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Box, C.; Cummins, A. 2019. San Francisco Bay Microplastics Project: Science-Supported Solutions and Policy Recommendations. SFEI Contribution No. 955. 5 Gyres: Los Angeles, CA.

Plastics in our waterways and in the ocean, and more specifically microplastics (plastic particles less than 5 mm in size), have gained global attention as a pervasive and preventable threat to marine ecosystem health. The San Francisco Bay Microplastics Project was designed to provide critical data on microplastics in the Bay Area. The project also engaged multiple stakeholders in both science and policy discussions. Finally, the project was designed to generate scientifically supported regional and statewide policy recommendations for solutions to plastic pollution.

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2021. San Francisco Bay North Bay Margins Sediment Report. Marine Pollution Studies Lab: Moss Landing, California.

This report contains information on the late summer/early fall field sampling efforts conducted
by the Marine Pollution Studies Lab at Moss Landing Marine Labs (MPSL-MLML) in support of
the San Francisco Bay Regional Monitoring Program (RMP) North Bay (San Pablo and Suisun
Bays) Margins study. The North Bay Margins is the third and final round of a larger San
Francisco Bay study collecting sediment and water in shallow margin areas of the bay. The first
round was conducted in Central Bay in 2015 and second round in South Bay in 2017. The work
was contracted through the San Francisco Estuary Institute (SFEI) to the San Jose State
University Research Foundation (SJSURF).
This report includes sample collections over a three week period (August 31st through September
16th) in 2020 encompassing two trips. A total of 40 sediment sites were sampled (Appendix A).
Duplicate sediment samples were collected at two sites (SPB039 and SUB25). Detailed sample
counts and protocols can be found in the 2020 RMP Bay Margins Sediment Cruise Plan prepared
by SFEI.

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Senn, D.; Trowbridge, P. 2016. San Francisco Bay Nutrient Management Strategy Observation Program. SFEI Contribution No. 877. San Francisco Estuary Institute: Richmond, CA.
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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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Zi, T.; Mckee, L.; Yee, D.; Foley, M. 2021. San Francisco Bay Regional Watershed Modeling Progress Report, Phase 1. SFEI Contribution No. 1038. San Francisco Estuary Institute: Richmond, CA.
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SFEI; CDHS,. 2001. The San Francisco Bay Seafood Consumption Study Report. SFEI Contribution No. 369. San Francisco Estuary Institute: Oakland, CA.
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McKee, L.; Peterson, D.; Braud, A.; Foley, M.; Dusterhoff, S.; Lowe, J.; King, A.; Davis, J. 2023. San Francisco Bay Sediment Modeling and Monitoring Workplan. SFEI Contribution No. 1100. San Francisco Estuary Institute: Richmond, CA.

This document was prepared with guidance gained through two RMP Sediment Workgroup workshops held in late 2022 and early 2023. Given the variety of participants involved, this Workplan encompasses interests beyond San Francisco Bay RMP funders. We thank the attendees for their contributions. 

In 2020, the Sediment Workgroup (SedWG) of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) completed a Sediment Monitoring and Modeling Strategy (SMMS) which laid out a conceptual level series of data and information gaps and generally recommended the use of both empirical data collection and modeling tools to answer initial high priority management questions (McKee et al., 2020). At the time, the SMMS promoted the use of surrogates such as time-continuous turbidity measurements for cross-section flux modeling within the Bay without an understanding of existing Bay hydrodynamic models, their strengths, weaknesses, and potential uses for understanding coupled Bay-mudflat-marsh processes. Since then, the Wetland Regional Monitoring Program (WRMP, www.wrmp.org) has generally promoted the use of coupling monitoring and modeling techniques to inform wetlands sediment management decisions. In addition, he completion of the Sediment for Survival report (a RMPEPA funded collaboration) and the further development of sediment conceptual models has also advanced the need for a coupled dynamic modeling and monitoring program that has the capacity to explore more complex management questions (Dusterhoff et al., 2021; SFEI, 2023). Such a program will take time to develop, but will be more cost-efficient and adaptable and allow for more timely answers to pressing questions. 

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Doehring, C.; Beagle, J.; Lowe, J.; Grossinger, R. M.; Salomon, M.; Kauhanen, P.; Nakata, S.; Askevold, R. A.; Bezalel, S. N. 2016. San Francisco Bay Shore Inventory: Mapping for Sea Level Rise Planning. SFEI Contribution No. 779. San Francisco Estuary Institute: Richmond, CA.

With rising sea levels and the increased likelihood of extreme weather events, it is important for regional agencies and local municipalities in the San Francisco Bay Area to have a clear understanding of the status, composition, condition, and elevation of our current Bay shore, including both natural features and built infrastructure.


The purpose of this Bay shore inventory is to create a comprehensive and consistent picture of today’s Bay shore features to inform regional planning. This dataset includes both structures engineered expressly for flood risk management (such as accredited levees) and features that affect flooding at the shore but are not designed or maintained for this purpose (such as berms, road embankments, and marshes). This mapping covers as much of the ‘real world’ influence on flooding and flood routing as possible, including the large number of non-accredited structures.
This information is needed to:

  1. identify areas vulnerable to flooding.
  2. identify adaptation constraints due to present Bay shore alignments; and
  3. suggest opportunities where beaches, wetlands, and floodplains can be maintained or restored and integrated into flood risk management strategies.

The primary focus of the project is therefore to inform regional planners and managers of Bay shore characteristics and vulnerabilities. The mapping presented here is neither to inform FEMA flood designation nor is it a replacement for site-specific analysis and design.


The mapping consists of two main elements:

  1. Mapping of Bay shore features (levees, berms, roads, railroads, embankments, etc.) which could affect flooding and flood routing.
  2. Attributing Bay shore features with additional information including elevations, armoring, ownership (when known), among others.

SFEI delineated and characterized the Bay shore inland to 3 meters (10ft) above mean higher high water (MHHW) to accommodate observed extreme water levels and the commonly used range of future sea level rise (SLR) scenarios. Elevated Bay shore features were mapped and classified as engineered levees, berms, embankments, transportation structures, wetlands, natural shoreline, channel openings, or water control structures. Mapped features were also attributed with elevation (vertical accuracy of <5cm reported in 30 meter (100ft) segments from LiDAR derived digital elevation models (DEMs), FEMA accreditation status, fortification (e.g., riprap, buttressing), frontage (e.g., whether a feature was fronted by a wetland or beach), ownership, and entity responsible for maintenance. Water control structures, ownership, and maintenance attributes were captured where data was available (not complete for entire dataset). The dataset was extensively reviewed and corrected by city, county, and natural resource agency staff in each county around the Bay. This report provides further description of the Bay shore inventory and methods used for developing the dataset. The result is a publicly accessible GIS spatial database.

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Beagle, J.; Lowe, J.; McKnight, K.; Safran, S. M.; Tam, L.; Szambelan, S. Jo. 2019. San Francisco Bay Shoreline Adaptation Atlas: Working with Nature to Plan for Sea Level Rise Using Operational Landscape Units. SFEI Contribution No. 915. SFEI & SPUR: Richmond, CA. p 255.

As the climate continues to change, San Francisco Bay shoreline communities will need to adapt in order to build social and ecological resilience to rising sea levels. Given the complex and varied nature of the Bay shore, a science-based framework is essential to identify effective adaptation strategies that are appropriate for their particular settings and that take advantage of natural processes. This report proposes such a framework—Operational Landscape Units for San Francisco Bay.

Printed copies available for purchase from Amazon.

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Ackerman, J.; Hartman, A.; Herzog, M. P.; Toney, M. 2016. San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants - 2016 Data Summary. U.S. Geological Survey: Dixon, CA. p 19 pp.

As part of the Regional Monitoring Program (RMP) and the USGS’s long-term Wildlife Contaminants Program, the USGS samples double-crested cormorant (Phalacrocorax auritus) and Forster’s tern (Sterna forsteri) eggs throughout the San Francisco Bay Estuary approximately every three years to assess temporal trends in contaminant concentrations. This sampling has been carried out in 2006, 2009, and 2012. Although RMP sampling was scheduled to take place in 2015, it was delayed until 2016. This document summarizes egg collections for 2016, as well as mercury concentrations in Forster’s tern eggs on an individual egg basis.

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Zi, T.; Braud, A.; McKee, L. J.; Foley, M. 2022. San Francisco Bay Watershed Dynamic Model (WDM) Progress Report, Phase 2. SFEI Contribution No. 1091. San Francisco Estuary Institute: Richmond, California.

The San Francisco Bay total maximum daily loads (TMDLs) call for a 50% reduction in mercury (Hg) loads by 2028 and a 90% reduction in PCBs loads by 2030. In support of these TMDLs, the Municipal Regional Permit for Stormwater (MRP) (SFBRWQCB, 2009, SFBRWQCB, 2015, SFBRWQCB, 2022) called for the implementation of control measures to reduce PCBs and Hg loads from urbanized tributaries. In addition, the MRP has identified additional information needs associated with improving understanding of sources, pathways, loads, trends, and management opportunities of pollutants of concern (POCs). In response to the MRP requirements and information needs, the Small Tributary Loading Strategy (STLS) was developed, which outlined a set of management questions (MQs) that have been used as the
guiding principles for the region’s stormwater-related activities. In recognition of the need to evaluate changes in loads or concentrations of POCs from small tributaries on a decadal scale, the updated 2018 STLS Trends Strategy (Wu et al., 2018) prioritized the development of a new dynamic regional watershed model for POCs (PCBs and Hg focused) loads and trends. This regional modeling effort will provide updated estimates of POC concentrations and loads for all local watersheds that drain to the Bay. The Watershed Dynamic Model (WDM) will also provide
a mechanism for evaluating the impact of management actions on future trends of POC loads or concentrations.

As a multi-use modeling platform, the WDM is being developed to include other pollutants, such as contaminants of emerging concern (CECs), sediment, and nutrients and to be coupled with a Bay fate model to form an integrated watershed-Bay modeling framework to address Regional Monitoring Program (RMP) management questions. As this model is developed, flexibility to link with other models will be an important consideration.

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Cohen, A. N. 1997. The San Francisco Estuary: A model system for invasions research. San Francisco Estuary Institute: Seattle, WA (abstract).
Ellisor, D.; Buzby, N.; Weaver, M.; Foley, M.; Pugh, R. 2021. The San Francisco Estuary Institute Collection at the NIST Biorepository. NIST Interagency/Internal Report (NISTIR) - 8370. SFEI Contribution No. 1039. National Institute of Standards and Technology: Gaithersburg, MD.

The National Institute of Standards and Technology (NIST) has been collaborating with the San Francisco Bay Estuary Institute (SFEI) since 2009, providing biobanking services at the NIST Biorepository in Charleston, South Carolina in support of their ongoing water quality monitoring program, the Regional Monitoring Program for Water Quality in the San Francisco Bay (RMP). Specimens (bivalve tissue, bird egg contents, fish tissue and sediment) are collected and processed by SFEI-partnering institutions according to their established protocols and shipped to the NIST Biorepository for archival. This report outlines NIST's role in the project, describes collection and processing protocols developed by SFEI and their collaborators, details shipping and archival procedures employed by biorepository staff and provides an inventory of the collection maintained by NIST from 2009 to 2020.

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Collins, J. N. 2002. San Francisco Estuary Wetalnds Regional Monitoring Program Plan: Version 1, Framework and Protocols. SFEI Contribution No. 248. San Francisco Estuary Institute: Oakland, CA. p 94.
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Salomon, M.; Dusterhoff, S. D.; Askevold, R. A.; Grossinger, R. M. 2016. San Francisquito Creek Baylands: Landscape Change Metrics Analysis. Flood Control 2.0. SFEI Contribution No. 784. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 12.

Major Findings
Over the past 150 years, lower San Francisquito Creek and the adjacent baylands have been modified for the sake of land reclamation and flood control. This study focused on developing an understanding of the magnitude of habitat change since the mid-19th century through comparisons of key historical and contemporary landscape-scale habitat features, as well as several key landscape metrics that relate to ecological functions and landscape resilience. The major findings from the analyses conducted for this study are as follows:
• Historically, the San Francisquito Creek Baylands included a mosaic of habitat types, including an extensive tidal marsh plain with salt pannes and an expansive tidal channel network, a broad bay flat, and a relatively wide contiguous low-gradient tidal-terrestrial transition zone.
• Since the late 19th century, a combination of land reclamation and the inland migration of the shoreline has resulted in a 55% decrease in tidal marsh area, a 67% decrease in total tidal channel length, a 40% reduction in channel flat area, a 20% increase in bay flat area, and a 95% decrease in tidal-terrestrial transition zone length.
• Land reclamation has also resulted in the creation of new features that did not exist in the area historically including tidal lagoons, non-tidal open water features, and non-tidal wetlands.
 

Recommendations
The findings from this study provide insight into the drivers for and magnitude of habitat change within the San Francisquito Creek Baylands, and can therefore help inform climate-resilient approaches for regaining some of the lost landscape features and ecological functions. Specific management recommendations developed from the study findings are as follows:
• The dramatic decrease in tidal marsh area and associated tidal channel length since the mid-1800s make tidal marsh restoration a high priority. To make restored areas sustainable over the long-term, restoration should include reestablishing regular tidal inundation as well as reestablishing a connection with San Francisquito Creek and the delivery of freshwater and fine sediment. Restoration efforts should focus on large contiguous areas with minimal infrastructure and should ideally be done sometime over the next decade to ensure the restored areas will have a chance of surviving the sharp increase in the rate of sea level rise that is predicted to occur around 2030 (Goals Update 2015).
• Similarly, the dramatic decrease in the tidal-terrestrial transition zone makes it a high priority for any restoration vision for this area. The transition zone provides distinct ecological services and marsh migration space, and is in need of restoration throughout the South Bay. Since most of the upland land along the historical tidal-terrestrial transition zone is currently developed, near-term restoration efforts should focus on creating transition zone habitats on the bayside of flood risk management levees (Goals Update 2015).
• The landscape metrics used in this study (tidal habitat area, tidal channel length, and tidal-terrestrial interface length) can be used to help design resilient landscape restoration and adaptation strategies around the mouth of San Francisquito Creek. Specifically, the metrics can be used to assess the long-term ecological benefit associated with various processes-based restoration approaches (i.e., approaches that create habitat features and establish physical processes required for habitat resilience). Additional useful landscape metrics are being developed as part of the Resilient Silicon Valley project (see Robinson et al. 2015).

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Davis, J.; Yee, D.; Fairey, R.; Sigala, M. 2017. San Leandro Bay PCB Study Data Report. SFEI Contribution No. 855. San Francisco Estuary Institute: Richmond, CA.
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Lowe, S. 2020. Santa Clara County Five Watersheds Assessment: A Synthesis of Ecological Data Collection and Analysis Conducted by Valley Water. Pearce, S., Salomon, M., Collins, J., Titus, D., Eds.. SFEI Contribution No. 963. San Francisco Estuary Institute: Richmond. CA. p 71.

This report synthesizes the baseline assessments for Santa Clara County’s five watersheds to present similarities, differences, and compare ecological condition in streams across watersheds and their subregions, San Francisco Bay-Delta ecoregion, and statewide based on CRAM. It also interprets the assessment results and comparisons to identify risks to stream conditions, and opportunities for stream stewardship. Project D5’s baseline assessments establish a monitoring and assessment framework for evaluating the performance of Valley Water’s programs, projects, maintenance activities, and on-the-ground stewardship actions.

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Collins, J. N.; Lowe, S.; Pearce, S.; Roberts, C. 2014. Santa Rosa Plain Wetlands Profile: A Demonstration of the CaliforniaWetland and Riparian Area Monitoring Plan. SFEI Contribution No. 726. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 46.
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Lin, D.; Sutton, R.; Sun, J.; Ross, J. 2018. Screening of Pharmaceuticals in San Francisco Bay Wastewater. SFEI Contribution No. 910. San Francisco Estuary Institute : Richmond, CA.
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Phillips, J. H.; Baumgartner, D. J. 1987. The Screening of Problems Relating to the San Francisco Bay_Delta. SFEI Contribution No. 138. San Francisco Estuary Insitute: Richmond, CA. p 77.
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Bigelow, P.; Pearce, S.; McKee, L. J. .; Gilbreath, A. N. 2008. A Sediment Budget for Two Reaches of Alameda Creek. SFEI Contribution No. 550. San Francisco Estuary Institute.
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Daum, T.; Lowe, S.; Toia, R.; Bartow, G.; Fairey, R.; Anderson, J.; Jones, J. 2000. Sediment Contamination in San Leandro Bay, CA. SFEI Contribution No. 48. San Francisco Estuary Institute: Oakland, CA.
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Thorne, K. M.; Bristow, M. L. 2023. Sediment Deposition and Accretion Data from a Tidal Salt Marsh in South San Francisco Bay, California 2021-2022. U.S. Geological Survey Western Ecological Research Center .

The U.S. Geological Survey, Western Ecological Research Center collected sediment and accretion data at a wave-exposed tidal salt marsh in South San Francisco Bay, California. Sediment traps and feldspar marker horizons (MH) were deployed along transects of increasing distance from the sediment source, at primary, secondary and tertiary marsh channels/bay. Data were collected bi-monthly over two month periods in summer 2021 and winter 2021/2022. Included here are trap and MH plot locations, calculated sediment fluxes at each station by deployment period, annual accretion rates, and covariates associated with sediment deposition and accretion including vegetation structure and elevation. This project aimed to assess the temporal and spatial patterns in sediment deposition in order to better understand sediment delivery and marsh resilience to sea-level rise.

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.; 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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Dusterhoff, S.; McKnight, K.; Grenier, L.; Kauffman, N. 2021. Sediment for Survival: A Strategy for the Resilience of Bay Wetlands in the Lower San Francisco Estuary. SFEI Contribution No. 1015. San Francisco Estuary Institute: Richmond, CA.

This report analyses current data and climate projections to determine how much natural sediment may be available for tidal marshes and mudflats and how much supplemental sediment may be needed under different future scenarios. These sediment supply and demand estimates are combined with scientific knowledge of natural physical and biological processes to offer a strategy for sediment delivery that will allow these wetlands to survive a changing climate and provide benefits to people and nature for many decades to come. The approach developed in this report may also be useful beyond San Francisco Bay because shoreline protection, flood risk-management, and looming sediment deficits are common issues facing coastal communities around the world.

The resilience of San Francisco Bay shore habitats, such as tidal marshes and mudflats, is essential to all who live in the Bay Area. Tidal marshes and tidal flats (also known as mudflats) are key components of the shore habitats, collectively called baylands, which protect billions of dollars of bay-front housing and infrastructure (including neighborhoods, business parks, highways, sewage treatment plants, and landfills). They purify the Bay’s water, support endangered wildlife, nurture fisheries, and provide people access to nature within the urban environment. Bay Area residents showed their commitment to restoring these critical habitats when they voted for a property tax to pay for large-scale tidal marsh restoration. However, climate change poses a great threat, because there may not be enough natural sediment supply for tidal marshes and mudflats to gain elevation fast enough to keep pace with sea-level rise.

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Mckee, L.; Lowe, J.; Dusterhoff, S.; Foley, M.; Shaw, S. 2020. Sediment Monitoring and Modeling Strategy. Sediment Monitoring and Modeling Strategy. SFEI Contribution No. 1016. San Francisco Estuary Institute: Richmond, CA.
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Thompson, B.; Lowe, S. 2008. Sediment Quality Assessments in the San Francisco Estuary. SFEI Contribution No. 574. San Francisco Estuary Institute: Oakland, Ca.
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Schoellhamer, D.; McKee, L.; Pearce, S.; Kauhanen, P.; Salomon, M.; Dusterhoff, S.; Grenier, L.; Marineau, M.; Trowbridge, P. 2018. Sediment Supply to San Francisco Bay. SFEI Contribution No. 842. San Francisco Estuary Institute : Richmond, CA.
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Barnard, P. L.; Schoellhamer, D. H.; Jaffe, B. E.; McKee, L. J. . 2013. Sediment transport in the San Francisco Bay Coastal System: An overview. Marine Geology Special Issue: A multi-discipline approach for understanding sediment transport and geomorphic evolution in an estuarine-coastal system.
Warner, J. C.; Burau, J. R.; Schoellhamer, D. H. 1997. A sediment transport pathway in the back of a nearly semienclosed subembayment of San Francisco Bay, California. Environmental and Coastal Hydraulics: Protecting the Aquatic Habitat(Proceedings of Theme B., F.M. Holly, A. Alsaffar, S.S.Y. Wang, T. Carstens eds.) 2, 1096-1101 . SFEI Contribution No. 29.
Grossinger, R. M. 1999. Seeing Time: A Historical Approach to Restoration. Ecological Restoration 17, 251-2. . SFEI Contribution No. 328.
Gunther, A. J. 1987. The Segmentation of the San Francisco Bay/Delta. SFEI Contribution No. 135. San Francisco Estuary Institute: Richmond, CA. p 18.
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Sun, J.; Davis, J.; Stewart, R. 2018. Selenium in Muscle Plugs of White Sturgeon from North San Francisco Bay, 2015-2017. SFEI Contribution No. 929. San Francisco Estuary Institute : Richmond, CA.
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Jabusch, T. W. 2010. Selenium in the Grasslands Watershed. San Francisco Estuary Institute: Oakland, CA. pp 267-294.
Sun, J.; Davis, J. A.; Stewart, R.; Palace, V. 2019. Selenium in White Sturgeon from North San Francisco Bay: The 2015-2017 Sturgeon Derby Study. SFEI Contribution No. 897. San Francisco Estuary Institute: Richmond, CA.

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) tissues collected during the 2015-2017 Sturgeon Derby events in North San Francisco Bay. The goal of this study was to investigate the distribution of selenium among sturgeon tissues to inform the toxicological and regulatory interpretation of selenium measured in non-lethally collected tissues, including muscle plugs and fin rays. This technical report provides documentation of the study and presents its major findings.

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Flegal, A. R.; Conaway, C. H.; Kerin, E. 2002. Sequential Extraction of Mercury from Sediments in San Francisco Bay Estuary. Environmental Science and Technology . SFEI Contribution No. 126.
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May, C. L.; Mohan, A.; Plane, E.; Ramirez-Lopez, D.; Mak, M.; Luchinsky, L.; Hale, T.; Hill, K. 2022. Shallow Groundwater Response to Sea-Level Rise: Alameda, Marin, San Francisco, and San Mateo Counties. Pathways Climate Institute and San Francisco Estuary Institute.

The response of shallow groundwater to sea-level rise is a relatively new field of study. For low-lying coastal communities, sea-level rise adaptation efforts must consider the potential for groundwater rise to avoid maladaptation. The need to better understand this slow and chronic threat was identified as a critical data gap in the San Francisco Bay Area’s (Bay Area’s) adaptation efforts during the Bay Area Groundwater and Sea-Level Rise Workshop in 2019.

Pathways Climate Institute LLC (Pathways) and the San Francisco Estuary Institute (SFEI) gathered and analyzed multiple data sets and collaborated with city and county partners to analyze and map the existing “highest annual” shallow groundwater table and its likely response to future sea-level rise. This effort covers four counties (Alameda, Marin, San Francisco, San Mateo) and was funded by the Bay Area Council’s California Resilience Challenge. The study focused on the San Francisco Bay side of each county and does not include the Pacific coastline of Marin, San Francisco, nor San Mateo Counties. An advisory committee composed of city and county representatives provided essential support by gathering data and reviewing depth-to-groundwater maps. Additional academic and agency advisors participated in project team meetings and informed project direction. This effort produced the following publicly available data and online tools to support adaptation efforts:

  • Existing and future condition depth to groundwater GIS data available for download (geodatabase format).
  • A StoryMap providing background information and graphical representations of the processes and impacts of groundwater rise.
  • Web maps showing: (1) existing depth to groundwater; and (2) a comparison of the extent of emergent groundwater to the extent of coastal flooding under various sea-level-rise scenarios.
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Cohen, A. N.; Schaeffer, K.; Cosentino-Manning, N. 2007. Shellfish Beds in Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. In Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. NOAA National Marine Fisheries Service: Santa Rosa, CA. pp 50-55.
Cohen, A. N.; Zabin, C. J. 2006. Shells as vectors. Proceedings of the 2006 West Coast Native Oyster Restoration Workshop.
Whipple, A.; Grossinger, R. M.; Davis, F. W. 2010. Shifting Baselines in a California Oak Savanna: Nineteenth Century Data to Inform Restoration Scenarios. Restoration Ecology 19 (101), 88-101 . SFEI Contribution No. 593.

For centuries humans have reduced and transformed Mediterranean-climate oak woodland and savanna ecosystems, making it difficult to establish credible baselines for ecosystem structure and composition that can guide ecological restoration efforts. We combined historical data sources, with particular attention to mid-1800s General Land Office witness tree records and maps and twentieth century air photos, to reconstruct 150 years of decline in extent and stand density of Valley oak (Quercus lobata Neé) woodlands and savannas in the Santa Clara Valley of central coastal California. Nineteenth century Valley oak woodlands here were far more extensive and densely stocked than early twentieth century air photos would suggest, although reconstructed basal areas (7.5 m2/ha) and densities (48.9 trees/ha) were not outside the modern range reported for this ecosystem type. Tree densities and size distribution varied across the landscape in relation to soil and topography, and trees in open savannas were systematically larger than those in denser woodlands. For the largest woodland stand, we estimated a 99% decline in population from the mid-1800s to the 1930s. Although most of the study area is now intensely developed, Valley oaks could be reintroduced in urban and residential areas as well as in surrounding rangelands at densities comparable to the native oak woodlands and savannas, thereby restoring aspects of ecologically and culturally significant ecosystems, including wildlife habitat and genetic connectivity within the landscape.