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Re-evaluation of the Floating Percentile Method for Deriving Dredged Sediment Screening Guidelines. SFEI Contribution No. 1143. San Francisco Estuary Institute: Richmond, California.
2023. This document summarizes a study conducted for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) to re-evaluate the use of the Floating Percentile Method
(FPM) to derive sediment screening guidelines for dredged material reuse in the San Francisco Bay Region. The Long Term Management Strategy (LTMS) has a goal to use at least 40% of the sediment dredged from San Francisco Bay for beneficial reuse (USACE, 1998). The suitability of dredged sediment for beneficial reuse is in part determined by concentrations of toxic pollutants.The San Francisco Regional Water Quality Control Board (SFB-RWQCB) issued draft screening criteria in 2000 to categorize the suitability of sediment for reuse as either “surface” sediment, that may be placed near the surface for re-use in wetlands, or “foundation” sediment, that is buried under sediment that meets surface criteria. Contaminant concentration guidelines for surface sediment are lower than foundation sediment, based on the assumption that biota are more likely to be exposed to surface sediment than deeper foundation sediment.
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Regional Analysis of Potential Beneficial Use Locations. Conducted for the San Francisco Bay Regional Dredged Material Management Plan. Prepared by the San Francisco Estuary Institute for the US Army Corps of Engineers, San Francisco District. SFEI Contribution No. 1178. San Francisco Estuary Institute: Richmond, CA.
2023. ![application/pdf](/modules/file/icons/application-pdf.png)
Regional Curves of Hydraulic Geometry for Wadeable Streams In Marin and Sonoma Counties, San Francisco Bay Area. Watershed Sciences Berkeley and Marin County Flood Control District.
2013. ![application/pdf](/modules/file/icons/application-pdf.png)
Regional Monitoring in San Francisco Bay: A Summary of Key Issues. SFEI Contribution No. 36.
1999. Regional Monitoring Program for Trace Substances in the San Francisco Estuary 2005 Program Plan. SFEI Contribution No. 389. San Francisco Estuary Institute: Oakland. p 16.
2005. ![application/pdf](/modules/file/icons/application-pdf.png)
The Regional Monitoring Program: Science in Support of Managing Water Quality in San Francisco Bay. SFEI Contribution No. 435.
2006. ![application/pdf](/modules/file/icons/application-pdf.png)
Regional Watershed Modeling and Trends Implementation Plan. SFEI Contribution No. 943. San Francisco Estuary Institute: Richmond, CA.
2019. ![application/pdf](/modules/file/icons/application-pdf.png)
Regional Watershed Spreadsheet Model (RWSM) Year 5 Progress Report. SFEI Contribution No. 788.
2016. ![application/pdf](/modules/file/icons/application-pdf.png)
Regional Watershed Spreadsheet Model (RWSM): Year 6 Progress Report. SFEI Contribution No. 811. San Francisco Estuary Institute: Richmond, CA.
2017. ![application/pdf](/modules/file/icons/application-pdf.png)
2008.
The Relationship between Landscape Features and Sport Fish Mercury in the Sacramento-San Joaquin Delta Watershed. SFEI Contribution No. 534. San Francisco Estuary Institute.
2007. ![application/pdf](/modules/file/icons/application-pdf.png)
Relationship Between Sediment Toxicity and Contamination in San Francisco Bay. SFEI Contribution No. 27. San Francisco Estuary Institute: Oakland, CA. pp 285-309.
1997. The relationship between trophic position, spatial location, and contaminant concentration for San Francisco Bay sport fish: a stable isotope study. SFEI Contribution No. 487. San Francisco Estuary Institute: Oakland, CA.
2002. Remote Sensing Recommendations for Tidal Wetland Indicators. SFEI Contribution No. 1047. San Francisco Estuary Institute: Richmond. CA. p 31.
2021. This document presents potential products and methods for monitoring a suite of tidal wetland habitat indicators designated for the Montezuma Wetlands Project using remote sensing technology. This document can also serve as a starting place for the Technical Advisory Committee of the San Francisco Estuary Regional Monitoring Program (WRMP) to develop a set of regional protocols for monitoring the same or similar habitat indicators.
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Re-Oaking North Bay. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.
2020. ![application/pdf](/modules/file/icons/application-pdf.png)
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Re-Oaking Silicon Valley: Building Vibrant Cities with Nature. SFEI Contribution No. 825. San Francisco Estuary Institute: Richmond, CA.
2017. In this report, we investigate how re-integrating components of oak woodlands into developed landscapes — “re-oaking” — can provide an array of valuable functions for both wildlife and people. Re-oaking can increase the biodiversity and ecological resilience of urban ecosystems, improve critical urban forest functions such as shade and carbon storage, and enhance the capacity of cities to adapt to a changing climate. We focus on Silicon Valley, where oak woodland replacement by agriculture and urbanization tells a story that has occurred in many other cities in California. We highlight how the history and ecology of the Silicon Valley landscape can be used as a guide to plan more ecologically-resilient cities in the Bay Area, within the region and elsewhere in California. We see re-oaking as part of, and not a substitute for, the important and broader oak woodland conservation efforts taking place throughout the state.
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Report of Science Advisors: Solano County Natural Community Conservation Plan Habitat Conservation Plan. SFEI Contribution No. 272.
2002. ![application/pdf](/modules/file/icons/application-pdf.png)
Report of the 2003 Program Review. SFEI Contribution No. 303. San Franciso Estuary Institute: Oakland.
2004. ![application/pdf](/modules/file/icons/application-pdf.png)
Report of the Bioaccumulation Workshop. San Francisco Estuary Institute: Richmond, CA.
. 1999. ![application/pdf](/modules/file/icons/application-pdf.png)
Report of the Pesticide Workgroup. San Francisco Estuary Institute: Richmond, CA.
. 1999. ![application/pdf](/modules/file/icons/application-pdf.png)
Report of the Puget Sound Expedition, September 8-16, 1998; A Rapid Assessment Survey of Nonindigenous Species in the Shallow Waters of Puget Sound. Washington State Department of Natural Resources, Olympia WA and United States Fish and Wildlife Service: Olympia WA.
1998. Report of the Washington State Exotics Expedition 2000. SFEI Contribution No. 355. Nearshore Habitat Program, Washington State Department of Natural Resources: Olympia WA.
2001. ![application/pdf](/modules/file/icons/application-pdf.png)
Research Recommendations for the San Francisco Estuary: Understanding the Ecosystem. SFEI Contribution No. 181. San Francisco Estuary Institue: Richmond, Ca. p 49.
1994. Resilient Landscape Vision for Lower Walnut Creek: Baseline Information and Management Strategies. Flood Control 2.0. An SFEI-ASC Resilient Landscape Program report developed in cooperation with the Flood Control 2.0 Regional Science Advisors and
Contra Costa County Flood Control and Water Conservation District. SFEI Contribution No. 782. San Francisco Estuary Institute-Aquatic Science Center: Richmond, CA.
2016. Lower Walnut Creek (Contra Costa County, CA) and its surrounding landscape have undergone considerable land reclamation and development since the mid-nineteenth century. In 1965, the lower 22 miles of Walnut Creek and the lower reaches of major tributaries were converted to flood control channels to protect the surrounding developed land. In the recent past, sediment was periodically removed from the lower Walnut Creek Flood Control Channel to provide flow capacity and necessary flood protection. Due to the wildlife impacts and costs associated with this practice, the Contra Costa County Flood Control and Water Conservation District (District) is now seeking a new channel management approach that works with natural processes and benefits people and wildlife in a cost-effective manner. Flood Control 2.0 project scientists and a Regional Science Advisory Team (RSAT) worked with the District to develop a long-term management Vision for lower Walnut Creek that could result in a multi-benefit landscape that restores lost habitat and is resilient under a changing climate.
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Resilient Landscape Vision for the Calabazas Creek, San Tomas Aquino Creek, and Pond A8 Area: Bayland-Creek Reconnection Opportunities. SFEI Contribution No. 870. San Francisco Estuary Institute-Aquatic Science Center: Richmond, CA. p 40.
2018. This report proposes a multi-faceted redesign of the South San Francisco Bay shoreline at the interface with Calabazas and San Tomas Aquino creeks. Recognizing the opportunities presented by changing land use and new challenges, such as accelerated sea-level rise, we explore in this report a reconfigured shoreline that could improve ecosystem health and resilience, reduce maintenance costs, and protect surrounding infrastructure.
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Resilient Landscape Vision for Upper Penitencia Creek. SFEI Contribution No. 894. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
2018. ![application/pdf](/modules/file/icons/application-pdf.png)
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RESILIENT STATEN ISLAND: Landscape Scenario Analysis Pilot Application. SFEI Contribution No. 1083. San Francisco Estuary Institute: Richmond, Ca.
2022. A central motivating question for the Sacramento-San Joaquin Delta science and management community is what should be done, where and when, to support future Delta landscapes that are ecologically and economically viable and resilient to change. Actions must be taken that have the greatest potential for achieving multiple benefits. This is especially important given the urgency to rapidly transition Delta landscapes to address biodiversity loss, erosion of ecosystem resilience, flood risk, water supply reliability, and cultural and economic sustainability. Landscape-scale planning is needed to examine how individual actions add up to meaningful change. Such planning involves figuring out how different areas can provide different functions at different times and helps show how choices made now can help shift trajectories toward desired outcomes. Too often, land use and management decisions are made based on a limited set of objectives or at the site scale, resulting in missed opportunities. Actions (or inaction) should not foreclose on critical opportunities. Moving forward, there is great need to more effectively compare possible future scenarios across a range of ecological and economic factors. This scenario analysis for Staten Island — a large Delta island managed for multiple uses and facing challenges similar to elsewhere in the Delta — provides an approach to help address this need.
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Restoration of the San Francisco Region: the Role of NGOs (Abstract). San Francisco, CA: Richmond, CA.
2001. ![application/pdf](/modules/file/icons/application-pdf.png)
Restoration Plan for the Laguna de Santa Rosa. SFEI Contribution No. 1123. San Francisco Estuary Institute: Richmond, CA.
2023. The Laguna de Santa Rosa is an expansive freshwater wetland complex that hosts a rich diversity of plant and wildlife species, and is also home to a thriving agricultural community. Since the mid-19th century, modifications to the Laguna and its surrounding landscape have degraded habitat conditions for both wildlife and people. Together with partners at the Laguna de Santa Rosa Foundation, and funded by Sonoma Water and the California Department of Fish and Wildlife, the goal of the Laguna de Santa Rosa Master Restoration Plan project is to develop a plan that supports ecosystem services in the Laguna—through the restoration and enhancement of landscape processes that form and sustain habitats and improve water quality—while considering flood management issues and the productivity of agricultural lands.
The first phase of the project was the creation of the Restoration Vision for the Laguna de Santa Rosa. The report details a long-term vision for the landscape which highlights opportunities for multi-benefit habitat restoration and land management within the Laguna’s 100-year floodplain. It presents an understanding of the landscape functioning from past, present, and potential future perspectives. Starting with a picture of the historical ecology of the Laguna that details the magnitude of change in habitat conditions over the past two centuries, the document then presents an understanding of key physical processes that affect today’s Laguna. The restoration concepts described in the Vision represent a potential future Laguna, and were developed and vetted through a series of workshops in which technical advisers, management advisers, tribal representatives, and local landowners and stakeholders shared their expertise and helped shape the concepts.
The second phase of this project was the development of a Restoration Plan for the Laguna de Santa Rosa that was built from the Vision. The Restoration Plan was developed through a collaborative process that focused on moving forward identified restoration opportunities into conceptual designs that can be used to establish implementable restoration projects. The Restoration Plan includes the following elements:
- A restoration framework that offers a planning structure for landscape scale restoration that can be further developed and refined over time.
- Restoration project concepts in the Laguna’s 100-year floodplain developed from selected restoration opportunity areas shown in the Vision.
- Criteria for prioritizing and sequencing restoration project concepts.
The utilization of the Restoration Plan and the ultimate success of restoration efforts in the Laguna will require local landowner support and adequate funding to implement the restoration and manage and sustain the benefits through long-term stewardship. It will also require coordination among all the agencies responsible for managing the land and water within the Laguna and its surrounding watershed. With commitment and collaboration the Laguna
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Restoration Vision for the Laguna de Santa Rosa. SFEI Contribution No. 983. SFEI: Richmond, CA.
2020. The Laguna de Santa Rosa, located in the Russian River watershed in Sonoma County, CA, is an expansive freshwater wetland complex that hosts a rich diversity of plant and wildlife species, many of which are federally or state listed as threatened, endangered, or species of special concern. The Laguna is also home to a thriving agricultural community that depends on the land for its livelihood. Since the mid-19th century, development within the Laguna and its surrounding watershed have had a considerable impact on the landscape, affecting both wildlife and people. Compared to pre-development conditions, the Laguna currently experiences increased stormwater runoff and flooding, increased delivery and accumulation of fine sediment and nutrients, spread of problematic invasive species, and decreased habitat for native fish and wildlife species. Predicted changes in future precipitation patterns and summertime air temperatures, combined with expanding development pressure, could exacerbate these problems. People who manage land and regulate land management decisions in and around the Laguna, including landowners; federal, state, and local agencies; and local stakeholders, are seeking a long-term management approach for the Laguna that improves conditions for the wildlife and people that call the Laguna home. The California Department of Fish and Wildlife and Sonoma Water funded the Laguna-Mark West Creek Watershed Master Restoration Planning Project to develop such a management approach, focusing on the need to identify restoration and management actions that enhance desired ecological functions of the Laguna, while also supporting the area’s agriculture and its local residents.
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Results of the Benthic Pilot Study 1994 - 1997, Part 1. SFEI Contribution No. 39. San Francisco Estuary Institute: Richmond, CA.
2000. ![application/pdf](/modules/file/icons/application-pdf.png)
Results of the Estuary Interface Pilot Study, 1996-1999, Final Report. (Technical Report of the Sources Pathways and Loading Work Group (SPLWG) of the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP)). SFEI Contribution No. 50. San Francisco Estuary Institute: Oakland, CA.
2002. ![application/pdf](/modules/file/icons/application-pdf.png)
Results of the San Francisco Bay Seafood Consumption Study. SFEI Contribution No. 230.
2001. Review of Alternative Aquatic Pest Control Methods For California Waters. SFEI Contribution No. 96. San Francisco Estuary Institute: Oakland, CA. p 109 pp.
2004. ![application/pdf](/modules/file/icons/application-pdf.png)
Review of methods to reduce urban stormwater loads. SFEI Contribution No. 429. San Francisco Estuary Institute: Oakland. p 150xx.
. 2006. ![application/pdf](/modules/file/icons/application-pdf.png)
Review of sediment gauging in Alameda Creek Watershed in relation to District needs. SFEI Contribution No. 571.
2009. ![application/pdf](/modules/file/icons/application-pdf.png)
Review of sediment gauging studies in Alameda Creek Watershed. SFEI Contribution No. 571. San Francisco Estuary Institute.
2008. A review of urban runoff processes in the Bay Area: Existing knowledge, conceptual models, and monitoring recommendations. SFEI Contribution No. 66. San Francisco Estuary Institute: Oakland, CA.
2003. ![application/pdf](/modules/file/icons/application-pdf.png)
A review of Zebra Mussels' Environmental Requirements. . SFEI Contribution No. 420. San Francisco Estuary Institute: Sacramento, CA.
2005. ![application/pdf](/modules/file/icons/application-pdf.png)
Riparian Zone Estimation Tool Hydrologic Connectivity Module: Documentation and Validation of Selected Methodology. San Francisco Estuary Institute: 745.
. 2015. ![application/pdf](/modules/file/icons/application-pdf.png)
Riparian Zone Estimation Tool: Hydrologic Connectivity Module Field Plan. San Francisco Estuary Institute: Richmond, CA.
. 2013. ![application/pdf](/modules/file/icons/application-pdf.png)
RipZET: The Riparian Zone Estimation Tool version 2.0. San Francisco Estuary Institute: Richmond, CA.
. 2015. ![application/pdf](/modules/file/icons/application-pdf.png)
RMP Field Sampling Report 2016. SFEI Contribution No. 826. San Francisco Estuary Institute: Richmond, CA.
2017. ![application/pdf](/modules/file/icons/application-pdf.png)
RMP Food Web Analysis; Data Report on Gut Contents of Four Fish Species. San Francisco Estuary Institute.
2008. ![application/pdf](/modules/file/icons/application-pdf.png)
RMP Sediment Study 2009-2010 Determining Causes of Sediment Toxicity in the San Francisco Estuary. SFEI Contribution No. 626. UC-Davis, Marine Pollutions Studies Laboratory.
2011. ![application/pdf](/modules/file/icons/application-pdf.png)
RMP Sediment TIE Study 2007-2008: Using Toxicity Identification Evaluation (TIE)Methods to Investigate Causes of Sediment Toxicity to Amphipods. SFEI Contribution No. 561. San Francisco Estuary Institute: Oakland, CA.
2008. ![application/pdf](/modules/file/icons/application-pdf.png)
RMP Small Tributaries Loading Strategy. San Francisco Estuary Institute: Richmond, CA.
2009. ![application/pdf](/modules/file/icons/application-pdf.png)
RMP Small Tributaries Loading Strategy: Modeling and Trends Strategy 2018. SFEI Contribution No. 886. San Francisco Estuary Institute : Richmond, CA.
2018. ![application/pdf](/modules/file/icons/application-pdf.png)
RMP Update 2020. SFEI Contribution No. 1008.
2020. The overarching goal of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is to answer the highest priority scientific questions faced by managers of Bay water quality. The RMP is an innovative collaboration between the San Francisco Bay Regional Water Quality Control Board, the regulated discharger community, the San Francisco Estuary Institute, and many other scientists and interested parties. The purpose of this document is to provide a concise overview of recent RMP activities and findings, and a look ahead to significant products anticipated in the next two years. The report includes a description of the management context that guides the Program; a brief summary of some of the most noteworthy findings of this multifaceted Program; and a summary of progress to date and future plans for addressing priority water quality topics.
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RMP Update 2021. SFEI Contribution No. 1057.
2021. The overarching goal of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is to answer the highest priority scientific questions faced by managers of Bay water quality. The RMP is an innovative collaboration between the San Francisco Bay Regional Water Quality Control Board, the regulated discharger community, the San Francisco Estuary Institute, and many other scientists and interested parties. The purpose of this document is to provide a concise overview of recent RMP activities and findings, and a look ahead to significant products anticipated in the next two years. The report includes a description of the management context that guides the Program; a brief summary of some of the most noteworthy findings of this multifaceted Program; and a summary of progress to date and future plans for addressing priority water quality topics.
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RMP Watershed Pilot Study: An Information Review with Emphasis on Contaminant Loading, Sources, and Effects. SFEI Contribution No. 19. San Francisco Estuary Institute: Richmond, CA.
1998. ![application/pdf](/modules/file/icons/application-pdf.png)
Robertson Park and Medeiros Parkway sUAS Surveys for the Sycamore Pilot Implementation Project. Prepared for Zone 7 Water Agency and US Environmental Protection Agency’s Water Quality Improvement Fund. In collaboration with San Francisco Estuary Institute.
2024. This memo summarizes the use of small Unoccupied Aerial Systems (sUAS) to survey Robertson Park and Medeiros Parkway and analysis of how this type of technology can be used to support site scale level mapping.
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The Role of Recycling in Community Collection of Hazardous Waste. . University of California: Berkeley CA.
1984. Sacramento-San Joaquin Delta Historical Ecology Investigation: Exploring Pattern and Process. SFEI Contribution No. 672. SFEI: Richmond.
2012. The Sacramento-San Joaquin Delta has been transformed from the largest wetland system on the Pacific Coast of the United States to highly productive farmland and other uses embodying California’s water struggles. The Delta comprises the upper extent of the San Francisco Estuary and connects two-thirds of California via the watersheds that feed into it. It is central to the larger California landscape and associated ecosystems, which will continue to experience substantial modification in the future due to climate change and continued land and water use changes. Yet this vital ecological and economic link for California and the world has
been altered to the extent that it is no longer able to support needed ecological functions. Approximately 3% of the Delta’s historical tidal wetland extent remains wetland today; the Delta is now crisscrossed with agricultural ditches replacing the over 1,000 miles of branching tidal channels.
Imagining a healthy Delta ecosystem in the future and taking bold, concrete steps toward that future requires an understanding and vision of what a healthy ecosystem looks like. For a place as extensive, unique, and modified as the Delta, valuable knowledge can be acquired through the study of the past, investigating the Delta as it existed just prior to the substantial human modifications of the last 160 years. Though the Delta is irrevocably altered, this does not mean that the past is irrelevant. Underlying geologic and hydrologic processes still influence the landscape, and native species still ply the waters, soar through the air, and move across the land. Significant opportunities are available to strategically reconnect landscape components in ways that support ecosystem resilience to both present and future stressors.
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Sampling and Analysis Plan for 2016 RMP Status and Trends Bird Egg Monitoring. SFEI Contribution No. 827. San Francisco Estuary Institute: Richmond, CA. p 31 pp.
2016. ![application/pdf](/modules/file/icons/application-pdf.png)
Sampling and Analysis Plan for Microplastic Monitoring in San Francisco Bay and Adjacent National Marine Sanctuaries. SFEI Contribution No. 819. San Francisco Estuary Institute: Richmond, CA.
2017. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Ambient Monitoring Interim Report. SFEI Contribution No. 751.
2003. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Atmospheric Deposition Pilot Study Part 1: Mercury. SFEI Contribution No. 72. San Francisco Estuary Institute: Richmond, CA.
2001. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Atmospheric Deposition Pilot Study Part 2: Trace Metals. SFEI Contribution No. 73. San Francisco Estuary Institute: Richmond, CA.
2001. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Atmospheric Deposition Pilot Study Part 3: Dry Deposition of PAHs and PCBs. SFEI Contribution No. 506.
2005. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Atmospheric Deposition Pilot StudyPart 3: Dry Deposition of PAHs and PCBs. SFEI Contribution No. 408.
2005. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Atmospheric Deposition Pilot Study (Trace Metals): Presentation at 2001 WEFTEC. SFEI Contribution No. 235. San Francisco Estuary Institute: Richmond, CA.
2001. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay California Toxics Rule Priority Pollutant Ambient Water Monitoring Report. SFEI Contribution No. 814. San Francisco Estuary Institute: Richmond.
2017. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Episodic Toxicity Report:1999 Progress Report. SFEI Contribution No. 346. San Francisco Estuary Institute: Richmond, CA.
2000. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Episodic Toxicity Report - 2000. SFEI Contribution No. 233. San Francisco Estuary Institute: Richmond, CA.
2001. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Interim Model Validation Report. SFEI Contribution No. 850. San Francisco Estuary Institute: Richmond, CA.
2017. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Microplastics Project: Science-Supported Solutions and Policy Recommendations. SFEI Contribution No. 955. 5 Gyres: Los Angeles, CA.
2019. 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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San Francisco Bay Nutrient Management Strategy: Detailed Modeling Workplan for FY15-FY21. San Francisco Estuary Institute: Richmond, CA.
2014. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Nutrient Management Strategy Observation Program. SFEI Contribution No. 877. San Francisco Estuary Institute: Richmond, CA.
2016. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay PCB Food - Web Model. SFEI Contribution No. 90. San Francisco Estuary Institute , Simon Fraser University, EVS Environmental Consultants: Oakland, Ca.
2003. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Regional Watershed Modeling Progress Report, Phase 1. SFEI Contribution No. 1038. San Francisco Estuary Institute: Richmond, CA.
2021. ![application/pdf](/modules/file/icons/application-pdf.png)
The San Francisco Bay Seafood Consumption Study Report. SFEI Contribution No. 369. San Francisco Estuary Institute: Oakland, CA.
. 2001. ![application/pdf](/modules/file/icons/application-pdf.png)
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San Francisco Bay Sediment Modeling and Monitoring Workplan. SFEI Contribution No. 1100. San Francisco Estuary Institute: Richmond, CA.
2023. 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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San Francisco Bay Shore Inventory: Mapping for Sea Level Rise Planning. SFEI Contribution No. 779. San Francisco Estuary Institute: Richmond, CA.
2016. 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:
- identify areas vulnerable to flooding.
- identify adaptation constraints due to present Bay shore alignments; and
- 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:
- Mapping of Bay shore features (levees, berms, roads, railroads, embankments, etc.) which could affect flooding and flood routing.
- 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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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.
. 2019. 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.
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San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants - 2016 Data Summary. U.S. Geological Survey: Dixon, CA. p 19 pp.
2016. 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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San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants, California—2018. U.S. Geological Survey: Reston, Virginia.
2019. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants - 2009 Data Summary. U. S. Geological Survey: Davis, CA.
2009. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Bay Watershed Dynamic Model (WDM) Progress Report, Phase 2. SFEI Contribution No. 1091. San Francisco Estuary Institute: Richmond, California.
2022. 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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The San Francisco Estuary: A model system for invasions research. San Francisco Estuary Institute: Seattle, WA (abstract).
1997. 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.
2021. 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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San Francisco Estuary National Water Quality Monitoring Network Pilot Study Report. SFEI Contribution No. 548. p 70.
2008. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Estuary Project Status and Trends Report on Pollutants in the San Francisco Estuary, Final Draft. SFEI Contribution No. 162. AHI: Richmond, CA. p 291.
1991. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Estuary Regional Monitoring Program (RMP) Annual Monitoring Results, 2002. SFEI Contribution No. 466. San Francisco Estuary Institute: Oakland, CA.
2004. 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.
2002. ![application/pdf](/modules/file/icons/application-pdf.png)
San Francisco Estuary Wetlands Regional Monitoring Program Plan: Protocols for Tier 3 (Intensive Monitoring). SFEI Contribution No. 249.
2002. San Francisco State University Site 1 Vegetated Infiltration Basin (Case Study Site and Technical Reports). SFEI Contribution No. 794.
2014. ![application/pdf](/modules/file/icons/application-pdf.png)
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San Francisco State University Site 3 Basin and Swale System (Case Study Site and Technical Reports). SFEI Contribution No. 795.
2014. ![application/pdf](/modules/file/icons/application-pdf.png)
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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.
2016. 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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