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Flegal, A. R.; Sanudo-Wilhelmy, S. A. 1996. Trace metal concentrations in the surf zone and in coastal waters off Baja California, Mexico. Environmental Science and Technology 30, 1575-1580 . SFEI Contribution No. 195.
Flegal, A. R.; Sanudo-Wilhelmy, S. A.; Rivera-Duarte, I. 1996. Silver contamination in aquatic environments. Reviews of Environmental Contamination and Toxicology 148, 139-162 . SFEI Contribution No. 192.
Flegal, A. R.; Abu-Saba, K. E. 1997. Particulate sources and sinks of dissolved chromium in the San Francisco Bay estuary. Environmental Science and Technology . SFEI Contribution No. 25.
Flegal, A. R. 1997. Lead levels in the oceans. Encyclopedia of Environmental Analysis and Remediation(H. Ben-Zvi, editor)John Wiley & Sons, Inc. In press . SFEI Contribution No. 24.
Flegal, A. R.; Bruland, K. W.; Sanudo-Wilhelmy, S. A.; Kozelka, P. B. 1997. Physicochemical speciation of lead in South San Francisco Bay. Estuarine, Coastal and Shelf Science 44, 649-658 . SFEI Contribution No. 26.
Flegal, A. R.; Rivera-Duarte, I. 1997. Benthic fluxes of silver in San Francisco Bay. Marine Chemistry 56, 15-26 . SFEI Contribution No. 214.
Foley, M. 2019. 2020 RMP Multi-Year Plan. SFEI Contribution No. 959. San Francisco Estuary Institute: Richmond, CA.
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Foley, M.; Christian, E.; Goeden, B.; Ross, B. 2020. Expert review of the sediment screening guidelines for the beneficial reuse of dredged material in San Francisco Bay. SFEI Contribution No. 978. San Francisco Estuary Institute: Richmond, CA.

The beneficial reuse of dredged sediment is one strategy in a broader portfolio that is being developed for San Francisco Bay to help marshes adapt to rising sea level. Dredged sediment is currently being used in restoration projects around the Bay, but additional sediment is needed to meet the demand. The guidelines for determining if sediment is appropriate for beneficial reuse were developed twenty years ago. As part of assessing the role of dredged sediment in Bay restoration and adaptation strategies, the Regional Monitoring Program for Water Quality (RMP) and stakeholders recognized the need to revisit the beneficial reuse guidelines for dredged sediment. In September 2019, the RMP convened a workshop that included four technical experts to review the beneficial reuse guidelines. The experts were asked to answer three questions: 1) Are the current screening guidelines appropriate for beneficial reuse? 2) Is the current screening process appropriate and adequate? If not, what are your recommendations for improving it? and 3) How should bioaccumulation potential be addressed for the beneficial reuse of sediment? Based on the discussion of these three questions, six recommendations emerged from the workshop.

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Foley, M. 2019. 2019 Bay RMP Multi-Year Plan. SFEI Contribution No. 940. San Francisco Estuary Institute: Richmond, CA.
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Foley, M.; Davis, J.; Yee, D. 2023. Multi-Year Plan 2023. SFEI Contribution No. 1096. San Francisco Estuary Institute: Richmond, California.

The purpose of this document is to guide efforts and summarize plans developed within the RMP. The intended audience includes representatives of the many organizations who directly participate in the Program. This document will also be useful for individuals who are not directly involved with the RMP but are interested in an overview of the Program and where it is heading.  

The organization of this Multi-Year Plan parallels the RMP planning process (Figure 2). Section 1 presents the long-term management plans of the agencies responsible for managing water quality in the Bay and the overarching management questions that guide the Program. The agencies’ long-term management plans provide the foundation for RMP planning (Figure 2). In order to turn the plans into effective actions, the RMP distills prioritized lists of management questions that need to be answered (Page 8). The prioritized management questions then serve as a roadmap for scientists on the Technical Review Committee, workgroups, and strategy teams to plan and implement scientific studies to address the most urgent information needs. This information sharpens the focus on management actions that will most effectively and efficiently improve water quality in the Bay. 

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Foley, M. 2022. 2023 Detailed Workplan and Budget. SFEI Contribution No. 1117. San Francisco Estuary Institute: Richmond, California.
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Foley, M.; Sutton, R.; Yee, D.; Salop, P. 2021. 2021 RMP Water Cruise Plan. SFEI Contribution No. 1050. San Francisco Estuary Institute: Richmond, California.

This report details plans associated with the annual Regional Monitoring Program for Water Quality in the San Francisco Estuary (RMP) water cruise. The RMP water sampling program was redesigned in 2002 to adopt a randomized sampling design at thirty-one sites in place of the twenty-six base program stations sampled previously. In 2007, the number of sites was decreased to twenty-two stations, and it remains as such for 2021. The analytes for 2021 have been modified based on the Status and Trends (S&T) Review process that started in 2020. The analytes that are being removed from the program include selenium and methylmercury (dissolved and particulate), while bisphenols and organophosphate esters (OPEs) have been added to S&T monitoring. 

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Foley, M. 2021. 2021 RMP Multi-Year Plan. SFEI Contribution No. 1027. San Francisco Estuary Institute: Richmond, CA.
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Foley, M. M. 2022. 2022 RMP Multi-Year Plan. SFEI Contribution No. 1058. San Francisco Estuary Institute: Richmond, California.
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Franz, A.; Salop, P. 2020. 2019 Bay RMP Water Cruise Plan. SFEI Contribution No. 971. San Francisco Estuary Institute: Richmond, CA.
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Franz, A.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Sediment Sampling and Analysis Plan. SFEI Contribution No. 904. San Francisco Estuary Institute: Richmond, CA.
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Fregoso, T. A.; Foxgrover, A. C.; Jaffe, B. E. 2023. Sediment deposition, erosion, and bathymetric change in San Francisco Bay, California, 1971–1990 and 1999–2020. United States Geological Survey Pacific Coastal and Marine Science Center: Santa Cruz, CA.

Bathymetric change analyses document historical patterns of sediment deposition and erosion, providing valuable insight into the sediment dynamics of coastal systems, including pathways of sediment and sediment-bound contaminants. In 2014 and 2015, the Office for Coastal Management, in partnership with the National Oceanic and Atmospheric Administration (NOAA) Office of Coastal Management, provided funding for new bathymetric surveys of large portions of San Francisco Bay. A total of 93 bathymetric surveys were conducted during this 2-year period, using a combination of interferometric sidescan and multibeam sonar systems. These data, along with recent NOAA, U.S. Geological Survey (USGS), U.S. Army Corps of Engineers, and private contractor surveys collected from 1999 to 2020 (hereinafter referred to as 2010s), were used to create the most comprehensive bathymetric digital elevation models (DEMs) of San Francisco Bay since the 1980s. Comparing DEMs created from these 2010s surveys with USGS DEMs created from NOAA’s 1971–1990 (hereinafter referred to as 1980s) surveys provides information on the quantities and patterns of erosion and deposition in San Francisco Bay during the 9 to 47 years between surveys. This analysis reveals that in the areas surveyed in both the 1980s and 2010s, the bay floor lost about 34 million cubic meters of sediment since the 1980s. Results from this study can be used to assess how San Francisco Bay has responded to changes in the system, such as sea-level rise and variation in sediment supply from the Sacramento-San Joaquin Delta and local tributaries, and supports the creation of a new, system-wide sediment budget. This report provides data on the quantities and patterns of sediment volume change in San Francisco Bay for ecosystem managers that are pertinent to various sediment-related issues, including restoration of tidal marshes, exposure of legacy contaminated sediment, and strategies for the beneficial use of dredged sediment.

Fregoso, T. A.; Jaffe, B. E.; Foxgrover, A. C. 2023. Bathymetric change analysis in San Francisco Bay, California, from 1971 to 2020. United States Geological Survey Pacific Coastal and Marine Science Center: Santa Cruz, CA.

This data release provides bathymetric change grids of four geographic areas of San Francisco Bay, California, comparing digital elevation models (DEMs) created from bathymetric data collected in the 1970s and 1980s with DEMs created from bathymetric data collected in the 2010s and 2020. These types of change analyses can provide information on the quantities and patterns of erosion and deposition in San Francisco Bay over the 9 to 47 years between surveys, and they reveals that the bay floor lost about 34 million cubic meters of sediment between the intervening time period. Results from this study can be used to assess how San Francisco Bay has responded to changes in the system such as sea-level rise and variation in sediment supply from the Sacramento-San Joaquin Delta and local tributaries, and supports the creation of a new, system-wide sediment budget. These bathymetric change grids can also provide data to ecosystem managers about the quantities and patterns of sediment volume change in San Francisco Bay to assist in decision-making for a variety of sediment-related issues, including restoration of tidal marshes, exposure of legacy contaminated sediment, and strategies for the beneficial use of dredged sediment.

Fregoso, T. A.; Jaffe, B. E.; Foxgrover, A. C. 2023. Bathymetric change analysis in San Francisco Bay, California, from 1971 to 2020. United States Geological Survey.

This data release provides bathymetric change grids of four geographic areas of San Francisco Bay, California, comparing digital elevation models (DEMs) created from bathymetric data collected in the 1970s and 1980s with DEMs created from bathymetric data collected in the 2010s and 2020. These types of change analyses can provide information on the quantities and patterns of erosion and deposition in San Francisco Bay over the 9 to 47 years between surveys, and they reveals that the bay floor lost about 34 million cubic meters of sediment between the intervening time period. Results from this study can be used to assess how San Francisco Bay has responded to changes in the system such as sea-level rise and variation in sediment supply from the Sacramento-San Joaquin Delta and local tributaries, and supports the creation of a new, system-wide sediment budget. These bathymetric change grids can also provide data to ecosystem managers about the quantities and patterns of sediment volume change in San Francisco Bay to assist in decision-making for a variety of sediment-related issues, including restoration of tidal marshes, exposure of legacy contaminated sediment, and strategies for the beneficial use of dredged sediment.

Fregoso, T. A.; Foxgrover, A. C.; Jaffe, B. E. 2023. Sediment Deposition, Erosion, and Bathymetric Change in San Francisco Bay, California, 1971–1990 and 1999–2020. United State Geological Survey: Santa Cruz, CA.

Bathymetric change analyses document historical patterns of sediment deposition and erosion, providing valuable insight into the sediment dynamics of coastal systems, including pathways of sediment and sediment-bound contaminants. In 2014 and 2015, the California Ocean Protection Council, in partnership with the National Oceanic and Atmospheric Administration (NOAA) Office of Coastal Management, provided funding for new bathymetric surveys of large portions of San Francisco Bay. A total of 93 bathymetric surveys were conducted during this 2-year period, using a combination of interferometric sidescan and multibeam sonar systems. These data, along with recent NOAA, U.S. Geological Survey (USGS), U.S. Army Corps of Engineers, and private contractor surveys collected from 1999 to 2020 (hereinafter referred to as 2010s), were used to create the most comprehensive bathymetric digital elevation models (DEMs) of San Francisco Bay since the 1980s. Comparing DEMs created from these 2010s surveys with USGS DEMs created from NOAA’s 1971–1990 (hereinafter referred to as 1980s) surveys provides information on the quantities and patterns of erosion and deposition in San Francisco Bay during the 9 to 47 years between surveys. This analysis reveals that in the areas surveyed in both the 1980s and 2010s, the bay floor lost about 34 million cubic meters of sediment since the 1980s. Results from this study can be used to assess how San Francisco Bay has responded to changes in the system, such as sea-level rise and variation in sediment supply from the Sacramento-San Joaquin Delta and local tributaries, and supports the creation of a new, system-wide sediment budget. This report provides data on the quantities and patterns of sediment volume change in San Francisco Bay for ecosystem managers that are pertinent to various sediment-related issues, including restoration of tidal marshes, exposure of legacy contaminated sediment, and strategies for the beneficial use of dredged sediment.

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Gilbreath, A.; Pearce, S.; Shimabuku, I.; McKee, L. 2018. Bay Area Green Infrastructure Water Quality Synthesis. SFEI Contribution No. 922. San Francisco Estuary Institute : Richmond, CA.
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Gilbreath, A. N.; Stark, K.; Pearce, S.; Mckee, L. 2023. Suspended Sediment Loads Analysis of Four Creeks in the San Francisco Bay Area. SFEI Contribution No. 1134. San Francisco Estuary Institute: Richmond, CA.
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Gilbreath, A.; McKee, L.; Shimabuku, I.; Lin, D.; Werbowski, L. M.; Zhu, X.; Grbic, J.; Rochman, C. 2019. Multi-year water quality performance and mass accumulation of PCBs, mercury, methylmercury, copper and microplastics in a bioretention rain garden. Journal of Sustainable Water in the Built Environment 5 (4) . SFEI Contribution No. 872.

A multiyear water quality performance study of a bioretention rain garden located along a major urban transit corridor east of San Francisco Bay was conducted to assess the efficacy of bioretention rain gardens to remove pollutants. Based on data collected in three years between 2012 and 2017, polychlorinated biphenyls (PCBs) and suspended sediment concentrations (SSCs) were reduced (>90%), whereas total mercury (Hg), methylmercury (MeHg), and copper (Cu) were moderately captured (37%, 49%, and 68% concentration reduction, respectively). Anthropogenic microparticles including microplastics were retained by the bioretention rain garden, decreasing in concentration from 1.6 particles/L to 0.16 particles/L. Based on subsampling at 50- and 150-mm intervals in soil cores from two areas of the unit, PCBs, Hg, and MeHg were all present at the highest concentrations in the upper 100 mm in the surface media layers. Based on residential screening concentrations, the surface media layer near the inlet would need to be removed and replaced annually, whereas the rest of the unit would need replacement every 8 years. The results of this study support the use of bioretention in the San Francisco Bay Area as one management option for meeting load reductions required by San Francisco Bay total maximum daily loads, and provide useful data for supporting decisions about media replacement and overall maintenance schedules.

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Gilbreath, A.; Hunt, J.; Mckee, L. 2019. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2018. SFEI Contribution No. 942. San Francisco Estuary Institute: Richmond, CA.
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Gilbreath, A.; McKee, L.; Hunt, J. 2021. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2020. SFEI Contribution No. 1061. San Francisco Estuary Institute: Richmond, CA.

The San Francisco Bay polychlorinated biphenyl (PCB) and mercury (Hg) total maximum daily loads (TMDLs) call for implementation of control measures to reduce PCB and Hg loads entering the Bay via stormwater. In 2009, the San Francisco Bay Regional Water Quality Control Board (Regional Water Board) issued the first Municipal Regional Stormwater Permit (MRP). This MRP contained a provision aimed at improving information on stormwater pollutant loads in selected watersheds (Provision C.8.) and piloted a number of management techniques to reduce PCB and Hg loading to the Bay from smaller urbanized tributaries (Provisions C.11. and C.12.). To address C8, a previously developed fixed station loads monitoring technique was refined that incorporated turbidity and stage sensors recording at 5-15 minute intervals with the collection of velocity and water samples using both manual and auto sampling techniques to compute loads. In 2015, the Regional Water Board issued the second iteration of the MRP. “MRP 2.0” placed an increased focus on identifying those watersheds, source areas, and source properties that are potentially the most polluted and are therefore most likely to be cost-effective areas for addressing load-reduction requirements.

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Gilbreath, A.; Hunt, J.; Mckee, L. 2020. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015 - 2019. SFEI Contribution No. 987. San Francisco Estuary Institute: Richmond, CA.

Reconnaissance monitoring for water years 2015, 2016, 2017, 2018 and 2019 was completed with funding provided by the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). This report is designed to be updated each year until completion of the study. At least one additional water year (2020) is underway. An earlier draft of this report was prepared for the Bay Area Stormwater Management Agencies Association (BASMAA) in support of materials submitted on or before March 31st 2020 in compliance with the Municipal Regional Stormwater Permit (MRP) Order No. R2-2015-0049.

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Gilbreath, A.; Wu, J.; Hunt, J.; McKee, L. 2018. Pollutants of Concern Reconnaissance Monitoring Water Years 2015, 2016, and 2017. SFEI Contribution No. 840. San Francisco Estuary Institute: Richmond, CA.
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Gilbreath, A. N.; McKee, L. J. . 2015. Concentrations and loads of PCBs, dioxins, PAHs, PBDEs, OC pesticides and pyrethroids during storm and low flow conditions in a small urban semi-arid watershed. Science of the Total Environment 526, 251-261 . SFEI Contribution No. 650.

Urban runoff has been identified in water quality policy documents for San Francisco Bay as a large and potentially controllable source of pollutants. In response, concentrations of suspended sediments and a range of trace organic pollutants were intensively measured in dry weather and storm flow runoff from a 100% urban watershed. Flow in this highly urban watershed responded very quickly to rainfall and varied widely resulting in rapid changes of turbidity, suspended sediments and pollutant concentrations. Concentrations of each organic pollutant class were within similar ranges reported in other studies of urban runoff, however comparison was limited for several of the pollutants given information scarcity. Consistently among PCBs, PBDEs, and PAHs, the more hydrophobic congeners were transported in larger proportions during storm flows relative to low flows. Loads for Water Years 2007-2010 were estimated using regression with turbidity during the monitored months and a flow weighted mean concentration for unmonitored dry season months. More than 91% of the loads for every pollutant measured were transported during storm events, along with 87% of the total discharge. While this dataset fills an important local data gap for highly urban watersheds of San Francisco Bay, the methods, the uniqueness of the analyte list, and the resulting interpretations have applicability for managing pollutant loads in urban watersheds in other parts of the world.

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Gobas, F.; Wilcockson, F. 2003. San Francisco Bay PCB Food - Web Model. SFEI Contribution No. 90. San Francisco Estuary Institute , Simon Fraser University, EVS Environmental Consultants: Oakland, Ca.
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Greenfield, B. K.; Jahn, A. 2010. Mercury in San Francisco Bay forage fish. San Francisco Estuary Institute: Oakland, Ca.
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Greenfield, B. K.; Davis, J. A.; Collins, J. N.; Grenier, J. Letitia. 2002. The tidal marsh food web. SFEI Contribution No. 472. University of California: Berkeley, CA. p 12 pp.
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Greenfield, B. K.; Ichikawa, G.; Stephenson, M.; Davis, J. A. 2002. Mercury in Sport Fish from the Delta Region (Task 2A). SFEI Contribution No. 252. San Francisco Estuary Institute / CALFED Final Project Report.: Oakland, CA. p 88 pp.
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Greenfield, B. K. 2004. APMP Alternatives Program Executive Summary. SFEI Contribution No. 118. San Francisco Estuary Institute: Oakland, CA.
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Greenfield, B. K.; Davis, J. A. 2004. A Simple Mass Balance Model for PAH Fate in the San Francisco Estuary. SFEI Contribution No. 115. San Francisco Estuary Institute: Oakland, CA.
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Greenfield, B. K.; Davis, J. A. 2004. A PAH Fate Model for San Francisco Bay. Chemosphere . SFEI Contribution No. 114.
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