice versa. The net 

inflow of water is assumed to be equal to river flow from the South Bay (Smith and 

Holibaugh, 2006). To estimate the net effect of exchange between two the two portions of 

the bay on selenium loads, we assumed selenium concentrations at a station near the 

boundary of the two bays (BC10 Yerba Buena Island) to be representative of net inflow 

concentration from the South Bay. Estimated freshwater inputs from local watersheds of 

South Bay are 664 Mm3

/yr (Davis et al. 2000). With the mean selenium concentration of 

0.16 !g/L at Yerba Buena Island (Table A-3), estimated selenium inputs from South Bay to 

the Central Bay is at 106.2 kg/yr. The estimated load is relatively small compared to other 

selenium sources to the North Bay. 

One of the tributaries in the South Bay, the Guadalupe River can be a major source of 

selenium to the South Bay because of high concentration. Observed average total selenium 

concentration at Guadalupe River (BW15) by RMP is at 4.76 !g/L. With the annual flow of 

39.9-141.9 cfs for 2003-2007 (USGS11169025), selenium loads from this tributary alone 

can be 169.6-603.2 kg/yr. Therefore, the estimated 106.2 kg/yr load from South Bay may be 

at the lower bound of the loads entering from South Bay or suggests that significant removal 

of selenium via deposition may be occurring in the South Bay. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-58 Tetra Tech, Inc. 

3.9. COMPARISON OF SELENIUM CONCENTRATIONS AND LOADS FROM DIFFERENT SOURCES

A comparison of total and dissolved selenium concentrations from several sources of 

interest is summarized in Table 3-17. In terms of concentrations, the refineries have the 

highest selenium concentrations compared to other sources such as Delta outflow, 

atmospheric deposition, municipal wastewater and the bay water, followed by local 

tributaries. 

A comparison of relative importance of loadings from various sources is listed in Table 

3-18. Input from Delta represents the largest source of total selenium and exhibits large 

variation depending on flow. Local tributaries and refineries are other two important 

sources. Loadings from atmospheric deposition and municipal wastewater are smaller. Bay 

sediment erosion contributes a notable portion of the particulate selenium loadings. 

Table 3-17 

Representative selenium concentration in different sources 

 Source Total 

(μg/L) 

Dissolved

(μg/L) 

Atmospheric deposition Mosher and Duce (1989) - 0.1-0.4 

Local tributaries (data for individual tributaries) SFRWCB, 2007a,b 0.4-4.01 0.3-3.9 

 BASMAA (1996) 0.46 

Municipal wastewater Data provided by SFBRWQCB <1 - 

Refineries Data provided by SFBRWQCB 12-282 12-28 

Mallard Island (outflow from Delta) Storm Values L. McKee, personal communication 0.46 - 

San Joaquin River @ Vernalis (1999-2000) Cutter and Cutter (2004) 0.68 

Sacramento River @ Freeport (1999-2000) Cutter and Cutter (2004) 0.07 

San Joaquin River near Mallard Island (BG30) RMP 0.18 0.16 

Sacramento River near Mallard Island (BG20) RMP 0.15 0.13 

Bay water (1993-2005) RMP 0.18 0.15 

1. Mean of downstream sites in North Bay (SFRWCB, 2007a, b), Table 3-2 

2. Mean concentrations at individual refineries listed in Table 3-1. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-59 

Table 3-18 

Relative importance of loadings from different sources 

Total 

(kg/yr) 

Dissolved 

(kg/yr) 

Particulate 

(kg/yr) Uncertainty 

Sources: 

Atmospheric deposition 17.8-163.5 13.7 – 78.1 4.1-85.4 High 

Local tributaries 354 -1511 (354-834 best 

estimate) 

- 118.21 High 

Municipal and industrial 

wastewater 

255 - - Low 

Refineries 538 - - Low 

Input from Delta 1,110-11,752 

(mean:3,962) 

814-9,736 

(mean: 3,354) 

151-1,5092 

(mean: 698) 

Moderate 

Sacramento River at 

Freeport 

 670-2,693 (mean: 1,577) 

for 1991-2007 

 Moderate 

San Joaquin River at 

Vernalis 

760-7,2705 (mean: 2,972) 

for 1994-2007 

838-4,711 (mean: 2,289) 

for 1991-2007 

 Moderate 

Sediment 293 18.24 275 Moderate 

South Bay 106 High 

Sinks: 

Outflow 45003 37503 7503 Moderate 

Sediment Dredging 82.5 82.5 Moderate 

1

Based on TSS loadings by Davis et al. (2000), times selenium content in particulate material of Sacramento River 

2

Based on TSS loadings by McKee et al. (2006) and mean selenium content in particulate material of Sacramento and San 

Joaquin Rivers 

3

Based on average Delta outflow of 25000 Mm3. Outflow only includes loads contributed by the northern reach. 

4

Sediment diffusion rate estimated by Meseck (2002). 

5

Based on SWAMP dataset 

A comparison of dry and wet season loadings from different sources (Table 3-19) indicates 

that during the dry season, the major source of selenium loadings is from the Delta. The 

local tributary contribution during the dry season is minimal. During the wet season, the 

Delta outflow and local tributaries are the main selenium sources to the Bay. Refineries have 

a relatively steady input during both dry and wet seasons. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-60 Tetra Tech, Inc. 

Table 3-19 

Summary of dry and wet season selenium loading from major sources 

 Dry season 

(kg) 

Wet season 

(kg) 

Annual total 

(kg) 

Delta (Total, RMP data) 1,007.4 2,930.7 3,938.2 (total) 

Delta (Dissolved, assuming 60% 

removal of San Joaquin River load) 

909.5 1,583.1 2,492.6 

Sacramento River at Freeport 564.1 1,012.7 1,576.9 

San Joaquin River at Vernalis 863.4 1,426.0 2,289.4 

Export through aqueducts 664.5 841.7 1,506.1 

Delta (dissolved, difference 

between river loads and export 

through aqueduct) 

855.5 1,840.4 2,595.9 

Tributaries1 75.8 1,434.8 1,510.6 

Refineries 204.2 322.2 526.4 

1

 Estimates from Method 2 

The estimated selenium loads from different sources were compared to previous studies of 

Presser and Luoma (2006), Meseck and Cutter (2006) and Abu-Saba and Ogle (2005) (Table 

3-20). Selenium loads from refineries compared well to loads estimated by Presser and 

Luoma (2006) and Abu-Saba and Ogle (2005). Loadings from the Delta on an annual basis 

were also comparable to estimates of Presser and Luoma and in the same range of Abu-Saba 

and Ogle (2005), principally because the estimated range is wide. However, dry season 

Delta to bay loads in this work are substantially higher than previous estimates by Presser 

and Luoma (2006): over 1,000 kg compared to 200 kg. Loadings from local tributaries were 

higher than estimates by Abu-Saba and Ogle (2005), most likely due to higher selenium 

concentrations and runoff values used in the calculation. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 3-61 

Table 3-20 

Comparison of alternative total selenium loadings estimates to North San Francisco Bay. 

Source Category 

Presser and 

Luoma (2006) 

Meseck and 

Cutter (2006) 

Abu-Saba and 

Ogle (2005) This report 

 All loads in kg 

Refineries: Prior to improved 

wastewater treatment in 1998, kg/yr 

1,850 2,890 610-1,660 No estimate 

Refineries: Subsequent to improved 

wastewater treatment in 1998, kg/yr 

6201 1,100 204-552 526 

Delta loads, kg/yr 200 kg/6 

months, 

critically dry 

season; 4,500 

kg/6 months, 

high flow 

season 

No estimate 

reported; value 

embedded in 

model 

calculations. 

330-10,200 

(Nov 1997- Nov 

1999) 

3,946 annual 

average; 1,007 

dry months and 

2,930 wet 

months 

Selenium inventory in sediment bed, 

kg 

No estimate No estimate 50,000 in upper 

15 cm of entire 

San Francisco 

Bay 

20,000 kg in top 

15 cm in North 

San Francisco 

Bay 

Sediment erosion No estimate No estimate No estimate 293 

Local tributaries and waste water to 

North San Francisco Bay, kg/yr 

No estimate No estimate 90-900 (to all 

San Francisco 

Bay) 

Local watershed 

runoff: 354-834 

POTWs No estimate No estimate 90-900 Wastewater, 

other than 

refineries: 255 

Atmospheric deposition, kg/yr No estimate No estimate No estimate 18-164 

1

From the value illustrated in Figure 26 (p93) of Presser and Luoma (2006). The number 506 kg/yr on page 1-1 was from Table 10 

(p35) of Presser and Luoma (2006) where the actual loads were estimated for 1999. 

3.10. LOW FLOW VS. HIGH FLOW CONCENTRATIONS

Selenium loadings and concentrations in water column and the suspended particulate 

material can vary with flow conditions. Under high flow, high loadings from Delta 

combined with short residence time can result in selenium concentrations in the bay that are 

similar to those in Delta inflows. During low flow periods, local sources from point 

dischargers may become a larger source. Under low flow, also due to the longer residence 

time and warmer temperature, selenium is more likely to accumulate in phytoplankton and 

bacteria. Zooplankton selenium concentrations have been found to be highest during low 

flow period (Pukerson et al. 2003). Therefore the low flow season is a critical time period 

for selenium bioaccumulation. The hydraulic residence time in NSFB can vary from 2 days 

during high flow to an average of 160 days during low flow (Cutter, 1989). 

To forecast the expected selenium concentrations in water column and suspended particulate 

material, a simple, completely-mixed, one-box model similar to Presser and Luoma (2006) 

was used to estimate possible concentrations in the bay under several flow conditions: high 

flow in a wet year (2006), low flow in a wet year (2006), and low flow in a critically dry 

year (2001). Loadings from various sources estimated in previous sections were used. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

3-62 Tetra Tech, Inc. 

Partition coefficient between dissolved and particulate selenium were derived from data of 

Doblin et al. (2006). 

Several processes besides outflow to ocean that may contribute to the selenium removal: 

methylation to form dimethylselenide followed by volatilization, influx of dissolved 

selenium into sediments, reduction followed by adsorption and settling, phytoplankton 

uptake, and settling of suspended sediment. Previous study has indicated that diffusion into 

and out of the sediment is negligible (Meseck, 2002). Due to the oxic water, reduction of 

selenium is less likely to occur in the water column. Sediments in Suisun and San Pablo Bay 

are erosional, therefore net deposition into sediments are unlikely to be an important 

removal mechanism. More details of the one-box model are provided in the Appendix. 

Predicted mean selenium concentrations using zero removal rates under high flow are 

generally similar to the observed concentrations from the RMP random sampling during 

2002-2005 (0.14 μg/L; Table 3-21), suggesting relatively conservative behavior during high 

flow. Predicted maximum selenium concentration under low flow of a critically dry year is 

at higher concentration of 0.36 μg/L. RMP sampling during a representative period in 

August 2001 indicated a North Bay average of 0.15 !g/L. Because the observed 

concentrations during this period are significantly lower than predictions with removal rates 

set to zero, removal process may indeed be significant during these periods. The one-box 

modeling described here is a preliminary effort to assess the data and will be refined in 

subsequent work on the conceptual model and detailed mechanistic model. 

Table 3-21 

Estimated selenium concentrations under different flow conditions (more detailed calculation 

listed in Appendix A). 

Delta outflow 

(Mm3/day) 

Delta 

loadings 

(kg/day) 

Loadings from 

other sources*

(kg/day) 

Predicted total 

selenium 

concentrations 

(μg/L) 

Concentrations in 

suspended 

particulate 

material** 

(μg/g) 

High flow, wet 

year (2006) 

202.2 19.0 9.6 0.14 0.94 

Low flow, wet 

year (2006) 

73.0 6.9 3.2 0.14 0.92 

Low flow, 

critically dry year 

(2001) 

14.2 2.0 3.2 0.33 2.20 

 *includes loadings from refineries, POTWs, local tributaries (proportional to delta outflow), and bed erosion. 

**based on average Kd of 7.4 L/g (Cutter and Cutter, 2004). 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

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4. SUMMARY

In this analysis selenium concentrations in water column and sediment were examined to 

provide a baseline for future modeling to be performed as part of the selenium TMDL in 

North San Francisco Bay. Major sources of monitoring data are the RMP and Prof. Greg 

Cutter’s research group at Old Dominion University. The RMP has obtained selenium data 

at regular intervals at fifteen stations in the North Bay between 1993 and 2002, at 12 random 

stations for water concentrations and at 24 stations for sediment concentrations between 

2002 and 2005. Selenium concentrations are generally low in the Bay water column with a 

whole North Bay average of 0.12 μg/L. Selenium concentrations in sediments are generally 

below 0.3 μg/g. Concentrations are lowest near the Golden Gate Bridge, with higher 

concentrations at lower salinities. More focused data sets that spanned a longer time frame 

and contained speciation data were also evaluated (Cutter, personal communication, 2007). 

The data show that there have been significant decreases in dissolved selenium 

concentrations and selenite in the North Bay since the mid-1980s, particularly in the lowflow season, following the implementation of more stringent controls on refinery discharges. 

Much of the selenium in the waters of the bay is in dissolved form, and consists of selenate, 

selenite, and organic selenide. 

The quantification of selenium loadings from different point and non-point sources 

including Sacramento River and San Joaquin River inputs through Delta, local refineries, 

POTWs, tributaries and sediments, during both dry and wet season, was another major 

component of this analysis. The results indicated that annual loadings from the Central 

Valley through the Delta are the largest source of selenium with high variability depending 

on total flow through the Delta. Concentrations from the RMP stations are weakly correlated 

to Delta outflows to the bay, and therefore loads in high flow years are estimated to be more 

than ten times higher than in low flow years. The average Delta load is estimated to be 3,962 

kg/yr. Local tributaries draining both urban and non-urban areas are also a large source of 

selenium (estimated average load of 354-834 kg/yr). Refineries are now estimated to be the 

third largest source of selenium to the North Bay (538 kg/yr), although these loads may have 

been higher prior to the late 1990s when wastewater controls were installed. Sediment 

resuspension/erosion and diffusion (293 kg/yr), other wastewater discharges (250 kg/yr), 

and atmospheric deposition (18-164 kg/yr) are other, smaller contributors of total selenium 

load. The point source loads (the refineries and the POTWs) contribute relatively uniform 

loads over the year, although the non-point source loads (the Delta and the local tributaries) 

contribute substantially more load in the wet season than in the dry season. 

Although numerical values of load estimates are provided here for comparison, it should be 

acknowledged that this process contains significant uncertainty, and more than one 

estimation method may be applied, sometimes leading to different answers as described 

below. This is particularly true of non-point source load estimates. These alternative values 

are described below for completeness. 

Selenium loads at Sacramento and San Joaquin River were estimated based on data collected 

by Cutter and Cutter (2004). Sacramento River at Freeport was estimated to have an average 

annual dissolved selenium loading of 1,577 kg/yr for 1991-2007. San Joaquin River at 

Vernalis has an average of dissolved selenium loading of 2,289 kg/yr for 1991-2007. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

4-2 Tetra Tech, Inc. 

We applied three different methods to compute loads, from the Delta to the bay, depending 

on available data: 

! The first approach used average concentration of two RMP stations in the Delta and 

multiplies it by the net tidally corrected Delta outflow. This resulted in an annual 

average load estimate of 3,962 kg/yr of total selenium from the Delta to the NSFB 

(1994-2006). 

! The second approach used selenium loadings from the Sacramento and the San 

Joaquin Rivers separately based on data from Cutter and Cutter (2004) and applied a 

“Delta removal constant” similar to Meseck (2002) to account for the possible 

selenium loss in the Delta. These concentrations were reported only as dissolved 

selenium, not total selenium. This resulted in an annual average load estimate of 

2,493 kg/yr of dissolved selenium (1993-2003). 

! The third approach was independent of the prior two: the loadings from Central 

Valley to the bay were estimated as the difference between inputs from the two 

rivers minus the export through aqueducts, and assuming minimal loss processes in 

the Delta. This resulted in an annual average load estimate of 2,696 kg/yr of 

dissolved selenium (1993 to 2003). 

In addition to these loads, the average particulate load was estimated as 698 kg/yr, based on 

loads of sediment from the Delta to the bay and by application of a constant selenium 

content in the sediments. 

Given the simplifications and assumptions employed in these load calculations, and given 

that some loads are in terms of dissolved selenium, the range of annual averages is small, 

and the methods are supportive of one another. Because the data used in the analysis was 

most abundant for Method 1, and both total and dissolved data were available, and because 

the flow volumes used in load calculation are tidally corrected, it is recommended that this 

method be used for describing Delta loads, resulting in an average Delta to bay export of 

3,962 kg/yr. 

Using the SWAMP selenium data from the tributaries, loads were computed using flow 

from different sources: modeled annual flows and measured flows from USGS gage stations. 

The modeled flows were used because of the limited availability of measured flow data. 

Driven in large part by relatively high concentrations in the tributaries in both the wet and 

dry seasons, the average annual loads from the tributaries can range from 354 kg/year to 

1,511 kg/year depending on the methods used for the load estimation. Much of this load 

(greater than 95%) is delivered to the bay in the wet months, consistent with the timing of 

flows, as shown in the calculation using the USGS gage data. The largest single sources of 

loads are the Napa River, Sonoma Creek, and the Concord hydrological area. 

Although the tributary concentration data are different between two datasets (SWAMP and 

BASMAA), the high average concentrations are not driven by one or two measurements. It 

is nonetheless clear that the load estimates above are based on a limited amount of data. 

Furthermore, the SWAMP concentration data are not independently corroborated. Given the 

underlying data limitations and uncertainty in flows, and the year-to-year variability, the 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 4-3 

wide range in the load estimates are not entirely surprising. For the purpose of this analysis, 

we recommend using a range of load estimates for the next stage of the analysis of 354-834 

kg/yr. 

North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 5-1 

5. KEY FINDINGS AND IMPLICATIONS FOR MODEL DEVELOPMENT

The analysis presented here is an important first step in the modeling to be performed for the 

selenium TMDL. Key findings from this analysis, including uncertainties and data gaps, that 

will carry forward to the next steps are listed below: 

! More than two-thirds of the selenium in bay waters is present in the dissolved form, 

with the majority in the selenate form. 

! Selenium concentrations vary according to the freshwater flows moving through the 

bay, and are highest in the in the mid-estuarine regions in the driest periods of the 

year. 

! Sediment selenium concentrations from the RMP data set, averaged over several 

years of sampling at fixed stations, vary over a narrow range 0.2 to 0.5 μg/g, with a 

few exceptions. These concentrations correlate well with TOC and percent fines. 

Almost all sediment data have been collected near the surface (15 cm deep or less). 

No data are available to estimate natural background levels of selenium in the bay 

sediments. 

! Refinery load reductions are consistent with reductions in selenium concentrations in 

NSFB in both wet and dry seasons. Concentrations of selenite, a major component of 

refinery discharges in the past, show dramatic declines from 1998. 

! Local tributary selenium concentrations are high (i.e., closer to San Joaquin River 

values than Sacramento River values) and result in significant loads to the NSFB, 

although more than 95% of this load is delivered in the wet months. The data used in 

this calculation have been collected by the SWAMP program and have not been 

corroborated by other monitoring programs. The Napa River was estimated to be the 

largest tributary load contributor. A sediment sample in the bay near the mouth of the 

Napa River showed significantly elevated concentrations. 

! Selenium loads in NSFB are dominated by non-point sources, and therefore 

correlated with runoff. Because of the region’s climate, with distinct seasonal 

patterns of rainfall, and significant variability from year to year, the non-point loads 

are highly variable both on a seasonal and annual basis. 

! Load estimates of the rivers to the bay showed that both San Joaquin and Sacramento 

Rivers are significant contributors of selenium to the NSFB. Their load contributions 

are of similar magnitude and occur in both wet and dry seasons. 

! The large Central Valley selenium sources are transported through the Delta, but data 

within the Delta are limited, and understanding of its role in the removal and/or 

export of selenium is based on a small amount of data. 

! Point source loads (refineries, POTWs, and other industrial dischargers) are among 

the best characterized loads into NSFB because both flow and concentration are 

measured simultaneously. These loads are also less variable through the year and the 

wet season and dry season loads similar. This contrasts with Delta loads and 

tributary loads which are far larger in the wet months. On an annual basis, point 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

5-2 Tetra Tech, Inc. 

source loads are relatively small; on a seasonal basis, point source loads are 

significant during the dry months. 

! POTW discharge concentrations of selenium are much smaller than refinery 

wastewater concentrations. However, because their flows are larger, on a load basis, 

POTW loads are about a third of the refinery loads. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. 6-1 

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proposed Basin Plan Amendment and Staff Report. Oakland, CA. 

SFBRWQCB. 2007a. Water quality monitoring and bioassessment in nine San Francisco 

Bay Region watersheds: Walker Creek, Lagunitas Creek, San Leandro Creek, Wildcat 

Creek/San Pablo Creek, Suisun Creek, Arroyo Las Positas, Pescadero Creek/Butano Creek, 

San Gregorio Creek, and Stevens Creek/Permanente Creek. Oakland, CA: Surface Water 

Ambient Monitoring Program, San Francisco Bay Regional Water Quality Control Board. 

SFBRWQCB 2007b. Water Quality Monitoring and Bioassessment in Four San Francisco 

Bay Region Watersheds in 2003-2004: Kirker Creek, Mt. Diablo Creek, Petaluma River, 

and San Mateo Creek. Surface Water Ambient Monitoring Program, San Francisco Bay 

Regional Water Quality Control Board, Oakland, CA 

SFBRWQCB. 2007c. Total maximum daily load for PCBs in San Francisco Bay. Proposed 

Basin Plan Amendment and Staff Report. California Regional Water Quality Control Board. 

San Francisco Bay Region. Oakland, CA. 
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SFEI. 2006. 2004-2005 Annual Monitoring Results. The Regional Monitoring Program for 

Water Quality in the San Francisco Estuary (RMP). San Francisco Estuary Institute, 

Oakland, CA. 

San Francisco Estuary Institute (SFEI). 2006b. RMP Annual Monitoring Results 2004-2005. 

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U.S. Geological Survey (USGS) 2001b. Historical Bathymetric Change in Suisun Bay, 

1867-1990, prepared by K. Cappiella, C. Malzone, R. Smith, and B. Jaffe, October 18. 

http://sfbay.wr.usgs.gov/access/Bathy/suisunbay/

Zawislanski, P.T., H.S. Mountford, E.J. Gabet, A.E. McGrath, H.C. Wong. 2001. Selenium 

distribution and fluxes in internal wetlands, San Francisco Bay, California. Journal of 

Environmental Quality 30: 1080-1091. 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. A-1 

APPENDICES

Table A-1 

Parameters and inputs of one-box model 

Category Value Unit References 

Water depth (mean) 6.1 m Conomos et al. 1985 

Surface area 

North Bay 434 km2 Tsai et al. 2001 

Central Bay 214 km2 Tsai et al. 2001 

Volume 

North Bay+ Central Bay 3953 Mm3 Calculated 

Delta outflow 

Wet year (2006), wet season average 202.2 Mm3/day http://iep.water.ca.gov/dayflow/ 

Wet year (2006), dry season average 73.0 Mm3/day http://iep.water.ca.gov/dayflow/ 

Critically dry year (2001), dry season 14.2 Mm3/day http://iep.water.ca.gov/dayflow/ 

Delta loads 

Wet year (2006), wet season 19.0 kg/day Average of daily loads 

Wet year (2006), dry season 6.9 kg/day Average of daily loads 

Critically dry year (2001), dry season 2.0 kg/day Average of daily loads 

Refineries loads (wet season) 1.53 kg/day 

Refineries loads (dry season) 1.36 kg/day 

Bed erosion 0.75 kg/day 

Local tributaries (wet) 6.80 kg/day 

Local tributaries (dry) 0.57 kg/day 

Local tributaries (dry, 2001) 0.14 kg/day Scaled from Napa 2001 dry 

season loads 

Wastewater 0.50 kg/day 

Residence time 

Wet year (2006), wet season 19.5 day Calculated 

Wet year (2006), dry season 54.2 day Calculated 

Critically dry year (2001), dry season 278.4 day Calculated 

Predicted mean concentrations (total) 

Wet year (2006), wet season 0.14 μg/L 

Wet year (2006), dry season 0.14 μg/L 

Critically dry year (2001), dry season 0.33 μg/L 

Concentrations in particulates 

Wet year (2006), wet season 0.94 μg/g 

Wet year (2006), dry season 0.92 μg/g 

Critically dry year (2001), dry season 2.2 μg/g 

Equations: Assuming completely mixed and steady state: 

(1). C = W/a, where W: loadings from all sources, a: assimilation coefficient, C: concentration 

(2). a = Q + kV+ "As, where Q: outflow, k: degradation/reaction coefficient, ": settling velocity, As: surface area. For simplicity, k and 

" are assumed to be 0. 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

A-2 Tetra Tech, Inc. 

(3) Cs = Kd*Cw, where Cs: concentration in particulate, Kd: partition coefficient, Cw: dissolved concentration. Cw is assumed to be 

90% of C. 

Table A-2 

Summary of dissolved selenium concentrations in water for the period of 1993-2005 for the whole 

Bay (data source: RMP). 

Site Code Site Name 

Median 

(μg/L) 

Mean 

(μg/L) 

Standard 

Deviation Count 

BA10 Coyote Creek 0.37 0.43 0.21 21 

BA20 South Bay 0.33 0.32 0.12 23 

BA30 Dumbarton Bridge 0.25 0.26 0.09 28 

BA40 Redwood Creek 0.17 0.18 0.05 24 

BB15 San Bruno Shoal 0.15 0.16 0.07 20 

BB30 Oyster Point 0.13 0.16 0.09 24 

BB70 Alameda 0.12 0.16 0.18 19 

BC10 Yerba Buena Island 0.11 0.14 0.08 27 

BC20 Horseshoe Bay 0.10 0.14 0.10 23 

BC30 Richardson Bay 0.13 0.14 0.10 23 

BC41 Point Isabel 0.10 0.14 0.09 24 

BC60 Red Rock 0.12 0.15 0.10 20 

BD15 Petaluma River 0.17 0.18 0.07 21 

BD20 San Pablo Bay 0.14 0.15 0.06 24 

BD30 Pinole Point 0.15 0.16 0.06 24 

BD40 Davis Point 0.16 0.17 0.06 25 

BD50 Napa River 0.16 0.16 0.06 24 

BF10 Pacheco Creek 0.15 0.17 0.08 24 

BF20 Grizzly Bay 0.13 0.14 0.06 25 

BF40 Honker Bay 0.11 0.12 0.05 22 

BG20 Sacramento River (near Mallard 

Island) 

0.12 0.13 0.09 29 

BG30 San Joaquin River (near Mallard 

Island) 

0.14 0.16 0.09 28 

BW10 Standish Dam 1.40 1.36 0.63 16 

BW15 Guadalupe River 4.72 4.21 2.10 13 

C-1-3 Sunnyvale 0.82 1.03 0.59 23 

C-3-0 San Jose 0.91 0.86 0.33 23 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. A-3 

Table A-3 

Summary of total selenium concentrations in water for the period of 1993-2005 for the whole Bay 

(data source: RMP). 

Site Code Site Name 

Median 

(μg/L) 

Mean 

(μg/L) 

Standard 

Deviation Count 

BA10 Coyote Creek 0.39 0.47 0.25 17 

BA20 South Bay 0.33 0.35 0.15 21 

BA30 Dumbarton Bridge 0.26 0.28 0.12 29 

BA40 Redwood Creek 0.19 0.20 0.06 20 

BB15 San Bruno Shoal 0.16 0.17 0.08 19 

BB30 Oyster Point 0.14 0.16 0.08 21 

BB70 Alameda 0.16 0.19 0.16 19 

BC10 Yerba Buena Island 0.12 0.16 0.09 23 

BC20 Horseshoe Bay 0.11 0.17 0.12 19 

BC30 Richardson Bay 0.11 0.13 0.08 22 

BC41 Point Isabel 0.12 0.14 0.07 20 

BC60 Red Rock 0.15 0.18 0.08 16 

BD15 Petaluma River 0.25 0.24 0.09 19 

BD20 San Pablo Bay 0.17 0.18 0.07 23 

BD30 Pinole Point 0.17 0.18 0.08 23 

BD40 Davis Point 0.18 0.21 0.08 23 

BD50 Napa River 0.19 0.20 0.05 22 

BF10 Pacheco Creek 0.19 0.19 0.07 22 

BF20 Grizzly Bay 0.17 0.17 0.07 23 

BF40 Honker Bay 0.15 0.16 0.05 22 

BG20 Sacramento River (near Mallard 

Island) 

0.13 0.15 0.08 27 

BG30 San Joaquin River (near Mallard 

Island) 

0.16 0.18 0.09 26 

BW10 Standish Dam 1.70 1.65 0.82 14 

BW15 Guadalupe River 5.59 4.76 2.58 12 

C-1-3 Sunnyvale 1.02 1.14 0.58 23 

C-3-0 San Jose 1.10 0.97 0.38 22 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

A-4 Tetra Tech, Inc. 

Table A-4 

Summary of selenium concentrations in sediments for the period of 1993-2005 for the whole Bay 

(data source: RMP) 

Site code Site Name 

Median 

(μg/g) 

Mean 

(μg/g) 

Standard 

Deviation (μg/g) Count 

BA10 Coyote Creek 0.32 0.31 0.10 16 

BA21 South Bay 0.34 0.44 0.25 16 

BA30 Dumbarton Bridge 0.33 0.35 0.10 16 

BA41 Redwood Creek 0.32 0.33 0.16 20 

BB15 San Bruno Shoal 0.30 0.28 0.07 14 

BB30 Oyster Point 0.29 0.33 0.13 16 

BB70 Alameda 0.30 0.34 0.11 14 

BC11 Yerba Buena Island 0.28 0.30 0.15 20 

BC21 Horseshoe Bay 0.19 0.25 0.14 16 

BC32 Richardson Bay 0.25 0.27 0.09 16 

BC41 Point Isabel 0.30 0.33 0.09 16 

BC60 Red Rock 0.07 0.11 0.11 13 

BD15 Petaluma River 0.29 0.31 0.12 14 

BD22 San Pablo Bay 0.32 0.41 0.32 18 

BD31 Pinole Point 0.28 0.36 0.27 20 

BD41 Davis Point 0.11 0.15 0.17 16 

BD50 Napa River 0.38 0.52 0.47 18 

BF10 Pacheco Creek 0.11 0.15 0.12 16 

BF21 Grizzly Bay 0.33 0.50 0.68 20 

BF40 Honker Bay 0.31 0.38 0.20 14 

BG20 Sacramento River (near 

Mallard Island) 

0.10 0.14 0.13 19 

BG30 San Joaquin River (near 

Mallard Island) 

0.30 0.29 0.16 20 

BW10 Standish Dam 0.51 0.49 0.17 10 

BW15 Guadalupe River 0.53 0.54 0.09 8 

C-1-3 Sunnyvale 0.31 0.33 0.19 15 

C-3-0 San Jose 0.33 0.33 0.11 15 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. A-5 

Table A-5 

Detailed Information on Selenium from POTWs in North San Francisco Bay 

NPDES Name Ports 

Flow 

(mgd) Period Count 

Conc. 

(ug/L) Period Count Load Total Note 

E-001-S (M001) 0.89 11/02-

11/04 355 1.16 12/02-6/05 32 1.42 2 ports, both included in calculation 

CA0038768 American Canyon 

E-003-R/S (M003) 0.99 5/04-

12/04 214 1.06 1/03-6/05 31 1.46 2.87 

CA0038091 Benicia E-001 2.99 8/99-

4/07 2830 0.85 10/99-4/07 98.00 3.50 

E-001 45.81 1/98-

5/07 3126 0.34 1/98-3/07 99 21.79 

Overflow occured only once in 

1998, not regular discharge, not 

included in load estimate 

CA0037648 CCC 

OV-001 

Overflow & 

Bypass 

102.50 1/98-

2/98 55 

CA0038628 Central Marin E-001/M-001 11.00 5/98-

3/07 3076 0.81 5/98-3/07 99 12.26 

CA0038547 Delta Diablo E-001-D 11.46 1/99-

4/07 2829 4.07 1/99-4/07 104 64.50 

CA0037702 EMUD E-001 74.64 8/98-

4/07 3194 0.34 9/98-4/07 294 34.76 

E-001-A 16.95 4/99-

5/07 2553 0.75 12/98-10/03 95 17.45 

Concentrations not reported for E001-S, E-002, E-003, E-004, used 

E-001-A conc. 

E-001-S 15.73 12/98-

5/07 2675 

Some flow record for 001-S are the 

same to 001-A, E001-S not used for 

final load calculation 

E-002 0.02 1/00-

4/06 1396 0.02 Mostly 0 

E-003 0.01 1/00-

4/06 1400 0.01 Mostly 0 

CA0038024 Fairfield-Suisun 

E-004 1.44 12/98-

4/07 1583 1.48 18.97 

E-001 Dry 

(May) 3.20 5/03-5/06 50 Dry weather concentration not available CA0037851 Las Gallinas 

E-001 Wet (Nov 

to Apr) 3.75 12/01-4/07 968 0.95 1/01-3/07 15 2.48 
July 2008 North San Francisco Bay Selenium Data Summary and Source Analysis 

A-6 Tetra Tech, Inc. 

NPDES Name Ports 

Flow 

(mgd) Period Count 

Conc. 

(ug/L) Period Count Load Total Note 

E-002 Wet (Nov 

to Apr) 1.44 11/06-4/07 181 0.95 3.43 E-002 concentration not available 

CA0037770 Mount View E-001 1.98 6/99-

4/07 2872 0.67 9/99-9/06 38 1.83 

E-001 Dry 

(May-October) 3.81 6/02-7/04 398 0.57 9/02-7/04 13 1.49 

CA0037575 Napa 

E-001 Wet (Nov 

- Apr) 13.98 1/99-5/04 573 0.27 1/99-5/04 26 2.60 4.10 

E-001 

(Recycling) 4.01 5/02-03/07 773 

Recycled water not discharging to 

the Bay, and not included in the 

load CA0037810 Petaluma 

E-001 7.61 1/00-

4/07 1377 0.65 1/99-4/07 119 6.88 

CA0037796 Pinole E-001 3.18 1/00-

5/07 2708 0.91 3/00-4/07 47 4.00 

CA0037826 Rodeo E-001 0.80 3/00-

4/07 2613 0.80 3/00-3/07 30 0.89 

CA0038067 Sausalito E-001 1.63 12/99-

4/07 2615 2.46 12/99-4/07 85 5.53 

E-001 

(Recycling) 2.701 5/00-11/01 170 Concentration reported with high DL of 5 ug/L, load not calculated 

CA0037800 Sonoma 

E-001 4.089 1/99-

7/04 1287 

CA0110116 Treasure Island E-001 0.534 10/00-

4/07 2433 0.48 8/00-7/04 46 0.36 

E-001 

Carquinez 

(deep) 

13.17 1/99-

4/07 0.96 5/00-4/07 79 17.47 

EPA PCS database has E-001 and 

E-002; load is the sum of E-001 and 

E-002 

E-002 Mare 

(deep) 2.69 1/00-4/06 154 0.767 1/02-4/06 15 2.85 20.32 CA0037699 Vallejo 

Mare (shallow) 7.38 1/99-

1/99 5 Mare (shallow) only 5 records. Not included. 

E-001 DC 

(Combined) 14.14 3/03-5/07 1520 1.727 2/02-4/07 CA0038539 West County/Richmond 60 33.74 Conc only reported for E-001-DC 

E-001 D1 (West 

County) 9.33 10/2-5/07 1672 Load is only calculated for E-001-DC 
North San Francisco Bay Selenium Data Summary and Source Analysis July 2008 

Tetra Tech, Inc. A-7 

NPDES Name Ports 

Flow 

(mgd) Period Count 

Conc. 

(ug/L) Period Count Load Total Note 

E-001 D2 

(Richmond) 8.37 10/2-5/07 1642 

E-001 Ignacio 

Dry 4.01 5/99-5/99 31 0.475 5/99-3/04 4 2.63 

E-001 Ignacio 

Wet 4.48 11/02-11/02 21 

E-002 Novato 

Wet 2.23 5/99-11/04 119 0.833 11/02-3/04 4 2.57 

CA0037958 Novato SD 

E-003 

Combined Dry 5.67 5/99-5/99 31 

CA0037711 Sewerage Agency of 

So. Marin E-001 3.3 1/99-5/07 3043 1.394 1/99-4/07 133 6.36 

CA0037753 Marin Co. S.D. no. 5 

(Triburon) E-001 1.02 1/00-4/07 2250 1.93 1/00-4/07 47 2.72 

E-001 (Dry) 0.87 1/00-

5/05 962 0.51 1/00-1/06 19 0.61 

CA0037966 City of Calistoga 

E-002 (Wet) 0.65 29 

E-001 1.114 1/04-

1/04 31 <0.5 0.38 Concentration taken from permit 

CA0038016 City of Saint Helena 

E-001S 1.452 

CA0037885 Contra Costa Co. S.D. 

No. 5 (Port Costa) 0.02 NA NA 

CA0037427 Marin Co. S.D. no. 5 

(Paradise Cove) 0.02 0.73 0.02 Concentration taken from permit