# T ECHNICAL 

# M EMORANDUM 

# 2: N ORTH 

# S AN 

# F RANCISCO 

# B AY 

# S ELENIUM 

# D ATA 

# S UMMARY AND 

# S OURCE 

# A NALYSIS

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 94549North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## A BBREVIATIONS



## BASMAA Bay Area Stormwater Mana gement 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) MaterialNorth San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## T ABLE OF 

## C ONTENTS 

## Abbrevia tions

.................................................................................................................. . i 1. Introduc tion

........................................................................................................... 1-1 2. Selenium Concentrations in Ba y Water and Botto m Sediments

........................... 2-1 2.1. Goals of Da ta Summary

............................................................................... 2-1 2.2. Data Descr iption

........................................................................................... 2-1 2.3. What is the distribution of se lenium in the water column?............................ 2-3 2.4. What are the long term trends of sel enium concentrations in water?

........... 2-6 2.5. What is the relative mix of dissolv ed and particulate selenium in the water co lumn?............................................................................................ 2-10 2.6. How does selenium correlate with salinity and freshw ater flows?

.............. 2-11 2.7. What was the impact of refinery se lenium load reductions in 1998?

.......... 2-19 2.8. How does selenium correlate with suspended sediments and chlorophy ll- a?............................................................................................. 2-21 2.9. What is the distribution of selenium in sediments?..................................... 2-30 3. Source Charac teriza tion

........................................................................................ 3-1 3.1. Overview of Previous Source Es timates

...................................................... 3-1 3.2. Direct Atmospheric Deposition

..................................................................... 3-2 3.3. Urban and Non-urban Stormwater Runo ff fro m Local Tributaries ................ 3-3 3.4. Inputs fro m San Joaquin and Sacr amento Rivers vi a the Delta ................. 3-19 3.5. Municipal and Industrial Wastewater Dischar gers

...................................... 3-43 3.6. Petroleum Re fineries

.................................................................................. 3-50 3.7. Internal Sources - Sediment Erosion

.......................................................... 3-56 3.8. Loads from the South Bay

.......................................................................... 3-57 3.9. Comparison of Selenium Concentr ations and Loads from Different Source s

...................................................................................................... 3-58 3.10. Low Flow vs. High Fl ow Concent rations

.................................................... 3-61 4. Summary

............................................................................................................... 4-1 5. Key Findings and Imp lications for Model Devel opment......................................... 5-1 6. Refer ences

............................................................................................................ 6-1 Appendice s ..................................................................................................................A- 1North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## L IST OF 

## F IGURES 

### 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 sele nium 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 sele nium 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 ................................................................... 2-24July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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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 sedim ents 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.................... 3-26North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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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. ........................................................................................................ 3-52July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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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. ....................................................................................................... 3-55North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## L IST OF 

## T ABLES 

### 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 conc entrations 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................................................................................................... 3-61July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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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-5North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## 1. I NTRODUCTION 

## 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 th e most up-to-date inform ation. 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 deve lop a quantitative estimate of the sources of selenium to the waters of the North Bay. In addition to this documen t, two other technical memorandums are under preparation. The first of these assesses th e scientific l iterature to develop recommendations for selenium toxico logical endpoints in the North Bay, and the second presents a conceptual model of sele nium behavior in the North Bay, with an emphasis on describing the biogeochemical processes relating selenium sources to concentrations in biological tissues. Info rmation in these memorandums will support the development of a mechanistic model of seleni um in NSFB linking sour ces to endpoints of interest in the TMDL. There has been a long history of research on selenium sour ces, 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 Cutte r, 2004; Presser and Luoma, 2006; Meseck and Cutter, 2006). Starting in th e mid-1980’s, selenium concentrations have been monitored in the bay across the salinity gradient and in different seasons refl ecting variations in freshwater flows. Major sources of selenium to the Bay-Delta identified in these previous studies include:

! San Joaquin River that receives discha rge from agricultural drainage from the western San Joaquin Valley

! Selenium discharged from the effl uents 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 cont ributions from various point and non-point sources. Over the past two decades, there have b een 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 la te 1990s and beyond than in the 1980s, although this is not clear cut. The data summary (Section 2) prov ides an overview of water and sediment data collected in and upstream of NSFB over the pa st two decades. Data on selenium in biota are discussed in the memo on toxicological endpoints (TM-3). Th e water and sediment data are presented in maps and plots to provide a visual summary a nd to identify major processes occurring in the North Bay. There are many ways to represent th is large and complex data set. The broad objective of the data summary was to provide a reader with the spatial and temporal extentJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## of the data collected to date, and to evaluate whether existing data co uld 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 conc entrations and flow volumes of each of the identified sources in NS FB, 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 cons idered include: atmospheric deposition, urban and non-urban runoff, Delta inflows and the re lative contributions of the Sacramento and San Joaquin Rivers, municipal wastewater effluents, petroleum refinery e ffluents, and inputs from the existing reservoir of selenium in the sediments of the North Bay. Accurate quantification of sources is a key input to se lenium 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.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## 2. S ELENIUM 

## C ONCENTRATIONS IN 

## B AY 

## W ATER AND 

## B OTTOM 

## S EDIMENTS



### 2.1. G OALS OF 

### D ATA 

### S UMMARY 

## A key objective of the data summary is to ev aluate 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 se lenium in the water column?

! What are the long term trends of se lenium 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 th is evaluation are first described, and plots and maps of the data are used to a ddress each of the questions above.

2.2. D ATA 

### D ESCRIPTION 

## 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 res earch group at Old Dominion University 1 

## . The RMP is a joint effort among San Francisco Estuary Institute (SFEI), the Regional Board, and local dischargers. All data collected by the Cutte r 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 contam inant concentrations in water, sediment and bivalves. Fifteen monitoring sites were loca ted 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 tim es a year during high flow, intermediate flow and low flow periods. Starting in 2002, EPA’s Generalized Random Tessellation Stratified (GRTS) sample desi gn 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 random ly 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 detecti on 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, Environmenta l Geochemistry and Biogeochemistry Initiative (Grant: OCE-9707946).July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## analyzed for dry weight concentrations wi th 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 Ri ver (USGS Station 757), during 1980s and again during 1997-1999 (Cutter and Cutter, 2004; Dob lin et al. 2006). Samples were taken along the salinity gradient at a pproximately equal salinity intervals and were analyzed for dissolved selenium and selenium species (selen ate, selenite, and orga nic dissolved selenide) at detection limits of 1.6 ng/L. Because salinity varied accord ing to the sampling year, the spatial locations varied slightly for indivi dual 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 se lenium 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 ha s 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 Wa ter, sediment, bivalve 1993-2005 BG30* Delta/San Joaquin River Wa ter, sediment, bivalve 1993-2005 *Sampling continued at these locations after 2002North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### Figure 2-1 Locations of RMP long-term monitori ng sites and sampling by Cutter and Cutter (2004) during November 1999.


### 2.3. W HAT 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 pe riod 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 se len ium (calculated as the difference between total and dissolved se lenium) accounts for approximately 10% of the total. During the most recent sampling ove r 1999-2005, i.e., following improved wastewater control in the oil refineries in 1998 (Presse r and Luoma, 2006), mean dissolved and total selenium concentrations pooled across all the long-term monito ring 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 marg inally higher in the mid-estuarine regions of Suisun and San Pablo Bays compared to the freshwater and marine portions ( Figure 2-2). Total se lenium concentrations in the Centra l Bay are lower, most likely due to ocean exchange and dilution. A few locations near the confluence of lo cal tributaries (e.g., Petaluma and Napa River) show higher total seleni um concentrations rela tive to the rest of the bay ( Figure 2-2). The trends ar e most apparent when m edi an values are considered.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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

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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 deviationJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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### Total SeleniumBC10 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 concentra tions are higher in the upper es tuary (Suisun Bay) than the San Pablo and Central Bays.

2.4. W HAT ARE THE LONG TERM TRENDS OF SELENIUM CONCENTRATIONS IN WATER 

### ? 

## Over the long-term, dissolved a nd 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 tim e is noted, beginning in 1993. In most instances, the data show a gene ral negative slope with time, a nd 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 Sel enium 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 fu nction of time in stations near Mallard Island and in Suisun Bay (data source: RMP).July 2008 North San Francisco Bay Sel enium 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 fu nction of time in the San Pablo and Central Bay (data source: RMP).


### 2.5. W HAT IS THE RELATIVE MIX OF DISSOLVED AN D PARTICULATE SELENIUM IN THE WATER COLUMN 

### ? 

## Pooling all the data from the RMP monito ring indicates a close correlation between dissolved and total selenium ( Figure 2-7), with the dissolved fraction rep resenting 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 0.5Dissolved Selenium ("g/L)



### 0.0 0.1 0.2 0.3 0.4 0.5

R 2 

### = 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. H OW DOES SELENIUM CORRELATE WITH SALINITY AND FRESHWATER FLOWS 

### ? 

## Freshwater inflows from the Delta and from lo cal 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, a nd 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 f rom Cutte r and Cutter (2004) were also included for comparison. During low flow periods, dissolved se lenium concentrations are low at salinity 0 psu, and increase in the middle of estuary (sa linity 5-20 psu), and thendecrease again with increase of salinity (> 25 ps u). During high flow periods, se lenium 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 Cu tter (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 concentr ations were relatively constant during high flow ( Figure 2-9).July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

2-12 Tetra Tech, Inc. 

### Low Flow

Salinity 0 5 10 15 20 25 30 35Dissolved 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 35Dissolved 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 1999 2



### .

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 definiti on for the Cutter data set were the classification reported in Doblin et al. (2006): NDOI < 1.5 x 10 10 

### l/d (low flow), NDOI > 8.5 x 10 10 

### l/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 35Dissolved 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 35Dissolved 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 Ba y 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. C oncentrations in the San Pabl o Bay remain relatively high compared to the head of estuary. Concentratio ns 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 Sel enium Data Summary and Source Analysis

2-14 Tetra Tech, Inc. 

## During a wet period of the same year (Febru ary 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 S uisun and San Pablo Ba y 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, disso lved selenium concentrations along several salinity transects sampled by Cutter and Cutter (2004) suggested eith er 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 incr ease of salinity with som e removal along salinity gradient, possibly due to phytoplankton uptake. Dissol ved selenium concentrations were lower in April 1999 compared to Apri l 1986 and June 1998. With the implementation of improved waste water treatment in the refine ries in 1998, the most si gnificant change in water column selenium was with respect to selenite (Cu tter and Cutter, 2004). For both April 1986 and June 1998, selenite concentrations indicated an increase in the mid-estuary. In contrast, selenite concen trations for April 1999 remained low throughout the Bay ( Figure 2-12). Selenate concentrations exhibited m o re conservative mixing behavior. Selenate concentrations in April 1999 we re lower than in April 1986 a nd June 1998. Organic selenideJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

2-16 Tetra Tech, Inc. 

## concentrations showed some variability along the salinity transect al though concentrations for the three high flow periods are similar. Dissolved selenium concentrations during lo w 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 S eptember 1986. However, total dissolved selenium concentrations are still sl ightly elevated in the mid-estuary. The most significant change is the observed decr ease in selenite concentrations ( Figure 2-13; Cutter and Cutter, 2004). Selenite concentrations for Nove mber 1999 are significantly lower than September 1986 and remain relatively constant throughout the Bay. Selenate concentrations were generally similar between the 1986 tr ansect and October 1998 and November 1999 transects. Selenate concentrations show slightly elevated concentrations between salinity 10- 20 psu. Organic selenide shows variable conc entrations along the salinity transects.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

Tetra Tech, Inc. 2-17Total dissolved Se("g/L)

0.05 0.10 0.15 0.20 0.25 0.30 0.35 Apr 86 Jun 98 Apr 99Selenite ("g/L)

0.00 0.02 0.04 0.06Selenate ("g/L)

0.00 0.05 0.10 0.15 0.20



### Salinity 0 5 10 15 20 25 30Organic 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 Sel enium 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 99Selenite ("g/L)

0.00 0.02 0.04 0.06 0.08 0.10 0.12Selenate ("g/L)

0.00 0.02 0.04 0.06 0.08 0.10 0.12



### Salinity 0 5 10 15 20 25 30 35Organic 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. W HAT WAS THE IMPACT OF REFINERY SELENIUM LOAD REDUCTIONS IN 

### 1998? 

## Cutter and Cutter (2004) sampled the effluents of five refineri es in the North Bay for three time periods during 1999-2000. Average dissolved se lenium concentrations in the effluents of the refineries was 16.4 μg/L, a 66% decrea se 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 ev ident for the low flow and high flow period (Figure 2-14). Speciation of refinery effluent also cha nged dram atically 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 wate r 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. Selena te 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 change s 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 ± 0.063July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

2-20 Tetra Tech, Inc. 

### Low Flow

Salinity 0 5 10 15 20 25 30 35Dissolved 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 35Dissolved 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. H OW 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 mate rial 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 sa linity gradient generally track the pattern in TSM, and decrease along the salinity gradient during high flow ( Figure 2-16). Chlorophyll-a concentratio ns show some occasional elevated values for the April 1986 transect. Selenium concentrations in particulate material are ge nerally 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 TS M concentration (Doblin et al. 2006).July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

2-22 Tetra Tech, Inc. 

## During low flow, TSM concentrations also decr ease slightly with an increase in salinity ( Figure 2-17). TSM concentrations show occa sional increases in the m iddle of estuary, possibly due to resuspension. Par ticulate selenium concentrations track the patterns in TSM (Doblin et al. 2006), most evidently for th e September 1986 and November 1999 transects. Selenium concentrations in particulate materi al exceed values measured during high flow and also show some increase with increase of sali nity (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 in creases in the Central Bay.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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

0 10 20 30 40 50 60 70 80Chlorophyll-a ("g/L)

0 2 4 6 8 10 12 14 16 Apr 86 June 98 Apr 99Particulate Se ("g/L)

0.000 0.005 0.010 0.015 0.020 0.025

Salinity 0 5 10 15 20 25 30Se 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, pa rticulate 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 Sel enium 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 99Chlorophyll-a ("g/L)

0 1 2 3 4 5 6 7 8Particulate 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 35Se 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, pa rticulate selenium and selenium in particulate material under low flow (September 1986, October 1998, and November 1999; Doblin et al. 2006). 

## Particulate selenium concentrations, expre ssed as μg/l, vary less over time than TSM ( Table 2-5), although selenium content in suspended particles differs between low flow and highNorth 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 roughl y similar during low and high flow periods. Speciation of particulate selenium along th e 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 concentratio ns 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 m ixing ( Figure 2-21).July 2008 North San Francisco Bay Sel enium 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 99Elemental Se ("g/L)

0.000 0.004 0.008 0.012 0.016 0.020 0.024Selenite and selenate ("g/L)

0.000 0.004 0.008 0.012

Salinity 0 5 10 15 20 25 30Organic 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. 2-27Particulate Se* ("g/L)

0.004 0.008 0.012 0.016 0.020 0.024
Nov 97 Oct 98 Nov 99Elemental Se ("g/L)

0.000 0.004 0.008 0.012 0.016Selenite and selenate ("g/L)

0.000 0.004 0.008 0.012 0.016

Salinity 0 5 10 15 20 25 30 35Organic 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 Sel enium Data Summary and Source Analysis

2-28 Tetra Tech, Inc. 

### TSM (mg/L) 0 10 20 30 40 50 60 70Particulate 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 R 2 =0.68

R 2 =0.57



### Figure 2-20 Correlation between particulate sel enium 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. 2-29TSM (mg/L)

0 10 20 30 40 50Chl a ("g/L)

0.8 1.2 1.6 2.0 2.4 2.8 3.2Particulate Se ("g/L)

0.004 0.008 0.012 0.016



### Salinity 0 5 10 15 20 25 30Se 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 Sel enium Data Summary and Source Analysis

2-30 Tetra Tech, Inc. 

### 2.9. W HAT 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 to tal range of concentrations is not large ( Figure 2-22). Sediment selenium concen tratio ns 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 Ba y, 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 th ese are single point concentrations and not averages. The majority of the sediment samp les 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 sedim ent selenium concentrations observed are well below the eco logical 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 sediment s are correlated to sediment grain size and organic carbon content. Sediment selenium con centrations were found to be highly related to percent fines < 0.00625 mm and percen t total organic carbon (TOC) (R 2 

## = 0.78 and R 2 

## = 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 relationshi p s are still observed. As illustrated in Figure 2-24, sites with low sedim ent selenium concentr ations correspond to low percent fines in the sediments and vice versa. Meseck (2002) obs erved a similar strong relationship between sediment selenium and organic carbon concentrations (R 2 

## = 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 se lenium (Meseck, 2002). Elemental selenium accounts for a median of 45% of the total seleni um in the sediments across the sites, with selenite and selenate accounting for a medi an of 17%. The difference between total, elemental and selenite and selenate is the or ganic 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 seasona l variations, concentrations are generally stable at the monitoring sites excep t 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 Sel enium Data Summary and Source Analysis

2-32 Tetra Tech, Inc. 

### Fines < 0.0625 mm (%) 0 20 40 60 80 100Se in Sediments ("g/g)



### 0.0 0.1 0.2 0.3 0.4 0.5 0.6

R 2 

### = 0.778 [Se] = 0.0537+ 0.0028 * % Fines

TOC (%) 0.0 0.5 1.0 1.5 2.0 2.5Se in Sediments ("g/g)



### 0.0 0.1 0.2 0.3 0.4 0.5 0.6

R 2 

### = 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 100Se 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 2.0Se in Sediments ("g/g)



### 0.0 0.1 0.2 0.3 0.4 0.5 R 2 

### = 0.385 [Se] = 0.0346+ 0.0028 * % Fines

R 2 

### = 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 Sel enium 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

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## 3. S OURCE 

## C HARACTERIZATION 

## The goal of the source characteri zation is to quantify the vari ous point and non-point sources that contribute selenium to North San Fran cisco Bay. The sources evaluated and their key features are listed below.

! Atmospheric deposition – includes both dr y and wet deposition to the bay water surface, and is usually consider ed as a small selenium source

! Urban and non-urban runoff from local trib utaries – includes both agricultural and urban stormwater runoff, and may be a sign ificant 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 efflue nts – which generally have low concentrations of selenium

! Petroleum refineries – which were the majo r sources of selenium (in the form of selenite) in the 1980’s and have decrea sed dramatically since 1999 because of improved wastewater treatment

! Input from bay sediment – net sedime nt erosion, resuspension, diffusion, and dredging activities can be poten tial 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 critic al period for selenium bioaccumulation due to longer residence time, while wet season has larger flow volumes and can potentially contribute larger loads of se lenium 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. O VERVIEW OF 

### P REVIOUS 

### S OURCE 

### E STIMATES 

## 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 su b-areas of western Sa n Joaquin Valley were also estimated under different dischargi ng scenarios by Presser and Luoma (2006). Of special relevance to any long-term evalua tion of selenium trends in NSFB is the reduction of loads from refineries that occurred because of ma jor improvements in wastewater treatment in the late 1990s. Sele nium loadings from oil refineries ranged between 928-2,116 kg/yr during 1987 and 1988 (Cu tter and San Diego-McGlone, 1990) and 1,415-3,400 kg/yr during 1986-1992 (SFBRWQCB, 19 93). Refinery discharge declined after July 1998 and selenium lo ads 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 estim ated to be 247 kg/yr during a critically dryJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## 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 concep tual model for selenium in the bay and estimated various sources including:

! Riverine fluxes via the Delta

! North Bay refinery effluent discharges

! Municipal wastewater, local tr ibutaries, and urban runoff Loading rates from the Delta were estimated by multiplying net freshwater discharge from the Delta and a “river end member con centration” 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 con centrations reported by Cutter and Cutter (2004) and ranged between 204-552 kg/yr. Urban and non-urban runoff and m unicipal wastewater loadings were estimated by some simple cal culations (Abu-Saba and Ogle, 2005). Average annual runoff volume (both urban and non-ur ban) for the Bay Area is about 900 Mm 3 

## (McKee et al., 2002) and annual discharge volume fr om wastewater is at a similar volume of 866 Mm 3 

## (Grovhoug et al., 2004). Selenium concen tration in local ru noff 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 thes e sources to range be tween 90-900 kg/yr with uncertainty. Cutter and Cutter (2004), based on data fo r 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 dissolve d selenium ranged between 773–26,195 g/day, with selenite inputs ranging between 110-2,446 g/day, selena te ranging between 497 – 17,121 g/day, and organic selenide ranging between 55 – 6,486 g/da y. 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 orga nic selenide ranging betw een 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 a nnual 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-po int 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. D IRECT 

### A TMOSPHERIC 

### D EPOSITION 

## Atmospheric deposition of selenium occurs both as dry and wet forms. Selenium is emitted to the atmosphere naturally as volatile dime thyl selenide, or as selenium dioxide andNorth San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## elemental selenium from fossil fuel com bustion (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 sele nite is the major species in wet de position 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 b een measured in the San Francisco Bay and estimates were made using data from other st udies. Atmospheric deposition of selenium is believed to represent only a sm all input to the wa ter surface and the watershed in other studies (EPA, 2002). Reported con centrations of selenium in precipitation are 0.1 - 0.4 μg/L in urban areas (Mosher and Duce, 1989). Concen trations 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 depo sition, 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 km 2 

## 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/m 3 

## . Concentrations measured in the Chesapeake Bay range from 1.4 – 1.8 ng/m 3 

## (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 associ ated with fine partic les; therefore a lower deposition velocity is expected. Based on a concentration ra nge of 0.3 – 2.4 ng/m 3 

## and deposition velocities of 0.1 cm/s and 0.26 cm/s, es timated 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 comparis on with other sources discussed below.

3.3. U RBAN AND 

### N ON 

### - URBAN 

### S TORMWATER 

### R UNOFF FROM 

### L OCAL 

### T RIBUTARIES 

## Local tributaries, that is, streams that discharg e directly into the Nort h 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 ag ricultural 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/km 2 

## vs. ~14 t/km 2 

## ; McKee et al. 2003). With respect to seleni um, 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 (med ian 0.38 μg/L) for the dry season and 0.56-9 μg/L (median 3.6 μg/L) for the wet seas on (EOA, 2006). Selenium concentrations observed in five tributaries of the North Bay in the Surface Water Ambient MonitoringJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## 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 an d 0.39- 3.14 μg/L (median 0.90 μg/L) during the wet season (SFBRWQCB, 2007a). Total seleni um 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 obser ved in the tributaries is mo stly 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 SWAMP 4 

## study by the San Francisco Bay Regional Water Quality C ontrol Board during 2001-2004 are listed in Table 3-1. SW AMP monitoring programs targeted both clean and polluted areas of the watershed. Therefore, many sampling site s are located in urban or agricultural areas. For each watershed, a number of stati ons 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 targ eted 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 concentr ations were found for all seasons ( Figure 3-1). The highest total selenium concentration was observe d at an urban influenced site during the dry season (8.1 ! g/L at KIR115-Kirker Creek Apartm ents). Average total selenium concentrations for the most downstream site s 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 m ore representative of the watershed condition by integrating all the land uses and therefor e only downstream sites were used in the calculations of loads to th e 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 di ssolved than total selenium concentrations were reported. For the purpose of the load ca lculations, estimates we re 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 Nort h Bay are mostly located in the Alameda County with two sites lo cated 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 BA SMAA dataset, with higher detection limit (at 0.2 ! g/L) and higher percentage of non-detect s 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 li mits. Measured concentrations seem to vary

4 

### Surface Water Ambient Monitoring Program, a statewide program to asse ss water quality conditions in surface water bodies.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## with detection limits. Land uses for watershe ds surrounding the samp ling 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
Wet 2003-2004 2.00 2.00 Mt. Diablo Creek MTD010 Spring 2003-2004 0.40 0.30
Wet 2003-2004 1.30 1.40 PET010 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 Spring 2001-2002 2.74 2.57 San Pablo Creek 206SPA020 Dry 2001-2002 1.60 1.53 Spring 2001-2002 0.90 1.04 Suisun Creek 207SUI010 Dry 2001-2002 0.32 0.17 Spring 2001-2002 0.39 1.41 Wildcat Creek 206WIL020 Dry 2001-2002 1.33 1.11
Wet 1.57 1.60 Spring 1.03 1.19 Average

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

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## (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

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## Three methods were used to estimate selenium loads from local tr ibutaries based on two different methods of estimating runoff from lo cal 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 1/1/04Total 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 Concentrati ons 

## Total annual runoff from local watersheds ha s been computed using a simple model by Davis et al. (2000). The predic ted 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 lo cal watersheds (hydrological areas) is shown in Figure 3-3. The average annual lo adings 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 wate rshed areas and high annual runoff. Runoff in the Bay area shows la rge year-to-year variation. Th erefore, loadings from local tributaries are expected to vary greatly with climate conditions. Waters heds in the Bay area show inter-annual variation with coefficien t of variation (CV) ranging from 0.65 to 1.01 (McKee et al. 2002). The 10 th 

## and 90 th 

## 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 di fferent climate conditions, 10 th 

## and 90 th 

## 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 Sel enium Data Summary and Source Analysis

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### Figure 3-3 Hydrological areas surrounding NSFB. Source: San Francisco Estuary InstituteNorth 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 (Mm 3 /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 39.1San 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 Concord 3 106 Mt. Diablo Creek 0.4 42.4 Concord 4 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 Concentrati ons 

## The second method is based on USGS flow data in the Bay area to estimate selenium loading from local tributaries. Daily flow r ecords from several USGS gaging stations for some major North Bay tributaries ar e available for di fferent 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 1 st 

## to Apr 30 th 

## ). Flow during the dry season (defined as May 1 st 

## to September 30 th 

## ) 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 re flect the current hydrologic regime of the watershed. The long-term average monthly flow and th e 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 estimat ed by multiplying flow and concentrations of the same river. For tributaries without observe d 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 volum es, total selenium is mainly delivered to the bay in wet s eason. Dry season loadings averag e 0.2 – 3.0% of wet season loadings for 6 of the 8 stations ( Table 3-5). An annual areal lo ading was also estimated forJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## each of the tributary, based on total annual se lenium loading and the drainage area. The estimated areal loadings were used to scal e up loading estimates of the entire hydrological area (e.g. Novato Creek at Novato was scaled up for the whole Nova to hydrological area). For hydrological areas without data (e.g., Sa n Rafael), areal lo ading 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 estim ated 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 con centration of the whole North Bay tributaries were used and therefore the estimates are subj ect 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 (mi 2 ) 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 1938-1977North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### 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) 151.3 203.5 206.1 846.1 250 5.3 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) 249.8 200.3 189.4 422.5 336.9 211.0 186.9 124.2July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

3-12 Tetra Tech, Inc. Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov DecLoading (kg)

0 1 2 3 4 5 6 USGS11459500 (Novato Creek at Novato)

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov DecLoading (kg)

0 2 4 6 8 10 USGS11459300 (San Antonio Creek nr. Petaluma)

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov DecLoading (kg)

0 2 4 6 8 10
USGS11459000 (Petaluma River at Petaluma)

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov DecLoading (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 DecLoading (kg)

0 20 40 60 80 100

USGS11456000 (Napa River nr. Napa)

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov DecLoading (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 DecLoading (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 DecLoading (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 monthl y selenium loadings at gaging stations of local tributaries.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

Tetra Tech, Inc. 3-13Novato Creek at NovatoSan Antonio Creek nr. PetalumaPetaluma River at PetalumaSonoma Creek at Agua Cal.Napa River nr. NapaWildcat Creek at RichmondWalnut Creek at ConcordPinole Creek at PinoleLoading (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 SW AMP 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 accumula ted to estimate seasonal loading for all the years. As a result of variations in hydrologi cal 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) ve rsus less than 100 kg/yr during a dry year (1994). The dry and wet year notation was ba sed on the classification system for San Joaquin and Sacramento River by th e Department of Water Resources ( http://cdec.water.ca.gov/c gi-progs/iodir/W SIHIST ). 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 1 st 

## to September 30 th 

## . The wet season is defined as October 1 st 

## to April 30 th



## .July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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### 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/mi 2 ) 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 5.71North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### Table 3-6 Estimated annual total selenium loadings for the hydrological areas in the North Bay.
Hydrological Areas Drainage Area (Mm 2 ) Area (mi 2 ) 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. Napa1991 (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 Sel enium Data Summary and Source Analysis

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### 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 Ba y PCB TMDL (KLI, 2002; SFBRWQCB, 2007c). Loads are estimated from five broad categor ies of land use (agricultural, open space, industrial, commercial and resi dential) 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 prev iously determined by Davis et al. (2000; Table 3-7). Best estimates of r unoff coefficient for each land us e 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 derive d from BASMAA (1996) and SWAMP study (SFBRWQCB 2007a, b). BASMAA (1996) sampling st ations 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 us e 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 concentrati ons from the BASMAA study are similar across land uses (Table 3-8). Stations from the SW AMP study are generally located in the urban areas, with Suisun Creek stations located in ag riculture-dominated areas. Therefore values from Suisun Creek were used to derive concen trations for the agricultural areas. Due to the differences in concentrations reported in tw o programs, values from BASMAA were used as lower bound of concentrations fr om local tributaries, while SWAMP data were used as an upper bound (Table 3-8). Overall, Method 3 results in a somewh at 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

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### 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 (Mm 2 ) 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 SWAMPJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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### Table 3-9 Estimated total selenium loadings (kg/yr) by la nd 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 loads 1 (kg/yr) 491.1 (148.2 lower bound)

1 Urban loads are the sum of residentia l, commercial, and industrial land uses.



## Estimated stormwater runoff from urba n areas surrounding the NSFB is 316.8 Mm 3 

## /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 agri cultural, 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). Estima ted loads from urban areas based on the BASMAA concentrations are at 148.2 kg/yr, abou t 43% of loads from all land use areas.

3.3.5 Tributary Load Summary 

## Three, somewhat overlapping methods were us ed to compute tribut ary loads. Using the SWAMP selenium data from the tributaries, lo ads were computed using flow from different sources: modeled annual flows from a recent st udy (Davis et al., 2000) and measured flows from USGS gage stations. The modeled flows we re 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 concen trations derived from BASMAA and SWAMP concentration data. Loads from urban areas ge nerally 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

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## Driven in large part by relativ ely 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 es timation. Much of this load (greater than 95%) is delivered to the bay in the wet months, consistent w ith 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 elem ent, 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 meas urements, it is nonetheless clear that the load estimates above are base d on a limited amount of data. Furthermore, the SWAMP and BASMAA concentrati ons differ: lower mean concen trations were observed in BASMAA dataset. However, the ra nge 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 uncer tainty in flows, and the year-to-year variability, estimated loads fr om 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 SWAM P concentrations and measured flow. For the purpose of this analysis, we go forward w ith 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 (T SS) loads for different hydrologi cal 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 1.91x10 8 

## kg/yr for the North Bay watershe ds. With a particulate selenium concentration of 0.62 ! g/g, estimated particulate selenium loads from local tributaries are 118.2 kg/yr.

3.4. I NPUTS FROM 

### S AN 

### J OAQUIN AND 

### S ACRAMENTO 

### R IVERS VIA THE 

### D ELTA 

## Although selenium inputs from the Central Va lley via the Delta are expected to be a significant source to the North Bay, accurately es timating 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). Theref ore, on an annual basis loads from both rivers to the Delta are significant. However, selenium processes in the Delta ar e not well characteri zed. Besides the normal processes of settling and mixing, a large portion of the water in th e Delta is also exported forJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## 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 Luom a, 2006). In this secti on, available flow and concentr ation 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 10/1/05Flow (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 10/1/06Flow (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, St ate 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 Malla rd Island at the BG20 (Sacramento River) and BG30 (San Joaquin Ri ver) stations. Observed total selenium concentrations at these stations (0.15 and 0.18 μg/L, re spectively) are more representative of Delta concentrations than of th e individual rivers. The concentr ations 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, andNorth San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## possibly tidal influences from the bay during low flow periods. Concentrations observed at BG20 and BG30 also correlate well (R 2 

## = 0.59) possibly due to mi xing of common sources. In a separate study, selenium concentrati ons were found to decrease by 60-80% during transport from the San Joaquin River at Vern alis into the estuary at Antioch (Cutter unpublished data; Meseck and Cutter, 2006).
Different methods have been used in previous studies to calcul ate 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 (BG2 0 and BG30) to estimate loads of different pollutants from Central Valley to the Bay. L eatherbarrow et al. (2005a) and McKee et al. (2006) used continuous monitori ng data of SSC at Mallard Island to estimate loads of sediments, mercury and organics to the Bay. With respect to seleni um, Presser and Luoma (2006) estimated loads from the two rivers (S acramento River at Freeport and San Joaquin River at Vernalis) separately to estimate selenium inputs to th e Bay. Cutter and Cutter (2004) and Abu-Saba and Ogle (2 005) used the approach of fl ow 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 availa ble data. The first approach is the simple approach similar to Davis et al. (2000), wh ich uses average concentration of two RMP stations in the Delta and multip lies it by the net Delta outflow. The second approach uses selenium loadings from the Sacramento and th e San Joaquin Rivers se parately based on data from Cutter and Cutter (2004) and applies a “Delta removal constant” similar to Meseck (2002) to account for the possi ble selenium loss in the De lta. The third approach is independent of the prior two, in which the lo adings from Central Valley to the bay were estimated as the difference between inputs fr om the two rivers minus the export through aqueducts. The third method can be used to esti mate 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
m easured at BG20 and BG30 also show year- to -year variations, and no correlation with the Delta outflow and no clear pattern in wet versus dr y 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 annua l 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. E xcluding 1998, estimated annual loadings vary by a factor 6 among the years. Loadings from the Delta are more significant in th e 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 Sel enium Data Summary and Source Analysis

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## There is some limited evidence that the Delta load may be higher than computed using this method and using BG-20 and BG-30 concen trations from the RMP. Selenium concentrations have been measured in the ou tflow 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 concen trations observed at Mallard Island during storm events suggest potential of higher load ings 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 relati onship was used to estim ate total selenium loadings during high flow. The result indicates a potential of 16-56% underestimate of total selenium loadings us ing BG20 and BG30 concen trations (e.g. 1,059 kg/yr vs. 1,590 kg/yr for a dry year 2001 an d 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 recomme nded for calculation of long term Delta loads. Leatherbarrow et al. (2005a) used concentratio ns measured at Mallard Island to estimate loads of PCB (polychlorinated biphenyls), PAH (polycycli c aromatic hydrocarbons), OC (Organochlorine) pesticides, and Hg from th e Delta to the Bay. Contaminant loads were estimated based on relationships between contaminants and SSC, and the estimated sediment loads using available flow info rmation 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 we re estimated. The relative contributions of the advective and dispersive load were estim ated using point velocity and concentration measured during water year 1994 and 1996 (McKee et al. 2006). During a wet period (mean discharge = 2116 m 3 

## /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 to tal load during low flow period. Estimated dispersive load for a low flow period (Apr il 15, 1994-June 4, 1994) was 49% of advective point load at surface and 52% at mid-depth (McK ee 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 app licability of this method fo r 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 calculati on appears at the e nd of this section.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### 1992 1994 1996 1998 2000 2002 2004 2006 2008Flow (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 Sel enium Data Summary and Source Analysis

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

Year Delta outflow
m 3 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 

### R 2 

### = 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 seleniu m 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 S acramento River at Freeport sampled by Cutter and Cutter (2004) on biweekly or monthly base s indicated relatively small changes from 1984 to 2000 ( Figure 3-11). Dissolved selenium concentrations in the Sacramento River (atNorth San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## 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 significan t decrease in selenium concentrations was observed for 1999-2000 compared to the 1 980s sampling. Mean dissolved selenium concentration for the period of 1999-2000 is 0.68 ± 0.20 ! g/L. Concentrations during 1999-2000 show some vari ations both in the Sacramento and San Joaquin River ( Figure 3-12). For the Sacramento River, higher concentrations were observed f or the months between April to July. For th e San Joaquin River, no clear seasonal pattern was observed. Concentrations in relation to flow are shown in Figure 3-13. For the Sacram ento 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 correla tion between river discharge and any dissolved selenium forms for the Sacramento River. For San Jo aquin River, a negativ e 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 con centration relationship derived was used to estimate daily concentrations based on flow. The daily loadi ng 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/nw is/dv/?referred_m odule=sw ). The estimated daily loadings were summed to calculate the seasonal loadings. The wet season was defined as Oct 1st to Apr. 30 th 

## and the dry season was de fined as May 1st to Sep 30 th 

## (Tetra Tech, 2006).July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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### 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 1/1/00Dissolved 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 1/1/00Dissolved 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

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### Sacramento River at Freeport (subset of data)

Date 10/1/98 2/1/99 6/1/99 10/1/99 2/1/00 6/1/00Dissolved 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 6/1/00Dissolved 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 Sel enium Data Summary and Source Analysis

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### Sacramento River at Freeport

y = -3E-08x + 0.0752 R 2 = 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 R 2 = 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 lo adings range between 703 – 2,693 kg/yr for the Sacramento River at Freeport and 867 – 4,710 kg/ yr for the San Joaqui n 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 S acramento River and 552- 3,048 kg/yr for SanNorth San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## Joaquin River. On average, dry season loadi ngs 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 ex ception (San Joaquin River in 1995). Estimated annual dissolved selenium loadings vary with water years ( Figure 3-14). Annual loadings can be as hi gh as 2,600-2,700 kg/yr during wet year s for the Sacram ento River (at Freeport) and approximately 750 – 1,000 kg/yr during dry years. Annual loadings for the San Joaquin River (at Vernalis) also vary w ith 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 loadi ngs are higher for the San Joaquin River (at Vernalis) than the Sacramento River (at Fr eeport) (2,380 kg/yr vs . 1,634 kg/yr during 1990- 2007).
Total selenium concentrations were also m easured 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 to tal selenium concentrations were higher during the 1980s and early 1990s compared to recent years ( Figure 3-15). Dissolved selen ium concentrations for the same peri od measured by Cutter an d Cutter (2004) agree relatively well with the total selenium con centrations observed in the SWAMP study but were slightly lower ( Figure 3-16). This is to be expect ed as dissolved selenium usually accounts for 80-95% of total selenium measur ed. The observed decreases of selenium concentration at Vernalis most likely resulte d 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 Crow s Landing). With transport downstream, the change in concentration was smaller, likely due to in flow 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 selen ium concentrations measured by SWAMP we re 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 calcula te 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 m ethods were observed.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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### Sacramento River at Freeport1991 (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 Vernalis1991 (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

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## 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 1/1/08Selenium ("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 6/1/00Selenium ("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 Sel enium Data Summary and Source Analysis

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### 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 1/1/08Selenium ("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 1/1/08Selenium ("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 1/1/08Selenium ("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 R 2

= 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 Sel enium 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 po tentially serve as a mechanism to remove high selenium concentrations originated fr om the San Joaquin River. As shown in Figure 3-21, during two low flow sa mpling events, dissol ved selenium concentrations were high in close proximity to the San Joaquin Rive r and decrease through the Delta. Dissolved selenium concentrations at the head of estu ary were much lower than the concentrations observed close to the river.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### Figure 3-21 Dissolved selenium concentrations at various locations of the Delta and North Bay in October 1998 (NDOI = 4.27x10 10 

### L/d) and November 1999 (NDOI = 1.07x10 10 

### 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, sele nium concentrations at Vernalis are reduced by 60-80% after being transported through Delta into the estuary at Antioch.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## Therefore, Meseck (2002) applied a “Delta rem oval” 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
com pared to Method 1, above, for each year. The percent absolute difference between the two methods for each individual year ra nges between 6.3-51.9% except for 1998, an unusually wet year. For 1998, previous method es timated 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 Delta1991 (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 th e 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 es timating selenium loads from the Delta. The previous method based on RMP monitoring data set 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 disc ussed next, an alterna tive is to consider outflow data from the Delta through aqueducts, an d the estimated selenium concentrations in these outflows, to evaluate th e net loads delivered to bay.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### 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 dom inated by Sacramento River water. During some periods, San Joaquin River water can al so dominate. Assuming equal volume mixing of the two rivers, the selenium concentra tion 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 aque ducts is likely to range between 700- 2,700 kg/yr. For critically dry years during 1986-199 8, 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 e xports can also be performed. The contribution of the Sacramento and San Joa quin Rivers or other re latively 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). Resu lts from DSM2 simulations indicated that during dry years or in the dry se ason, 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 sim ulations 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-04Percent 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 Sel enium 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 aqueduc t, Qsac is export flow originating from the Sacramento River, Csac is daily selenium con centration at the Sacram ento 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), a nd Qexp is total flow through the aqueducts (includes the Central Valley Project, State Wate r Project, Contra Costa Water District, and North Bay Aqueduct). We made the assumpti on 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 da ily loads. Estimated loads exported through aqueducts for the years between 19 93-2003 range between 883 – 1,985 kg/yr ( Figure 3-24). Dry season loads are co mparable to wet season loads, largely because aqueduct exports are less variable than riverine flows over the c ourse 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 de termined previously, i.e., 700-2,700 kg/yr. Contribution of loads to aqueducts from the tw o rivers was also estimated based on modeled contribution of flow from the two rivers an d concentrations at each river. The results indicated that the San Joaquin Ri ver 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, co mpared to 600-1,780 kg/yr from the San Joaquin River. Although the Sacramento River do minates in terms of flow in the aqueducts most of the time, due to higher selenium con centrations, 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 tw o 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 approxim ately 1,000 kg/yr (e.g. 1994, 2001). Loads in wet years can be much larger (n early 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. Estimat ed loads from the two rivers to the Delta are generally comparable. Annual selenium load s from the San Joaquin River are normally below 1,000 kg/yr. However during wet years la rger 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 be tween 200-300 kg. However for a few wet years, dry season loads from the San Joaquin Ri ver are approximatel y 1,000 kg. An average dissolved selenium load of 2,696 kg/yr fr om 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

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## Observed selenium concentra tions at Delta-Mendota Canal near Tracy Headworks (Milepost 3.50) obtained from U.S. Bureau of Reclamati on are higher than th e estimated selenium concentrations in the aqueducts using the fl ow-weighted method described above (Figure 3- 23). Note the observed concentration at Delt a-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 wate r 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 highe r end of our estimates of 700- 2700 kg/yr.
Selenium concentration data from the Stat e 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 b ecause 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 thr ee different methods to compute loads, and to compare these values. Note that for the seco nd and third methods, da ta was available to compute only the dissolved selenium loads and not the total load.

! The first approach used average concentra tion of two RMP stations in the Delta and multiplies it by the net tidally corrected Delt a 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 load ings from the Sacramento and the San Joaquin Rivers separately based on data fr om Cutter and Cutter (2004) and applied a “Delta removal constant” si milar to Meseck (2002) to account for the possible selenium loss in the Delta. These concentr ations 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 th e prior two: the loadings from Central Valley to the bay were estimated as th e 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 av erage load estimate of 2,696 kg/yr of dissolved selenium (1993 to 2003). Given the simplifications and assumptions empl oyed 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 di ssolved data were av ailable, and because the flow volumes used in load calculation are tidally corrected, it is recommended that thisJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## method be used for describing Delta loads, re sulting in an average De lta 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 continuou s 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 calculati on 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 es timated 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 aqueducts1993(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 export1993(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 export1993(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 thro ugh the aqueducts and contributions from the Sacramento River and the San Joaquin River.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

3-42 Tetra Tech, Inc. Delta loads to the Bay1993(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 River1993(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 River1993(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

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### 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 1/1/08Se 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. M UNICIPAL AND 

### I NDUSTRIAL 

### W ASTEWATER 

### D ISCHARGERS 

## 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 treatm ent although a few incorporate advanced treatment (i.e., City of American Canyon, Napa Sanitation District). Dry weather flows from these facili ties range from <1 to 120 mgd. Flow at five largest municipal discha rgers in the North Bay is shown in Figure 3-28. Flow at municipal discharges generally follows a seas onal pattern of higher concentration during the wet season, most likely due to storm water runoff. Concentrations in effluents of m unicipal dischargers generally are below 1 ! g/L, with many samples below detection limit ( Figure 3-29).

Ef fluent total selenium concentrations at a m onthly interval are reported for these facilities. Total selenium concentrations in the effluents are generally near 1 μg/L ( Table 3-11). Ef fluent concentrations at two facilities with the largest discharges (i .e., East Bay Municipal Utility District, EBMUD and Central Contra Costa Sanitation Dist rict, CCCSD) average 0.34 ± 0.19 μg/L and 0.34 ± 0.50 μg/L. Reported concentrations compared well to the dissolves selenium concentrations observe d by Cutter and San Diego-McGlone (1990) during 1987-1988 sampling (24-hour composite sa mple 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 Sel enium Data Summary and Source Analysis

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## Two methods were used in calcu lating 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 lo adings were estimated base d 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 disreg arded. Estimated daily loadings show large temporal variations ( Figure 3-30) related to th e flow variability.
Estim ated annual selenium loadings from POTWs in the North Bay are 255.3-255.8 kg/yr ( Table 3-12). More detailed information on flows a nd concentrations, as well as identification of individual ports used in lo ad estimates is presented in Appendix A5. The loadings are roughly half of values previous ly estimated by Cutter and San Diego-McGlone (1990) for the entire bay (1.08 kg/day or 394 kg/yr). Effluents from municipal discha rgers 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 indus trial facilities are minor compared to other sources ( Table 3-13).North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### Figure 3-27 POTW discharge locations in and around San Francisco Bay (source: SFBRWQCB, Basin Plan).July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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

Municipal dischargers Outfall Location (Fig. 3-27) Mean 1 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 A gency 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 (Ti buron) 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 Di strict 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 Pe rmit 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 permitsNorth 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 08Flow (mgd)

0 20 40 60 80 100 120 140 160

EBMUD

Year 98 00 02 04 06 08Flow (mgd)

50 100 150 200 250 300

Fairfield - Suisun

Year 00 02 04 06 08Flow (mgd)

0 10 20 30 40 50 Vallejo Sanitation

Year 98 00 02 04 06 08Flow (mgd)

0 20 40 60 80 100 120 140 160 180

West County Agency

Year 02 03 04 05 06 07 08Flow (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 Sel enium Data Summary and Source Analysis

3-48 Tetra Tech, Inc. Central Contra Costa

Year 98 00 02 04 06 08Concentrations ("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 08Concentrations ("g/L)

0.0 0.4 0.8 1.2 1.6 2.0

Vallejo

Year 00 02 04 06 08Concentrations ("g/L)

0 1 2 3 10 11 12 Fairfield - Suisun

Year 98 00 02 04Concentrations ("g/L)

0.0 0.4 0.8 1.2 1.6 2.0

West County Agency

Year 02 04 06 08Concentrations ("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

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

POTW Facility Name Outfall Location Average Flow (mgd) Estimated Se Loadings 1

(kg/yr) Estimated Se Loadings 2

(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 Calistoga 3 (E-001 dry) (E-002 wet) 4 0.87 0.65 0.60 0.46 0.20

City of Saint Helena E-001 3 30 1.11 0.38 Central Contra Costa S.D. 5 45.8 21.8 15.0 Central Marin Sanitati on 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 (T iburon) 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 Sout h 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 aver age concentration and average daily flow 2 - Estimated based on flow and conc entrations 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 Sel enium Data Summary and Source Analysis

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### 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 1/1/07Daily loading (g/day)



### 0 100 200 300 400 500 600

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


### 3.6. P ETROLEUM 

### R EFINERIES 

## Mean selenium concentrations at the refineries range between 11.9 – 27.7 ! g/L ( Table 3-14). Concentrations show relatively large variations over tim e ( Figure 3-31). Daily flow
m easurement at the refineries indicates some seasonal high flows, probably due to storm water runoff ( Figure 3-32). Concentrations generally s how 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 dail y maximum concentrations for the refineries range between 12 – 28 μg/L. No relationship between concentrations and flow were observed. The annual loadings were calcul ated by summing the daily loadings. TheNorth San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## estimated total daily loading from these refine ries is 1.47 kg/day or an average of 537 kg/yr during 1999-2007 ( Table 3-15). Current loadings are si gnif icantly lower than the previous years (1,407 – 3,382 kg/yr in 1986 – 1992) fo llowing the improvement in waste water treatment practices at the refi neries (Presser and Luoma, 2006). To calculate seasonal loads, daily loads were calculated by multiplying daily flow with weekly concentration extrapol ated to the week and then adding up for dry and wet season. Wet season was defined as Oct. 1st to Apr. 30t h. 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 lo adings are generally 62-78% of the average wet season loadings at four of the refineries. Average dr y 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 (compare d to 64% in 1987-1988, Cutter and Cutter, 2004). The speciation in refineries is similar to that in muni cipal 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 loading 1 (kg/day) Mean daily loading 2 (kg/day) Annual loading 1 (kg/yr) Annual loading 2 (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 c oncentrations extrapolated to the rest of the week 2 – Calculated based on daily flow and concentrations on sampling dates onlyJuly 2008 North San Francisco Bay Sel enium 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 co ncentrations for the refineries in the North Bay.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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98 99 00 01 02 03 04 05 06Flow (mgd)

0 5 10 15 20 25 30 35

Conoco Phillips

98 99 00 01 02 03 04 05 06 07 08Flow (mgd)

0 2 4 6 8 10

Shell Martinez

Year 98 99 00 01 02 03 04 05 06 07 08Flow (mgd)

0 2 4 6 8 10 Tesoro

99 00 01 02 03 04 05 06 07 08Flow (mgd)

0 2 4 6 8 10 12 14 16 18

Valero

98 99 00 01 02 03 04 05 06 07 08Flow (mgd)

0 1 2 3 4 5



### Figure 3-32 Daily average effluent flow rate from the refineries.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

3-54 Tetra Tech, Inc. Valero

Flow (cfs) 0 1 2 3 4 5Conc. ("g/L)

0 10 20 30 40 50 60 Tesoro

Flow (cfs) 0 2 4 6 8 10 12 14 16 18Conc. ("g/L)

0 10 20 30 40 50

Shell Martinez

Flow (cfs) 2 3 4 5 6 7 8 9Conc. ("g/L)

0 20 40 60 80 100 Chevron

Flow (cfs) 0 5 10 15 20 25 30Conc. ("g/L)

0 10 20 30 40 50

R 2 =0.04

R 2 =0.002 R 2 =0.05

R 2 =0.002 Conoco Phillips

Flow (cfs) 0 10 20 30 40 50Conc. ("g/L)

0 2 4 6 8 10 R 2 =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

1 9 9 9 ( w e t )

2 0 0 0 ( w e t )

2 0 0 1 ( d r y )

2 0 0 2 ( d r y )

2 0 0 3 ( w e t )

2 0 0 4 ( d r y )

2 0 0 5 ( w e t )

2 0 0 6 ( w e t )

2 0 0 7 ( d r y )Selenium loading (kg)

0 25 50 75 100 125 150
Dry Season Wet Season

Chevron

1 9 9 9 ( w e t )

2 0 0 0 ( w e t )

2 0 0 1 ( d r y )

2 0 0 2 ( d r y )

2 0 0 3 ( w e t )

2 0 0 4 ( d r y )

2 0 0 5 ( w e t )

2 0 0 6 ( w e t )

2 0 0 7 ( d r y )Selenium loading (kg)

0 25 50 75 100 125 150 Dry Season Wet Season

Shell Martinez

1 9 9 9 ( w e t )

2 0 0 0 ( w e t )

2 0 0 1 ( d r y )

2 0 0 2 ( d r y )

2 0 0 3 ( w e t )

2 0 0 4 ( d r y )

2 0 0 5 ( w e t )

2 0 0 6 ( w e t )

2 0 0 7 ( d r y )Selenium loading (kg)

0 50 100 150 200 250 300 Dry Season Wet Season Tesoro

1 9 9 9 ( w e t )

2 0 0 0 ( w e t )

2 0 0 1 ( d r y )

2 0 0 2 ( d r y )

2 0 0 3 ( w e t )

2 0 0 4 ( d r y )

2 0 0 5 ( w e t )

2 0 0 6 ( w e t )

2 0 0 7 ( d r y )Selenium loading (kg)

0 25 50 75 100 125 150 Dry Season Wet Season Valero

1 9 9 9 ( w e t )

2 0 0 0 ( w e t )

2 0 0 1 ( d r y )

2 0 0 2 ( d r y )

2 0 0 3 ( w e t )

2 0 0 4 ( d r y )

2 0 0 5 ( w e t )

2 0 0 6 ( w e t )

2 0 0 7 ( d r y )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 Sel enium Data Summary and Source Analysis

3-56 Tetra Tech, Inc. 

### 3.7. I NTERNAL 

### S OURCES 

### - S EDIMENT 

### E ROSION 

## 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 (Leatherbarro w et al. 2005b). Given the sediment mass for the upper 15 cm of the whole bay (1.4 x 10 11 

## 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 mobili zed to the water column through resuspension, erosion, diffusion and bioturbati on. Resuspension rates in the San Francisco Bay were found to be 2 to 5 times greater than the accumulati on rates, indicating sedi ment is resuspended 2 to 5 times before settling (Leatherbarrow et al. 2005b). Previous studie s 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 resu spension redistributes sediments to a wider area. Localized sediment erosion also occurs due to decreases in sediment supply from the surrounding watershe ds. Net sediment eros ion was found to occur both in the Suisun Bay and Sa n Pablo Bay. For San Francisc o Bay, the abundance of organisms has been found to potentially enhan ce mobilization of sediments to the water column. Diffusion of dissolved selenium from the sediment por ewater 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 mob ilization, but this has not been quantified for the source analysis. Selenium in sediments can also undergo a se ries of transformations (Meseck and Cutter, 2006). In deeper layers of sedi ment, 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 se diments. Organic selenide in surface sediment can also be oxidized to se lenite and selenate or methylated by microbes. Studies in San Pablo and Suisun Bay indicated th at more erosion than burial is occurring in these two areas in the recent years (USGS 2001 a, b). In Suisun Bay, net sediment erosion was 1-2 Mm 3 

## /yr from 1887 to 1990 (USGS 2001a ). During 1942 to 1990, Suisun Bay experienced a net loss of 61 Mm 3 

## of sediment, with a net loss of 1.27 Mm 3 

## /yr at an erosion rate of 1.2 cm/m 2 

## /yr. Erosion in San Pablo Bay is at a slower rate and only occurred after 1950s. San Pablo Bay lost approximately 7 Mm 3 

## of sediments between 1951 and 1983 at a rate of 0.22 Mm 3 

## /yr (USGS 2001b). This net loss of se diments can be a potential source of selenium from sediments to the water colum n. 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 re sults in selenium loadings due to sediment erosion of 275 kg/yr.

5 

### Assuming North and Central Bay area of 434 km 2 

### and 214 km 2 

### , over the total area of 1133 km 2 

### for the whole Bay (Tsai et al. 2001).North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## 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 acr es/yr in San Pablo Bay). Loss of tidal mudflats may introduce contaminants previous ly deposited in thes e areas to the Bay (Marvin-DiPasquale et al., 2003). Sediment dredging from navigatio n channels and dispos al in locations insi de 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 o cean disposal and upland/wetla nd reuse are 142.5 kg Se/yr and 225 kg Se/yr respectively. The dry mass of selenium was cal culated assuming a particle density of 2.65 kg/L and a 50% solid per unit mass sediment, sim ilar 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 (m 3 ) Average volume (m 3 /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. L OADS FROM THE 

### S OUTH 

### B AY 

## Water in the South Bay and Central Bay is su bject 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 sele nium concentrations at a station near the boundary of the two bays (BC10 Yerba Buena Is land) to be represen tative of net inflow concentration from the South Bay. Estimated fr eshwater inputs from local watersheds of South Bay are 664 Mm 3 

## /yr (Davis et al. 2000). With the mean selenium concentration of 0.16 ! g/L at Yerba Buena Island (Table A-3), estim ated 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, th e Guadalupe River can be a major source of selenium to the South Bay because of high c oncentration. Observed average total selenium concentration at Guadalupe Ri ver (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 estimate d 106.2 kg/yr load from South Bay may be at the lower bound of the loads entering from So uth Bay or suggests that significant removal of selenium via deposition may be occurring in the South Bay.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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### 3.9. C OMPARISON OF 

### S ELENIUM 

### C ONCENTRATIONS AND 

### L OADS FROM 

### D IFFERENT 

### S OURCES 

## A comparison of total and dissolved selenium concentrations from several sources of interest is summarized in Table 3-17. In terms of concentra tions, the refineries have the highest selenium concentrati ons compared to other sources such as Delta outflow, atmospheric deposition, municipal wastewat er and the bay water, followed by local tributaries. A comparison of relative importance of load ings 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. Lo cal 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 partic ulate 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 0.4-4.0 1 0.3-3.9 BASMAA (1996) 0.46 Municipal wastewater Data provided by SFBRWQCB <1 - Refineries Data provided by SFBRWQCB 12-28 2 12-28 Mallard Island (outflow from Delta) Storm Values L. McK ee, 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 concent rations at indi vidual refineries listed in Table 3-1.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### Table 3-18 Relative importance of loadings from different sources Total (kg/yr) Dissolved (kg/yr) Particulate (kg/yr) Uncertainty Sources: Atmospheric deposition 17.8-1 63.5 13.7 – 78.1 4.1-85.4 High
Local tributaries 354 -1511 (354-834 best estimate) - 118.2 1 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) 151-1,509 2 (mean: 698) Moderate

Sacramento River at Freeport 670-2,693 (mean: 1,577) for 1991-2007 Moderate

San Joaquin River at Vernalis 760-7,270 5 (mean: 2,972) for 1994-2007 838-4,711 (mean: 2,289) for 1991-2007 Moderate

Sediment 293 18.2 4 275 Moderate South Bay 106 High Sinks: Outflow 4500 3 3750 3 750 3 Moderate Sediment Dredging 82.5 82.5 Moderate

1 Based on TSS loadings by Davis et al. (2000), times seleni um content in particulate material of Sacramento River
2 Based on TSS loadings by McKee et al. (2006) and mean selenium content in particula te material of Sacramento and San Joaquin Rivers
3 Based on average Delta outflow of 25000 Mm 3 . Outflow only includes loads cont ributed by the northern reach.
4 Sediment diffusion rate estimated by Meseck (2002).
5 Based on SWAMP dataset 

## A comparison of dry and wet season lo adings from different sources ( Table 3-19) indicates that during the dry season, the m ajor source of selenium loadings is from the Delta. The local tributary contribution dur ing 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 duri ng both dry and wet seasons.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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### 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 Ve rnalis 863.4 1,426.0 2,289.4 Export through aqueduc ts 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

Tributaries 1 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 s ources were compared to previous studies of Presser and Luoma (2006), Meseck and Cutte r (2006) and Abu-Saba and Ogle (2005) ( Table 3-20). Selen ium loads from refineries compared well to loads estimated by Presser and Luoma (2006) and Abu-Saba and Ogle (2005). Lo adings 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 estim ated range is wide. However, dry season Delta to bay loads in this work are substant ially 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

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### 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 620 1 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 estima te 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. L OW 

### F LOW VS



### . H IGH 

### F LOW 

### C ONCENTRATIONS 

## 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. Unde r low flow, also due to the longer residence time and warmer temperature, selenium is mo re 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 cr itical time period for selenium bioaccumulation. The hydraulic resi dence 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 concentratio ns 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 va rious sources estimated in pr evious sections were used.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## Partition coefficient between dissolved and part iculate selenium were derived from data of Doblin et al. (2006). Several processes besides outflow to ocean th at may contribute to the selenium removal: methylation to form dimethylselenide fo llowed by volatilization, influx of dissolved selenium into sediments, reduction fo llowed by adsorption and settling, phytoplankton uptake, and settling of suspended sediment. Prev ious study has indicated that diffusion into and out of the sediment is negligible (Mes eck, 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 us ing zero removal rates under high flow are generally similar to the observed concentr ations from the RMP random sampling during 2002-2005 (0.14 μg/L; Table 3-21), suggesting relatively co nservative behavior during high flow. Predicted m aximum selenium concentration under low flow of a crit ically dry year is at higher concentration of 0.36 μg/L. RMP sa mpling during a representative period in August 2001 indicated a North Bay average of 0.15 ! g/L. Because the observed concentrations during this peri od are significantly lower than pr edictions 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 mode l and detailed mechanistic model.

Table 3-21 Estimated selenium concentrations under differen t 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, PO TWs, local tributaries (proportional to delta outflow), and bed erosion. **based on average K d 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. S UMMARY 

## 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 m onitoring data are the RMP and Prof. Greg Cutter’s research group at Old Dominion Univ ersity. 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 concentrati ons and at 24 stations for se diment concentrations between 2002 and 2005. Selenium concentrations are genera lly 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 n ear 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 (Cutte r, personal communication, 2007). The data show that there have been sign ificant decreases in dissolved selenium concentrations and selenite in the North Ba y 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, a nd 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 De lta, local refineries, POTWs, tributaries and sediments, during bo th dry and wet season, was another major component of this analysis. The results indica ted 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 lo w 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/y r). Refineries are now estimated to be the third largest source of selenium to the Nort h Bay (538 kg/yr), although these loads may have been higher prior to the late 1990s when wastewater co ntrols 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 cont ributors 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 lo ads (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 ar e provided here for comparison, it should be acknowledged that this process contains significant uncertainty, and more than one estimation method may be applied, sometimes l eading to different answers as described below. This is particularly tr ue of non-point source load estim ates. 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 se lenium loading of 2,289 kg/yr for 1991-2007.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## We applied three different methods to compute loads, from the Delta to the bay, depending on available data:

! The first approach used average concentra tion of two RMP stations in the Delta and multiplies it by the net tidally corrected Delt a 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 load ings from the Sacramento and the San Joaquin Rivers separately based on data fr om Cutter and Cutter (2004) and applied a “Delta removal constant” si milar to Meseck (2002) to account for the possible selenium loss in the Delta. These concentr ations 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 th e prior two: the loadings from Central Valley to the bay were estimated as th e 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 av erage load estimate of 2,696 kg/yr of dissolved selenium (1993 to 2003). In addition to these loads, the average particul ate load was estimated as 698 kg/yr, based on loads of sediment from the Delta to the ba y and by application of a constant selenium content in the sediments. Given the simplifications and assumptions empl oyed 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 di ssolved data were av ailable, and because the flow volumes used in load calculation are tidally corrected, it is recommended that this method be used for describing Delta loads, re sulting in an average De lta 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 a nd measured flows from USGS gage stations. The modeled flows were used because of the li mited availability of measured flow data. Driven in large part by relativ ely high concentrations in the tributaries in both the wet and dry seasons, the average annual loads from th e 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 US GS gage data. The largest single sources of loads are the Napa River, Sonoma Cr eek, 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 th at 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 unc ertainty in flows, and the year-to-year variability, theNorth San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## wide range in the load estimates are not entire ly surprising. For the purp ose 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

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## 5. K EY 

## F INDINGS AND 

## I MPLICATIONS FOR 

## M ODEL 

## D EVELOPMENT 

## The analysis presented here is an important firs t 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 ba y 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 th e 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 correl ate 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 natura l 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. Concentra tions of selenite, a major component of refinery discharges in the past, show dramatic declines from 1998.

! Local tributary selenium concentrations ar e 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 deli vered 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. Th e 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 significan tly elevated concentrations.

! Selenium loads in NSFB are dominate d by non-point sources, and therefore correlated with runoff. Because of the regi on’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 s howed that both San Jo aquin and Sacramento Rivers are significant contribu tors of selenium to the N SFB. Their load contributions are of similar magnitude and occu r 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 understandi ng of its role in the removal and/or export of selenium is based on a small amount of data.

! Point source loads (refineries, POTWs, a nd other industrial di schargers) are among the best characterized loads into NSFB because both flow and concentration are measured simultaneously. These loads are al so less variable thr ough 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, pointJuly 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## source loads are relatively small; on a seasonal basis, point source loads are significant during the dry months.

! POTW discharge concentrations of sele nium 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

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## 6. R EFERENCES 

## Abu-Saba, K., and S. Ogle. 2005. Selenium in San Francisco Bay: Conceptual Model/Impairment Assessment. Final Report, prepared for Clean Es tuary Partnership. BASMAA (Bay Area Stormwater Management Agencies Association), 1996. San Francisco Bay Area Stromwater Runoff Monitoring Da ta Analysis 1988-1995. Final Report. Conomos, T.J., Smith, R.E., Gartner, J.W. 1985. Environmental Setting of San Francisco Bay. Hydrobiologia 129: 1-12. Cutter, G.A. 2007. Personal communication, electronic dataset containing data from all published studies from the Cutter research grou p at Old Dominion Univer sity. Available at: ftp://rd.tetratech.com/NSFB_Se. Cutter, G.A., and T.M. Church. 1986. Selenium in western Atlantic precipitation. Nature 322: 720-722. Cutter, G.A. 1978. Species determination of sele nium in natural waters. Anal. Chim. Acta 98: 59-66. Cutter, G.A. 1989. The estuarine behavior of se lenium in San Francisc o Bay. Estuar. Coast. Shelf Sci. 28: 13-34. Cutter, G.A., L.S. Cutter. 2004. Selenium biogeochemistry in the San Francisco Bay estuary: changes in water column behavior. Estuarine, Coastal and Shelf Science 61: 463- 476. Cutter, G.A., M. L.C. San Diego-McGlone. 1990. Te mporal variability of selenium fluxes in San Francisco Bay. The Science of the Total Environment 97/98: 235-250. Davis, J.A., L.J. McKee, J.E. Leatherbarro w, and T.H. Daum. 2000. From Stormwater to Coastal Waters in the San Francisco Bay Region. Comparison to other pathways and recommended approach for future evaluation. San Francisco Estuary Institute, September 2000. Davis, J.A. 2003. The long-term fate of PCBs in San Francisco Bay. SFEI Contribution 47. San Francisco Estuary Institute, Oakland, California. Department of Water Resources (DWR). 2004. Methodology for flow and salinity estimates in the Sacramento-San Joaquin Delta and Suisun Marsh. http://baydeltaoffice.water.ca.gov/mode ling/deltam odeling/annualreports.cfm

. Doblin, M.A. S.B. Baines, L.S. Cutter, G. A. Cutter. 2006. Sources and biogeochemical cycling of particulate selenium in the San Francisco Bay estuary. Estuarine, Coastal and Shelf Science 67: 681-694.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## Duce, R.A., B.J., Ray, G.L. Hoffman, P.R. Walsh. 1976. Trace metal concentration as a function of particle si ze in marine aerosols from Berm uda. Geophysical Research Letters 3: 339-342. EOA, Inc. 2006. Screening-level Monitoring of Permanente Creek, Stevens Creek, Calabazas Creek, Matadero/Barron Creek, and Sunnyvale East/West Channel Watersheds. SCVURPPP FY 05-06 Watershed Monitoring a nd Assessment Summary Report Submitted in fulfillment of NPDES Permit Provision C.10(b). Gray, J.R., G.D. Glysson, L.M. Turcios, and G. E. Schwarz. 2000. Comparability of suspended sediment concentration and tota l suspended solids data. Water Resources Investigation Report 00-4191. United States Geological Survey, Reston, Virginia. Grovhoug T., G. Lau, K.E. Abu-Saba. 2004. Mercur y management by Bay area wastewater treatment plants. San Francisco Bay Clean Es tuary Partnership, Oakl and, California. Johnson, T.M., T.D. Bullen, P. T. Zawislansk i. 2000. Selenium stable isotope ratios as indicators of sources and cycling of selenium: results from the northern reach of San Francisco Bay. Environmental Science and Technology 34: 2075-2079. KLI (Kinnetic Laboratories, Inc.) 2002. Joint stormwater agency project to study urban sources of mercury, PCBs and Organochlorine pesticides. April 2002. Leatherbarrow, J.E., L.J. McKee, D. H. Schoellhamer, N.K. Ganju, A. R. Flegal. 2005a. Concentrations and loads of organic contamin ants and mercury associated with suspended sediment discharged to San Francisco Bay from the Sacramento-San Joaquin River Delta, Claifornia. RMP Technical Report. SFEI Contri bution 405. San Francisco Estuary Institute, Oakland, CA. Leatherbarrow, J., J. Ross, N. David, D. Yee. 2005b. Fate of contaminants in sediment of San Francisco Estuary: A review of literature and data. San Francisc o Estuary Institute, March 2005. Lemly, A.D., and G.J. Smith. 1987 . Aquatic cycling of selenium : implications of fish and wildlife. United States Department of the In terior, Fish and Wildlife Service, Fish and Wildlife Leaflet 12. Washington, D.C. Marvin-DiPasquale, M.C., J.L. Agee, R.M. Bo use, B.E. Jaffe. 2003. Microbial cycling of mercury in contaminated pelagic and wetland sediments of San Pablo Bay, California. Environmental Geology 43: 260-267. McKee, L., N. Ganju, D. Schoellhamer, J. Davis, D. Yee, J. Leatherbarrow, R. Hoenicke. 2002. Estimates of suspended-sediment flux entering San Francisco Bay from the Sacramento and San Joaquin Delta. San Fran cisco Estuary Institute, December 2002. 36pp. McKee, L., J. Leatherbarrow, S. Pearce, J. Davis. 2003. A review of urban runoff processes in the Bay area: existing know ledge, conceptual models, and monitoring recommendations. San Francisco Estuary Institute, September 2003. 162pp.North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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## McKee, L.J., N.K. Ganju, D.H. Schoellhamer. 2006. Estimates of suspended sediment entering San Francisco Bay from the Sacramen to and San Joaquin Delta, San Francisco Bay, California. Journal of Hydrology 323: 335-352. Meseck, S.L. 2002. Modeling the biogeochemical cycle of selenium in the San Francisco Bay. Ph.D. Dissertation, Ol d Dominion University. Meseck and Cutter. 2006. Evaluating the biogeoch emical cycle of selenium in San Francisco Bay through modeling. Limnology and Oceanography 51(5): 2018-2032. Mosher, B.W., R.A. Duce. 1989. The Atmosphe re, in Occurrence and Distribution of Selenium, Ed. by Milan Ihnat, CRC Press, Inc. Florida, 309pp. Presser, T.S. and S. N. Luoma. 2006. Forecasting Selenium Discharges to the San Francisco Bay-Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension. USGS Professional paper 1646. Purkerson, D.G., M.A. Doblin, S.M. Bollens, S.N. Luoma, G.A. Cutter. 2003. Selenium in San Francisco Bay zooplankton: potentia l effects of hydrodynamics and food web interactions. Estuaries 26: 956-969.Schoellhamer, D.H., P.A. Buchanan, N.K. Ganju. 2002. Ten years of continuous suspendedsediment concentration monitoring in San Fran cisco By and Delta. Proceedings of Turbidity and Other Sediment Surrogates Wo rkshop. April 30-May 2, 2002, Reno, NV. SFBRWQCB. 1992. Mass emissions reduction st rategy for selenium: California San Francisco Bay Regional Water Qualit y Control Board, Oakland, CA, 53pp. SFBRWQCB. 2004. Mercury in San Francisco Ba y: Total Maximum Daily Loads (TMDL) proposed Basin Plan Amendment a nd Staff Report. Oakland, CA. SFBRWQCB. 2007a. Water quality monitoring a nd bioassessment in nine San Francisco Bay Region watersheds: Walker Creek, La gunitas Creek, San Leandro Creek, Wildcat Creek/San Pablo Creek, Suisun Creek, Arroyo La s Positas, Pescadero Creek/Butano Creek, San Gregorio Creek, and Stevens Creek/Per manente Creek. Oakland, CA: Surface Water Ambient Monitoring Program, San Francisco Bay Regional Water Quality Control Board. SFBRWQCB 2007b. Water Quality M onitoring and Bioassessment in Four San Francisco Bay Region Watersheds in 2003 -2004: Kirker Creek, Mt. Diab lo 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. Califo rnia Regional Water Quality Control Board. San Francisco Bay Region. Oakland, CA.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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## SFEI. 2006. 2004-2005 Annual Monitoring Results. The Regional Monitoring Program for Water Quality in the San Francisco Estuar y (RMP). San Francisco Estuary Institute, Oakland, CA. San Francisco Estuary Institute (SFEI). 2006b. RMP Annual Monitoring Results 2004-2005. SEFI Contribution 519. San Francisco Estuary Institute, Oakland, CA. Smith, S.V., and J.T. Hollibaugh. 2006. Water, salt, and nutrient exchanges in San Francisco Bay. Limnology and Oceanography 51(1): 504-517. Sweet, C.W., A. Weiss, S.J. Vermette. 1998. Atmo spheric deposition of tr ace metals at three sites near the Great Lakes. Water, Air, and Soil Pollution 103: 423-439. Tetra Tech, 2006. Organic Carbon in the Cent ral Valley and Sacramento – San Joaquin Delta. Final Report to USEPA Region IX and Central Valley Drinking Water Policy Workgroup. Tetra Tech, 2007. Technical Memorandum #4: C onceptual Model and Data Analysis of Selenium in North San Francisco Bay: Draft. Tsai, P. R. Hoenicke, E. Hansen, K. Lee. 2001. San Francisco Bay Atmospheric Deposition Pilot Study Part 2: Trace Metals. SFEI Cont ribution 73. San Francisco Estuary Institute, Oakland, CA. U.S. EPA. 1996. Chesapeake Bay atmospheric deposition study final report. EPA 903-R-96- 005. U.S. EPA Region 9. 2002. Total Maximum Daily Loads for Toxic Pollutants San Diego Creek and Newport Bay, California. Technica l Support Document, Part D: Selenium. U.S. Geological Survey (USGS) 2001a. Se dimentation Changes in San Pablo Bay, 1856- 1983, prepared by B. Jaffe, R. Smith, and L. Zink, October 16. http://sfbay.wr.usgs.gov/access/sanpablobay/bathy/home.html U.S. Geological Survey (USGS) 2001b. Historic al Bathymetric Change in Suisun Bay, 1867-1990, prepared by K. Cappiella, C. Malz one, R. Smith, and B. Jaffe, October 18. http://sfbay.wr.usgs.gov/access/Bathy/suisunbay/ Zawislanski, P.T., H.S. Mountford, E.J. Ga bet, 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

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## A PPENDICES



### 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 km 2 Tsai et al. 2001 Central Bay 214 km 2 Tsai et al. 2001 Volume North Bay+ Central Bay 3953 Mm 3 Calculated Delta outflow Wet year (2006), wet season average 202.2 Mm 3 /day http://iep.wate r.ca.gov/dayflow/ Wet year (2006), dry season average 73.0 Mm 3 /day http://iep.wate r.ca.gov/dayflow/ Critically dry year (2001), dry season 14.2 Mm 3 /day http://iep.wate r.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), dr y 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 (200 1), 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 (200 1), dry season 2.2 μg/g Equations: Assuming completely mixed and steady state: (1). C = W/a, where W: loadings from all source s, a: assimilation coefficient, C: concentration (2). a = Q + kV+ " As, where Q: outflow, k: deg radation/reaction coefficient, " : settling velocity, As: surface area. For simplicity, k and
" are assumed to be 0.July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

A-2 Tetra Tech, Inc. (3) Cs = Kd*Cw, where Cs: concentration in particulate, Kd: parti tion coefficient, Cw: dissolved c oncentration. Cw is assumed t o 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 Bri dge 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 23North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### 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 Bri dge 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 22July 2008 North San Francisco Bay Sel enium Data Summary and Source Analysis

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### 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 Bri dge 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 15North San Francisco Bay Selenium Data Summary and Source Analysis July 2008

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### 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 NoteE-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 2.48July 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 60 33.74 Conc only reported for E-001-DC CA0038539 West County/Richmond
E-001 D1 (West County) 9.33 10/2- 5/07 1672 Load is only calculated for E-001- DCNorth 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