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Regional Monitoring Program for Water Quality in the SF Estuary. 2007. 2006 RMP Annual Monitoring Results. SFEI Contribution No. 542. San Francisco Estuary Institute: Oakland.
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Regional Monitoring Program for Water Quality in the SF Estuary. 2007. 2007 RMP Annual Monitoring Results. SFEI Contribution No. 572. San Francisco Estuary Institute: Oakland, CA.
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Program, H. Ecology. 2012. Historical Ecology of the McCormack-Williamson Tract: A Landscape Framework for Restoration. SFEI Contribution No. 674. Aquatic Science Center / San Francisco Estuary: Richmond, CA.
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Plane, E.; Lowe, J. 2022. Adaptation Pathways: San Leandro Operational Landscape Unit. SFEI Contribution No. 1077. San Francisco Estuary Institute: Richmond, CA.
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Plane, E.; Lowe, J.; Miller, G.; Robinson, A.; Crain, C.; Grenier, L. 2023. Baylands Resilience Framework for San Francisco Bay: Wildlife Support. SFEI Contribution No. 1115. 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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Phillips, A. 1988. Executive Summary of the Monitoring of Toxic Contaminants in the San Francisco Bay-Delta: A Crtical Review. SFEI Contribution No. 151. San Francisco Estuary Institue: Richmond, CA. p 14.
Phillips, D. J. H. 1987. Executive Summary of Toxic Contaminats in the San Francisco Bay - Delta and Their Possible Biological Effects. SFEI Contribution No. 139. San Francisco Estuary Institute: Richmond, CA. p 15.
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Phillips, D. J. H. 1987. Toxic Contaminants in the San Francisco Bay-Delta and their Possible Biological Effects. SFEI Contribution No. 145. Aquatic Habitat Institute: Richmond, CA. p 472.
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Peterson, D.; Baumgarten, S.; Stark, K.; Vaughn, L.; Dusterhoff, S. 2024. Petaluma River Watershed Contemporary Riparian Condition Assessment. Petaluma River Watershed Contemporary Riparian Condition Assessment. SFEI Contribution No. 1160. San Francisco Estuary Institute: Richmond, CA.
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Pearce, S.; Whipple, A.; Harris, K.; Lee, V.; Hegstad, R.; McClain, C. 2023. Sycamore Alluvial Woodland Restoration and Enhancement Suitability Study. In collaboration with Alameda County Flood Control and Water Conservation District, Zone 7. Prepared for the US Environmental Protection Agency’s Water Quality Improvement Fund. SFEI Contribution No. 1128. San Francisco Estuary Institute: Richmond, CA.

The “Sycamore Alluvial Woodland Restoration and Enhancement Suitability Study” addresses distribution and regeneration patterns and restoration strategies of sycamore alluvial woodland (SAW) habitat, a unique and relatively rare native vegetation community adapted to California’s intermittent rivers and streams. The report was produced by SFEI and H. T. Harvey & Associates, as part of the US EPA Water Quality Improvement Fund Preparing for the Storm grant, led by Zone 7 Water Agency.

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Pearce, S. A.; Stark, K. 2023. Translating Sediment Science Into Action: Documenting Beneficial Sediment Reuse. SFEI Contribution No. 1124. San Francisco Estuary Institute: Richmond, CA.

The Preparing for the Storm project, led by Zone 7 Water Agency (Zone 7) and funded by the US Environmental Protection Agency (EPA) Water Quality Improvement Fund, aims to develop science-based plans, strengthen existing and new partnerships, and pilot new methodologies for tackling these issues surrounding coarse sediment. As a task within this larger project, this report describes four projects in the East Bay that serve as case studies for beneficial reuse of sediment. Each example highlights a project with sediment that could be reused (in lieu of landfilling) or a project that needs additional sediment and could benefit from deliveries of sediment that normally would not have been beneficially reused.

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Pearce, S.; Mckee, L.; Whipple, A.; Church, T. 2021. Towards a Coarse Sediment Strategy for the Bay Area. SFEI Contribution No. 1032. San Francisco Estuary Institute: Richmond, CA.

Historic and current regional management of watersheds and channels for water supply and flood control across the San Francisco Bay Area has cut off much of the coarse sediment that was historically delivered to the Bay. Here we define coarse sediment as having grain sizes larger than 0.0625 mm, which includes sand, gravel and even cobble, as opposed to fine sediment that includes clay, mud and silt. Future projections indicate that sediment supply will not meet the demand from extant and restored tidal marshes to keep up with sea level rise.


The US EPA Water Quality Improvement Fund Preparing for the Storm grant has funded the Zone 7 Water Agency, the San Francisco Estuary Institute and the San Francisco Bay Joint Venture to support the future development of a successful regional coarse sediment reuse strategy. Development of such a strategy requires an understanding of logistical and regulatory hurdles and identification of key strategies for breaking down barriers. One potential solution for meeting the sediment demand along the Bay margin is to utilize coarse sediment that is removed from flood control channels by public agencies. To-date, very little of this sediment that is removed is beneficially reused for restoration along the Bay shoreline. The current economic and regulatory framework around sediment removal presents many challenges, barriers and lack of incentives for agencies to reuse their sediment.

This document represents a step forward towards beneficially reusing coarse flood control channel sediment by outlining reuse challenges, and identifying incentives for participation and potential solutions.

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Pearce, S.; McKee, L. 2020. Summary of Water Year 2017 precipitation, discharge, and sediment conditions at selected locations in Arroyo de la Laguna watershed, with a focus on Arroyo Mocho. SFEI Contribution No. 912. San Francisco Estuary Institute: Richmond, CA.

This report summarizes the precipitation, discharge, and sediment conditions observed from October 1, 2016 to September 30th, 2017 (Water Year (WY) 2017) in the Arroyo de la Laguna watershed, with a focus on the Arroyo Mocho watershed. This information was collected by the Zone 7 Water Agency to support operation and maintenance of their flood control facilities. Additionally, this and similar information collected in WY 2018 and 2019 will be utilized to update the Arroyo Mocho watershed sediment budget (Pearce et al, 2020).

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Pearce, S.; McKee, L. J. . 2009. Alameda Creek Bulk Sediment Study Technical Memorandum. San Francisco Estuary Institute: Oakland,Ca.
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Panlasigui, S.; Baumgarten, S.; Spotswood, E. 2021. E-Bikes and Open Space: The Current State of Research and Management Recommendations. SFEI Contribution No. 1064. San Francisco Estuary Institute: Richmond, CA.
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Panlasigui, S.; Spotswood, E.; Beller, E.; Grossinger, R. 2021. Biophilia beyond the Building: Applying the Tools of Urban Biodiversity Planning to Create Biophilic Cities. Sustainability 13 (5).

In response to the widely recognized negative impacts of urbanization on biodiversity, many cities are reimagining urban design to provide better biodiversity support. Some cities have developed urban biodiversity plans, primarily focused on improving biodiversity support and ecosystem function within the built environment through habitat restoration and other types of urban greening projects. The biophilic cities movement seeks to reframe nature as essential infrastructure for cities, seamlessly integrating city and nature to provide abundant, accessible nature for all residents and corresponding health and well-being outcomes. Urban biodiversity planning and biophilic cities have significant synergies in their goals and the means necessary to achieve them. In this paper, we identify three key ways by which the urban biodiversity planning process can support biophilic cities objectives: engaging the local community; identifying science-based, quantitative goals; and setting priorities for action. Urban biodiversity planning provides evidence-based guidance, tools, and techniques needed to design locally appropriate, pragmatic habitat enhancements that support biodiversity, ecological health, and human health and well-being. Developing these multi-functional, multi-benefit strategies that increase the abundance of biodiverse nature in cities has the potential at the same time to deepen and enrich our biophilic experience in daily life.

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Panlasigui, S.; Pearce, S.; Hegstad, R.; Quinn, M.; Whipple, A. 2020. Wildlife Habitat and Water Quality Enhancement Opportunities at Castlewood Country Club. SFEI Contribution No. 1003. San Francisco Estuary Institute: Richmond, CA.

Meeting human and ecological needs within San Francisco Bay’s watersheds is increasingly challenged by flooding, water quality degradation, and habitat loss, exacerbated by intensified urbanization and climate change. Addressing these challenges requires implementing multi-benefit strategies through new partnerships and increased coordination across the region’s diverse landscapes. Actions to improve water quality and enhance habitat for biodiversity in our highly developed and managed landscapes can help the region as a whole to build resilience to withstand current pressures and future change. The EPA-funded project, “Preparing for the Storm,” aims to address these challenges at the site- and landscape-scale through studies and implementation projects in the Livermore-Amador Valley. As part of this larger project, this technical report presents a synthesis of water quality and habitat improvement opportunities for a golf course of Castlewood Country Club.

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Palenik, B.; Flegal, R. A. 1999. Cyanobacterial Populations in San Francisco Bay. SFEI Contribution No. 42. San Francisco Estuary Institute: Richmond, CA.
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Overdahl, K. E.; Sutton, R.; Sun, J.; DeStefano, N. J.; Getzinger, G. J.; P. Ferguson, L. 2021. Assessment of emerging polar organic pollutants linked to contaminant pathways within an urban estuary using non-targeted analysis. SFEI Contribution No. 1107. Environmental Sciences: Processes and Impacts.

A comprehensive, non-targeted analysis of polar organic pollutants using high resolution/accurate mass (HR/AM) mass spectrometry approaches has been applied to water samples from San Francisco (SF) Bay, a major urban estuary on the western coast of the United States, to assess occurrence of emerging contaminants and inform future monitoring and management activities. Polar Organic Chemical Integrative Samplers (POCIS) were deployed selectively to evaluate the influence of three contaminant pathways: urban stormwater runoff (San Leandro Bay), wastewater effluent (Coyote Creek, Lower South Bay), and agricultural runoff (Napa River). Grab samples were collected before and after deployment of the passive samplers to provide a quantitative snapshot of contaminants for comparison. Composite samples of wastewater effluent (24 hours) were also collected from several wastewater dischargers. Samples were analyzed using liquid-chromatography coupled to high resolution mass spectrometry. Resulting data were analyzed using a customized workflow designed for high-fidelity detection, prioritization, identification, and semi-quantitation of detected molecular features. Approximately 6350 compounds were detected in the combined data set, with 424 of those compounds tentatively identified through high quality spectral library match scores. Compounds identified included ethoxylated surfactants, pesticide and pharmaceutical transformation products, polymer additives, and rubber vulcanization agents. Compounds identified in samples were reflective of the apparent sources and pathways of organic pollutant inputs, with stormwater-influenced samples dominated by additive chemicals likely derived from plastics and vehicle tires, as well as ethoxylated surfactants.

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Oros, D. R.; Taberski, K. 2000. Closing in on unidentified contaminants. pp p. 18-19 . SFEI Contribution No. 274.
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Oros, D. R. 2005. Emerging Contaminants: Endocrine Disrupting Chemicals (EDCs). RMP Regional Monitoring News, San Francisco Estuary Regional Monitoring Program for Trace Substances 10, p.1-11 . SFEI Contribution No. 502.
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Oros, D. R. 2002. Polar aromatic biomarkers in the miocene Maritza-East Lignite, Bulgaria. Organic Geo-chemistry . SFEI Contribution No. 476.
Oros, D. R. 2005. Pelagic Organism Decline. SFEI Contribution No. 511.
Oros, D. R.; Simoneit, B. R. T.; Mazurek, M. A.; Baham, J. E. 2002. Organic Tracers from Wild Fire Residues in Soils and Rain/River Wash-Out. Water, Air and Soil Pollution 137, p.203-233 . SFEI Contribution No. 479.
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Oram, J. J.; Greenfield, B. K.; Davis, J. A.; David, N.; Leatherbarrow, J. E. 2006. Organochlorine Pesticide Fate in San Francisco Bay. SFEI Contribution No. 433. San Francisco Estuary Institute: Oakland, CA. p 48.
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Oram, J. J.; McKee, L. J. .; Davis, J. A.; Hetzel, F. 2007. Polychlorinated biphenyls (PCBs) in San Francisco Bay. Environmental Research 105, 67-86 . SFEI Contribution No. 526.
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Oram, J. J.; Leatherbarrow, J. E.; Davis, J. A. 2005. DRAFT REPORT: A Model of Long-Term PCB Fate and Transport in San Francisco Bay, CA. SFEI Contribution No. 388. San Francisco Estuary Institute: Oakland, CA.
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Oram, J. J.; McKee, L. J. .; Davis, J. A.; Sedlak, M.; Yee, D. 2008. Sources, Pathways and Loadings Workgroup: Five-Year Workplan (2008-12). SFEI Contribution No. 567. San Francisco Estuary Institute: Oakland.
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Oram, J. J.; Melwani, A. R. 2006. Dredging Impacts on Food-Web Bioaccumulation of DDTs in San Francisco Bay, CA. SFEI Contribution No. 418. San Francisco Estuary Institute: Oakland, CA.
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O'Connor, J. M. 1991. Evaluation of Turbidity and Turbidity Related Effects on the Biota of the San Francisco Bay-Delta Estuary. SFEI Contribution No. 169. San Francisco Estuary Institute: Richmond, CA. p 84.
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O'Connor, J. M.; Daum, T. H. 1992. Status and Assessment of Selected Monitoring Programs in the San Francisco Esturary. SFEI Contribution No. 172. San Francisco Estuary Institute: Richmond, Ca. p 128.