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Introduced Tidal Marsh Plants in the San Francisco Estuary: Regional Distribution and Priorities for Control. SFEI Contribution No. 321. San Francisco Estuary Institute: Richmond CA. p 42.
1998. (155.6 KB)The Way It Was: Mythology, Memory, and Maps of the Early San Francisco Bay Area (Abstract for American Society for Environmental History Conference, March 2000). SFEI Contribution No. 269. San Francisco Estuary Institute.
2000. (8.69 KB)Wetland Habitat Changes in the Rodeo Lagoon Watershed, Golden Gate National Recreation Area, Marin County, CA. SFEI Contribution No. 116. San Francisco Estuary Institute: Oakland, CA.
2004. (13.65 MB)Documenting Local Landscape Change: The Bay Area Historical Ecology Project. In The Historical Ecology Handbook: A Restorationist's Guide to Reference Ecosystems.. . The Historical Ecology Handbook: A Restorationist's Guide to Reference Ecosystems. Island Press: Washington D.C.
2001. T-Sheet User Guide: Application of the Historical U.S. Coast Survey Maps to Environmental Management in the San Francisco Bay Area. SFEI Contribution No. 427. San Francisco Estuary Institute: SF. p 45.
2005. (8.6 MB)Novato Creek Baylands Vision: Integrating ecological functions and flood protection within a climate-resilient landscape. SFEI Contribution No. 764.
2015. (21.5 MB)This report explores the potential for integrating ecological functions into flood risk management on lower Novato Creek. It presents an initial vision of how ecological elements could contribute to flood protection, based on a broad scale analysis and a one day workshop of local and regional experts. The Vision is not intended to be implemented as is, but rather adapted and applied through future projects and analysis. Other actions (e.g., floodwater detention basins) may also need to be implemented in the interim to meet flood risk objectives.
2007.
The Historical Ecology of Napa Valley: An Introduction. SFEI Contribution No. 557.
2008. (33.68 MB) (5.01 MB)Historical Ecology of South Santa Clara County: Preliminary Findings. A Technical Memorandum to the Santa Clara Valley Habitat Conservation Plan/Natural Community Conservation Plan. SFEI Contribution No. 527.
2007. (36.53 MB)Oak Landscapes in the Recent Past. In Oaks in the Urban Landscape: Selection, Care, and Preservation. . Oaks in the Urban Landscape: Selection, Care, and Preservation. University of California Agriculture and Natural Resources: Richmond, CA.
2011. WRAMP Training and Outreach Plan. SFEI Contribution No. 1136. p 39.
2023. (5.8 MB)The goal of this Training and Outreach Plan is to increase the overall awareness and use of the WRAMP datasets and tools in support of wetland resource planning, management, and project performance tracking in California. Specifically, a near-term goal is to develop modular training sessions that can be linked together in different ways to customize how the datasets, monitoring methods, and online tools might be used for different purposes.
Online 401: From Pilot to Production. San Francisco Estuary Institute: Richmond, CA.
2014. (3.15 MB)2016. EcoAtlas - Lake Tahoe Environmental Improvement Program: Tool Integration White Paper. SFEI Contribution No. 800.
(703.29 KB)Priority pollutant loads from effluent discharges to the San Francisco Estuary. Water Environment Research 64, 134-140 . SFEI Contribution No. 171.
1992. Status and Trends Report on Pollutants in the San Francisco Estuary. SFEI Contribution No. 161. San Francisco Estuary Project: Oakland, CA.
1991. The Segmentation of the San Francisco Bay/Delta. SFEI Contribution No. 135. San Francisco Estuary Institute: Richmond, CA. p 18.
1987. (1.23 MB)Executive Summary of an Assessment of the Loading of Toxic Contaminants to the San Francisco Bay-Delta. SFEI Contribution No. 136. San Francisco Estuary Institute: Richmond, Ca. p 27.
1987. San Francisco Bay Episodic Toxicity Report:1999 Progress Report. SFEI Contribution No. 346. San Francisco Estuary Institute: Richmond, CA.
2000. (45.66 KB)An Assesssment of the Loading of Toxic Contaminants to the San Francisco Bay-Delta. SFEI Contribution No. 137. San Francisco Estuary Institute: Richmond. p 330.
1987. The Loading of Toxic Contaminants to the San Francisco Bay -Delta in Urban Runoff. SFEI Contribution No. 167. San Francisco Estuary Institue: Richmond, CA. p 82.
1991. An evaluation of bioaccumulation monitoring with transplanted bivalves in the RMP. SFEI Contribution No. 322. San Francisco Estuary Institute: Richmond, CA. pp 187-200.
1998. Status and Trends Report on Pollutnats in the San Francisco Estuary. San Francisco Bay-Delta Aquatic Habitat Institute: Richmond CA. p 291.
1991. Status and Trends Report on Dredging and Waterway Modification in the San Francisco Estuary. SFEI Contribution No. 159. San Francisco Estuary Project: Oakland, CA.
1990. Development of Environmental Indicators of the Condition of San Francisco Estuary. SFEI Contribution No. 113. San Francisco Estuary Institute: Oakland.
2004. (770.99 KB)The Bioavailability of Toxic Contaminants in the San Francisco Bay-Delta: Proceedings of a Two-Day Seminar Series. SFEI Contribution No. 142. San Francisco Bay - Delta Aquatic Habitat Institute, Richmond, CA: Berkeley, CA.
1988. Urban Ecological Planning Guide for Santa Clara Valley. SFEI Contribution No. 941. San Francisco Estuary Institute: Richmond, CA.
This document provides some of the scientific foundation needed to guide planning for urban biodiversity in the Santa Clara Valley region, grounded in an understanding of landscape history, urban ecology and local setting. It can be used to envision the ecological potential for individual urban greening projects, and to guide their siting, design and implementation. It also can be used to guide coordination of projects across the landscape, with the cooperation of a group of stakeholders (such as multiple agencies, cities and counties). Users of this report may include a wide range of entities, such as local nonprofits, public agencies, city planners, and applicants to the Open Space Authority’s Urban Open Space Grant Program.
2019. (42.6 MB)This document provides some of the scientific foundation needed to guide planning for urban biodiversity in the Santa Clara Valley region, grounded in an understanding of landscape history, urban ecology and local setting. It can be used to envision the ecological potential for individual urban greening projects, and to guide their siting, design and implementation. It also can be used to guide coordination of projects across the landscape, with the cooperation of a group of stakeholders (such as multiple agencies, cities and counties). Users of this report may include a wide range of entities, such as local nonprofits, public agencies, city planners, and applicants to the Open Space Authority’s Urban Open Space Grant Program.
An Introduction to EcoAtlas: Applied Aquatic Science. San Francisco Estuary Institute: Richmond, CA. p 16 pages.
2016. (5.84 MB)This memo was developed by SFEI to introduce the EcoAtlas tools, their intended (target) user community, and the short- and long-term intended applications.
GreenPlan-IT Tracker.
2018. (1.43 MB)This technical memo describes the purpose, functions, and structure associated with the newest addition to the GreenPlan-IT Toolset, the GreenPlan-IT Tracker. It also shares the opportunities for further enhancement and how the tool can operate in concert with existing resources. Furthermore, this memo describes a licensing plan that would permit municipalities to use the tool in an ongoing way that scales to their needs. The memo concludes with a provisional roadmap for the development of future features and technical details describing the tool’s platform and data structures.
Enhancing the Vision for Managing California's Environmental Information. SFEI Contribution No. 792. Delta Stewardship Council: Sacramento, CA.
2015. (1.16 MB)The Environmental Data Summit, convened under the auspices of the Delta Stewardship Council’s Delta Science Program in June 2014, witnessed remarkable participation from experts across California, the nation, and even the world. Summit attendees from the public, private, federal, and non-profit sectors shared their views regarding the urgent needs and proposed solutions for California’s data-sharing and data-integration challenges, especially pertaining to the subject of environmental resource management in the era of “big data.” After all, this is a time when our data sources are growing in number, size, and complexity. Yet our ability to manage and analyze such data in service of effective decision-making lags far behind our demonstrated needs.
In its review of the sustainability of water and environmental management in the California Bay-Delta, the National Research Council (NRC) found that “only a synthetic, integrated, analytical approach to understanding the effects of suites of environmental factors (stressors) on the ecosystem and its components is likely to provide important insights that can lead to enhancement of the Delta and its species” (National Research Council 2012). The present “silos of data” have resulted in separate and compartmentalized science, impeding our ability to make informed decisions. While resolving data integration challenges will not, by itself, produce better science or better natural resource outcomes, progress in this area will provide a strong foundation for decision-making. Various mandates ranging from the California Water Action Plan to the President’s executive order demanding federal open data policies demonstrate the consensus on the merits of modern data sharing at the scale and function needed to meet today’s challenges.
This white paper emerges from the Summit as an instrument to help identify such opportunities to enhance California’s cross-jurisdictional data management. As a resource to policymakers, agency leadership, data managers, and others, this paper articulates some key challenges as well as proven solutions that, with careful and thoughtful coordination, can be implemented to overcome those obstacles. Primarily featured are tools that complement the State’s current investments in technology, recognizing that success depends upon broad and motivated participation from all levels of the public agency domain. Executive Summary
This document describes examples, practices, and recommendations that focus on California’s Delta as an opportune example likely to yield meaningful initial results in the face of pressing challenges. Once proven in the Delta, however, this paper’s recommended innovations would conceivably be applied statewide in subsequent phases.
Applied Aquatic Science: A Business Plan for EcoAtlas. San Francisco Estuary Institue: Richmond, CA.
2017. (1.69 MB) (323.4 KB) (214.45 KB)The following plan is intended to ensure the continued vitality of the toolset. The plan’s success will depend upon the continued collaboration of the public agencies that have supported the toolset thus far, but it must also integrate principles of resilience as it accounts for the tensions that arise as organizations move in different strategic directions.
A living tool for the continued exploration of microplastic toxicity. Microplastics and Nanoplastics 2 (13).
2022. Throughout the past decade, many studies have reported adverse effects in biota following microplastic exposure. Yet, the field is still emerging as the current understanding of microplastic toxicity is limited. At the same time, recent legislative mandates have required environmental regulators to devise strategies to mitigate microplastic pollution and develop health-based thresholds for the protection of human and ecosystem health. The current publication rate also presents a unique challenge as scientists, environmental managers, and other communities may find it difficult to keep up with microplastic research as it rapidly evolves. At present, there is no tool that compiles and synthesizes the data from these studies to allow for visualization, interpretation, or analysis. Here, we present the Toxicity of Microplastics Explorer (ToMEx), an open access database and open source accompanying R Shiny web application that enables users to upload, search, visualize, and analyze microplastic toxicity data. Though ToMEx was originally created to facilitate the development of health-based thresholds to support California legislations, maintaining the database by the greater scientific community will be invaluable to furthering research and informing policies globally. The database and web applications may be accessed at https://microplastics.sccwrp.org/.
Research recommendations to better understand the potential health impacts of microplastics to humans and aquatic ecosystems. Microplastics and Nanoplastics 2 (18).
2022. (466.11 KB)To assess the potential risk of microplastic exposure to humans and aquatic ecosystems, reliable toxicity data is needed. This includes a more complete foundational understanding of microplastic toxicity and better characterization of the hazards they may present. To expand this understanding, an international group of experts was convened in 2020–2021 to identify critical thresholds at which microplastics found in drinking and ambient waters present a health risk to humans and aquatic organisms. However, their findings were limited by notable data gaps in the literature. Here, we identify those shortcomings and describe four categories of research recommendations needed to address them: 1) adequate particle characterization and selection for toxicity testing; 2) appropriate experimental study designs that allow for the derivation of dose-response curves; 3) establishment of adverse outcome pathways for microplastics; and 4) a clearer understanding of microplastic exposure, particularly for human health. By addressing these four data gaps, researchers will gain a better understanding of the key drivers of microplastic toxicity and the concentrations at which adverse effects may occur, allowing a better understanding of the potential risk that microplastics exposure might pose to human and aquatic ecosystems.
Pharmaceuticals and Personal Care Products in Wastewater Treatment Plant Influent and Effluent and Surface Waters of Lower South San Francisco Bay. San Francisco Estuary Institute: Oakland, Ca.
2009. Increases in Anthropogenic Gadolinium Anomalies and Rare Earth Element Concentrations in San Francisco Bay over a 20 Year Record. Environ. Sci. Technol. 50 (8).
2016. We evaluated both the spatial distribution of gadolinium (Gd) and other rare earth elements (REE) in surface waters collected in a transect of San Francisco Bay (SFB) and their temporal variations within the Bay over two decades. The REE were preconcentrated using the NOBIAS PA-1 resin prior to analysis by high-resolution inductively coupled plasma mass spectrometry. Measurements revealed a temporal increase in the Gd anomaly in SFB from the early 1990s to the present. The highest Gd anomalies were observed in the southern reach of SFB, which is surrounded by several hospitals and research centers that use Gd-based contrast agents for magnetic resonance imaging. Recent increases in that usage presumably contributed to the order of magnitude increase in anthropogenic Gd concentrations in SFB, from 8.27 to 112 pmol kg–1 over the past two decades, and reach the northeast Pacific coastal waters. These measurements (i) show that “exotic” trace elements used in new high-tech applications, such as Gd, are emerging contaminants in San Francisco Bay and that anthropogenic Gd concentrations increased substantially over a 20 year period; (ii) substantiate proposals that REE may be used as tracers of wastewater discharges and hydrological processes; and (iii) suggest that new public policies and the development of more effective treatment technologies may be necessary to control sources and minimize future contamination by REE that are critical for the development of new technologies, which now overwhelm natural REE anomalies.
A Proposed Lentic Benthic Bioassessment Procedure for California (Protocol Brief for Biological Sampling in Lakes, Reservoirs, and Ponds). SFEI Contribution No. 315. San Francisco Estuary Institute.
2004. (455.8 KB)Aquatic Pesticides Monitoring Program Phase 3 (2005) Bioassessment of Waterbodies Treated With Aquatic Pesticides. SFEI Contribution No. 393. San Francisco Estuary Institute: Oakland, CA.
2005. (1.22 MB)Current-Use Pesticides, Fragrance Ingredients, and Other Emerging Contaminants in San Francisco Bay Margin Sediment and Water. SFEI Contribution No. 934. San Francisco Estuary Institute: Richmond, CA.
2020. (2.8 MB)The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) has recently focused attention on better characterization of contaminants in nearshore “margin” areas of San Francisco Bay. The margins of the Lower South Bay are mudflats and shallow regions that receive direct discharges of stormwater and wastewater; as a result, they may have higher levels of urban contaminants than the open Bay. In the summer of 2017, the RMP collected samples of margin
sediment in the South and Lower South Bay for analysis of legacy contaminants. The study described here leveraged that sampling effort by adding monitoring of sediment and water for two additional sets of emerging contaminants: 1) current-use pesticides; and 2) fragrance ingredients including the polycyclic musk galaxolide, as well as a range of other commonly detected emerging contaminants linked to toxicity concerns such as endocrine disruption.
Historical Ecology of Lower San Francisquito Creek Phase 1. San Francisco Estuary Institute: Oakland, Ca.
2009. (3.99 MB)DGT (Diffusive Gradient in Thinfilm) as a tool to assess sources of bioavailable methylmercury in San Francisco Bay. SFEI Contribution No. 640. SFEI: Oakland.
2011. (8.12 MB)Integrated Coastal Reserve Planning, Making the Land—Sea Connection. Front Ecol Environ 3 (8), 429-436.
2005. (2.41 MB)Watershed Management and Land Use. CCMP Implementation Committee.
2007. The Estuary Interface Pilot Study: 1998 Progress Report. SFEI Contribution No. 49. San Francisco Estuary Institute.
2000. San Francisco Bay Atmospheric Deposition Pilot Study Part 1: Mercury. SFEI Contribution No. 72. San Francisco Estuary Institute: Richmond, CA.
2001. (1.35 MB)Atmospheric Concentrations and Fluxes of Organic Compounds in the Northern San Francisco Estuary. Environmental Science and Technology 36 (22), 4741-4747 . SFEI Contribution No. 474.
2002. Regional Monitoring in San Francisco Bay: A Summary of Key Issues. SFEI Contribution No. 36.
1999. Forecasting Multiple Watershed-level Benefits of Alternative Storm Water Management Approaches in the Semi-arid Southwest: Required Tools for Investing Strategically. . SFEI Contribution No. 602.
2010. (2.29 MB)Creating data-quality objectives: A case study. Water Environment Laboratory Solutions 7-9 . SFEI Contribution No. 31.
1997. 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. (152.89 KB)SWAMP Collaboration Workshop. SFEI Contribution No. 407.
2005. Atmospheric Deposition of Trace Metals in San Francisco Bay. SFEI Contribution No. 278. San Francisco Estuary Institute: Richmond, CA.
2002. A Watershed Monitoring Strategy for Napa County. SFEI Contribution No. 428. San Francisco Estuary Institute: Napa,. p 34.
2005. (1.14 MB)PCB intercalibration exercise with Regional Monitoring Program water sample extracts. SFEI Contribution No. 204. San Francisco Estuary Institute: Richmond, CA. pp 234-239.
1997. San Francisco Bay Atmospheric Deposition Pilot Study Part 2: Trace Metals. SFEI Contribution No. 73. San Francisco Estuary Institute: Richmond, CA.
2001. (1.54 MB)San Francisco Bay Atmospheric Deposition Pilot StudyPart 3: Dry Deposition of PAHs and PCBs. SFEI Contribution No. 408.
2005. (1.54 MB)San Francisco Bay Atmospheric Deposition Pilot Study Part 3: Dry Deposition of PAHs and PCBs. SFEI Contribution No. 506.
2005. (1.54 MB)Effective Application of Monitoring Information: The Case of San Francisco Bay. Environmental Monitoring and Assessment 81, 15-25 . SFEI Contribution No. 291.
2003. San Francisco Bay Atmospheric Deposition Pilot Study (Trace Metals): Presentation at 2001 WEFTEC. SFEI Contribution No. 235. San Francisco Estuary Institute: Richmond, CA.
2001. (636.66 KB)San Francisco Bay Interim Model Validation Report. SFEI Contribution No. 850. San Francisco Estuary Institute: Richmond, CA.
2017. (34.98 MB)Development of Semi-Empirical Light Extinction Estimates for Biogeochemical Modeling Applications in San Francisco Bay. SFEI Contribution No. 1177. San Francisco Estuary Institute: Richmond, CA.
2024. (8.71 MB)Nutrient Management Strategy Science Program. SFEI Contribution No. 879. San Francisco Estuary Institute: Richmond, CA.
2017. (49.7 MB)Poly- and perfluoroalkyl substances in wastewater: Significance of unknown precursors, manufacturing shifts, and likely AFFF impacts. Water Research . SFEI Contribution No. 780.
2016. In late 2014, wastewater effluent samples were collected from eight treatment plants that discharge to San Francisco (SF) Bay in order to assess poly- and perfluoroalkyl substances (PFASs) currently released from municipal and industrial sources. In addition to direct measurement of twenty specific PFAS analytes, the total concentration of perfluoroalkyl acid (PFAA) precursors was also indirectly measured by adapting a previously developed oxidation assay. Effluent from six municipal treatment plants contained similar amounts of total PFASs, with highest median concentrations of PFHxA (24 ng/L), followed by PFOA (23 ng/L), PFBA (19 ng/L), and PFOS (15 ng/L). Compared to SF Bay municipal wastewater samples collected in 2009, the short chain perfluorinated carboxylates PFBA and PFHxA rose significantly in concentration. Effluent samples from two treatment plants contained much higher levels of PFASs: over two samplings, wastewater from one municipal plant contained an average of 420 ng/L PFOS and wastewater from an airport industrial treatment plant contained 560 ng/L PFOS, 390 ng/L 6:2 FtS, 570 ng/L PFPeA, and 500 ng/L PFHxA. The elevated levels observed in effluent samples from these two plants are likely related to aqueous film forming foam (AFFF) sources impacting their influent; PFASs attributable to both current use and discontinued AFFF formulations were observed. Indirectly measured PFAA precursor compounds accounted for 33%–63% of the total molar concentration of PFASs across all effluent samples and the PFAA precursors indicated by the oxidation assay were predominately short-chained. PFAS levels in SF Bay effluent samples reflect the manufacturing shifts towards shorter chained PFASs while also demonstrating significant impacts from localized usage of AFFF.
Sycamore Alluvial Woodland Pilot Study Implementation Guidelines. Prepared for Zone 7 Water Agency and US Environmental Protection Agency’s Water Quality Improvement Fund. In collaboration with San Francisco Estuary Institute.
. 2023. (13.23 MB)This document supports planting-based approaches for sycamore enhancement by providing site-level revegetation techniques for installing, maintaining and monitoring sycamore plantings.
Methods Matter: Methods for Sampling Microplastic and Other Anthropogenic Particles and Their Implications for Monitoring and Ecological Risk Assessment. Integrated Environmental Assessment and Management 16 (6) . SFEI Contribution No. 1014.
2020. To inform mitigation strategies and understand how microplastics affect wildlife, research is focused on understanding the sources, pathways, and occurrence of microplastics in the environment and in wildlife. Microplastics research entails counting and characterizing microplastics in nature, which is a labor‐intensive process, particularly given the range of particle sizes and morphologies present within this diverse class of contaminants. Thus, it is crucial to determine appropriate sampling methods that best capture the types and quantities of microplastics relevant to inform the questions and objectives at hand. It is also critical to follow protocols with strict quality assurance and quality control (QA/QC) measures so that results reflect accurate estimates of microplastic contamination. Here, we assess different sampling procedures and QA/QC strategies to inform best practices for future environmental monitoring and assessments of exposure. We compare microplastic abundance and characteristics in surface‐water samples collected using different methods (i.e., manta and bulk water) at the same sites, as well as duplicate samples for each method taken at the same site and approximate time. Samples were collected from 9 sampling sites within San Francisco Bay, California, USA, using 3 different sampling methods: 1) manta trawl (manta), 2) 1‐L grab (grab), and 3) 10‐L bulk water filtered in situ (pump). Bulk water sampling methods (both grab and pump) captured more microplastics within the smaller size range (<335 μm), most of which were fibers. Manta samples captured a greater diversity of morphologies but underestimated smaller‐sized particles. Inspection of pump samples revealed high numbers of particles from procedural contamination, stressing the need for robust QA/QC, including sampling and analyzing laboratory blanks, field blanks, and duplicates. Choosing the appropriate sampling method, combined with rigorous, standardized QA/QC practices, is essential for the future of microplastics research in marine and freshwater ecosystems.
Estuary News RMP Insert 2005. Estuary News.
2005. (419.37 KB)Contaminant Concentrations in Sport Fish from San Francisco Bay, 2006. SFEI Contribution No. 554. Oakland,CA.
2008. (15.89 MB)Aquatic Pesticide Monitoring Program Modeling Workgroup Final Report. SFEI Contribution No. 104.
2003. (950.69 KB)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. (298.16 KB)Pollutant Monitoring in the North Richmond Pump Station: A Pilot Study for Potential Dry Flow and Seasonal First Flush Diversion for Wastewater Treatment. San Francisco Estuary Institute: Richmond, CA.
2012. (1.4 MB)Estuary News RMP Insert 2007. Estuary News.
2007. (1.33 MB)LTMS Symposium on Methylmercury in Dredging Operations and Dredged Sediment Reuse in the San Francisco Estuary. San Francisco Estuary Institute: Oakland, Ca.
2010. Estuary News RMP Insert 2006. Estuary News.
2006. (1.71 MB)