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A Broad Scan of Bay Contaminants. San Francisco Estuary Institute: Richmond, CA.
2015. (1.34 MB)Brominated and Chlorinated Flame Retardants in San Francisco Bay Sediments and Wildlife. Environment International 47, 56-65.
2012. (565.23 KB)Building a regionally consistent base map for the Bay Area: The National Hydrography Data Set. Abstracts of the 5th Biannual State of the Estuary Conference – San Francisco Estuary: Achievements, trends and the future, pp 108.
2001. Building Capacity of the California Wetland Program Plan to Protect and Restore Vernal Pools. SFEI Contribution No. 1087. San Francisco Estuary Institute: Richmond. CA. p 30.
2022. (2.07 MB)This report describes the updates to the vernal pool habitat map, the development of the ambient baseline ecological condition survey of vernal pool systems within the Central Valley, and the development and results of the habitat development curve. A fictional project example shows how CRAM and the vernal pool complex CDFs and HDCs can help project proponents and the regulatory agencies think critically about project designs (using CRAM Attributes and Metrics as a standard measure), evaluate project conditions within a regional landscape context, and monitor project performance over time to ensure that project goals are met.
Funding for this report was provided through an agreement with the U.S. Environmental Protection Agency (USEPA). This report does not necessarily reflect the views and policies of USEPA nor does the mention of trade names or commercial products within this report constitute endorsement or recommendation for use.
Building Ecological Resilience in Highly Modified Landscapes.
2018. (4.93 MB)Ecological resilience is a powerful heuristic for ecosystem management in the context of rapid environmental change. Significant efforts are underway to improve the resilience of biodiversity and ecological function to extreme events and directional change across all types of landscapes, from intact natural systems to highly modified landscapes such as cities and agricultural regions. However, identifying management strategies likely to promote ecological resilience remains a challenge. In this article, we present seven core dimensions to guide long-term and large-scale resilience planning in highly modified landscapes, with the objective of providing a structure and shared vocabulary for recognizing opportunities and actions likely to increase resilience across the whole landscape. We illustrate application of our approach to landscape-scale ecosystem management through case studies from two highly modified California landscapes, Silicon Valley and the Sacramento–San Joaquin Delta. We propose that resilience-based management is best implemented at large spatial scales and through collaborative, cross-sector partnerships.
CALFED's Fish Mercury Project. SFEI Contribution No. 531. San Francisco Estuary Institute and CALFED.
. 2007. (21.81 MB)CALFED's FIsh Mercury Project FACT SHEET-- Monitoring and Reducing Methylmercury Exposure in the Bay Delta Watershed. SFEI Contribution No. 538. SFEI.
. 2007. Calibration and evaluation of five indicators of benthic community condition in two California bay and estuary habitats. Marine Pollution Bulletin 59 (1-3), 5-13.
2009. (332.88 KB)Calibration of the Multivariate AZTI Marine Biotic Index (M-AMBI) for Potential Inclusion into California Sediment Quality Objective Assessments in San Francisco Bay. SFEI Contribution No. 939. San Francisco Estuary Institute: Richmond, CA.
2019. (2.45 MB) (119.95 KB) (44.53 KB) (23.92 KB) 2004.
California Bay-Delta Authority Fish Mercury Project, Year 2 (2006) Annual Report. Sport Fish Sampling and Analysis. SFEI Contribution No. 535. San Francisco Estuary Institute.
2007. (14 MB)California Rapid Assessment Method (CRAM) Fact Sheet, Level 2, State version. SFEI Contribution No. 562. p 2 pages.
. 2008. (390.99 KB)California Rapid Assessment Method (CRAM) - Part 2. SFEI Contribution No. 285. San Francisco Estuary Institute.
2003. (2.79 MB)California Rapid Assessment Method for Wetlands v. 1.0. SFEI Contribution No. 246. San Francisco Estuary Institute. p 18.
2002. California Trash Monitoring Methods and Assessments Playbook. SFEI Contribution No. 1025. San Francisco Estuary Institute: Richmond, Calif.
2021. (299.99 MB)As municipalities and water-quality regulatory agencies have implemented programs and policies to improve management of the trash loading to storm drain conveyances, there has been increased interest in using a common set of methods to quantify the effectiveness of management actions. To create a foundation for developing a consistent, standardized approach to trash monitoring statewide, the project team performed a method comparison analysis, based on two seasons of fieldwork. This analysis facilitated the assessment of the accuracy, repeatability, and efficiency of some already developed trash monitoring methodologies already in use, as well as help to investigate a new, innovative method (cf. Fielding Testing Report on trashmonitoring.org). Methods developed by the Bay Area Stormwater Management Agencies Association (BASMAA) for use in the San Francisco Bay Area were compared to methods developed by the Southern California Stormwater Monitoring Coalition (SMC) for use in coastal southern California. One of the chief goals of these comparisons was to understand the similarities and differences between the already existing methods for detecting, quantifying, and characterizing trash in selected environments. Readers will find that the data bear out remarkable levels of accuracy and precision with quantitative metrics that help to align methods and management concerns. Furthermore, the degree of correlation among tested methods were especially high, offering greater opportunities for inter-method comparisons.
The findings of this project are intended for use by public agencies, non-profit organizations, private consultants, and all of their various partners in informing a statewide effort to adopt rigorous, standardized monitoring methods to support the State Water Board’s Trash Amendments. Over the next couple of decades, such public mandates will require all water bodies in California to achieve water quality objectives for trash.
California Wetland and Riparian Area Protection Policy. Technical Advisory Team. Technical Memorandum No. 1: Technical Advisory Team. SFEI Contribution No. 997. SFEI: Oakland, CA.
. 2009. (281.31 KB)California Wetland and Riparian Area Protection Policy. Technical Advisory Team. Technical Memorandum No. 3: Landscape Framework for Wetlands and Other Aquatic Areas. SFEI Contribution No. 999.
. 2012. (2.98 MB)California Wetland and Riparian Area Protection Policy. Technical Advisory Team. Technical Memorandum No. 2: Wetland Definition. SFEI Contribution No. 998.
. 2012. (1.35 MB)California Wetland and Riparian Area Protection Policy. Technical Advisory Team. Technical Memorandum No. 4: Wetland Identification and Delineation. SFEI Contribution No. 1000.
. 2012. (2.44 MB)California Wetland and Riparian Area Protection Policy. Technical Advisory Team. Technical Memorandum No. 5: Stream Definition (Final Draft). SFEI Contribution No. 1001.
. 2016. (816.97 KB)Carbamates, Diazinon, Imidacloprid and Piperonyl Butoxide in Sediments by Liquid Chromatography/Mass Spectrometry-Mass Spectrometry. Analytical Chemistry . SFEI Contribution No. 443.
2006. Carbamates, Diazinon, Imidacloprid and Piperonyl Butoxide in Surface Water by Liquid Chromatography/Mass Spectrometry-Mass Spectrometry. J. of Agricultural and Food Chemistry . SFEI Contribution No. 442.
2006. Carbon-isotope, diatom, and pollen evidence of late Holocene salinity changes in a brackish marsh in the San Francisco Estuary. Quaternary Research 55, 66-76 . SFEI Contribution No. 467.
2003. Cardiac toxicity of 5-ring polycyclic aromatic hydrocarbons is differentially dependent on the aryl hydrocarbon receptor 2 isofrom during zebrafish development. Toxicology and Applied Pharmacology 257, 242-249.
2011. (1.33 MB)Cartographic analysis of historical and modern baylands boundaries for Marin County, California. SFEI Contribution No. 229. Marin County Community Develpment Agency. p 88 pp.
1998. "Case studies" on exotic species transported with oyster and marine baitworm shipments. In Toolkit on Best Practices for Prevention and Management. Toolkit on Best Practices for Prevention and Management. UN Global Invasive Species Programme.
2000. Case Study 2.5: Petition for U.S. federal action on the green seaweed Caulerpa taxifolia. . United Nations Global Invasive Species Program. CAB International, Wallingford, Oxon, UK. p 31.
2001. Case Study 3.16: Transfer of pathogens and other species via oyster culture. . United Nations Global Invasive Species Program. CAB International: Wallingford, Oxon, UK. p p 92.
2001. Case study: hitchhikers in or on marine baitworms and their packing material. In Toolkit for Managing Invasive Species. Toolkit for Managing Invasive Species. United Nations Global Invasive Species Program.
2001. Case study: transfer of pathogens and other species via oyster culture. In Toolkit for Managing Invasive Species. Toolkit for Managing Invasive Species. United Nations Global Invasive Species Program.
2001. Castro Valley Atmospheric Deposition Study. SFEI Contribution No. 430. Brake Pad Partnership.
2005. (2.61 MB)Causes of Sediment Toxicity to Mytilus galloprovincialis in San Francisco Bay, California. Archive of Environmental Contamination Toxicology 45, 486-491 . SFEI Contribution No. 296.
2003. CECs in California’s Ambient Aquatic Ecosystems: Occurrence and Risk Screening of Key Classes. . ASC Contribution. SFEI Contribution No. 1066. Aquatic Science Center: Richmond, CA.
2022. (1.01 MB) (441.1 KB)Cesar Chavez Streetscape Improvement Project (Case Study Site and Technical Reports). SFEI Contribution No. 797.
2015. (651.3 KB) (1.59 MB)Changing Channels: Regional Information for Developing Multi-benefit Flood Control Channels at the Bay Interface. Flood Control 2.0. SFEI Contribution No. 801. San Francisco Estuary Institute: Richmond, CA.
2017. (62.69 MB) (23.02 MB)Over the past 200 years, many of the channels that drain to San Francisco Bay have been modified for land reclamation and flood management. The local agencies that oversee these channels are seeking new management approaches that provide multiple benefits and promote landscape resilience. This includes channel redesign to improve natural sediment transport to downstream bayland habitats and beneficial re-use of dredged sediment for building and sustaining baylands as sea level continues to rise under a changing climate. Flood Control 2.0 is a regional project that was created to help develop innovative approaches for integrating habitat improvement and resilience into flood risk management at the Bay interface. Through a series of technical, economic, and regulatory analyses, the project addresses some of the major elements associated with multi-benefit channel design and management at the Bay interface and provides critical information that can be used by the management and restoration communities to develop long-term solutions that benefit people and wildlife.
This Flood Control 2.0 report provides a regional analysis of morphologic change and sediment dynamics in flood control channels at the Bay interface, and multi-benefit management concepts aimed at bringing habitat restoration into flood risk management. The findings presented here are built on a synthesis of historical and contemporary data that included input from Flood Control 2.0 project scientists, project partners, and science advisors. The results and recommendations, summarized below, will help operationalize many of the recommendations put forth in the Baylands Ecosystem Habitat Goals Science Update (Goals Project 2015) and support better alignment of management and restoration communities on multi-benefit bayland management approaches.
Channel Geomorphology Assessment: A component of the watershed management plan for the Carneros Creek watershed, Napa County, California. SFEI Contribution No. 67. San Francisco Estuary Institute: Oakland, CA.
2003. (4.87 MB)Channel Geomorphology Assessment: A component of the watershed management plan for the Sulphur Creek watershed, Napa County, California. SFEI Contribution No. 68. San Francisco Estuary Institute: Oakland, CA.
2003. (4.64 MB)Characterization of brominated, chlorinated, and phosphate flame retardants in San Francisco Bay, an urban estuary. Science of the Total Environment 652, 212-223 . SFEI Contribution No. 859.
2019. Flame retardant chemical additives are incorporated into consumer goods to meet flammability standards, and many have been detected in environmental matrices. A uniquely wide-ranging characterization of flame retardants was conducted, including polybrominated diphenyl ethers (PBDEs) and 52 additional brominated, chlorinated, or phosphate analytes, in water, sediment, bivalves, and harbor seal blubber of San Francisco Bay, a highly urbanized estuary once considered a hot spot for PBDE contamination. Among brominated flame retardants, PBDEs remained the dominant contaminants in all matrices, though declines have been observed over the last decade following their phase-out. Hexabromocyclododecane (HBCD) and other hydrophobic, brominated flame retardants were commonly detected at lower levels than PBDEs in sediment and tissue matrices. Dechlorane Plus (DP) and related chlorinated compounds were also detected at lower levels or not at all across all matrices. In contrast, phosphate flame retardants were widely detected in Bay water samples, with highest median concentrations in the order TCPP > TPhP > TBEP > TDCPP > TCEP. Concentrations in Bay water were often higher than in other estuarine and marine environments. Phosphate flame retardants were also widely detected in sediment, in the order TEHP > TCrP > TPhP > TDCPP > TBEP. Several were present in bivalves, with levels of TDCPP comparable to PBDEs. Only four phosphate flame retardants were detected in harbor seal blubber: TCPP, TDCPP, TCEP, and TPhP. Periodic, multi-matrix screening is recommended to track contaminant trends impacted by changes to flammability standards and manufacturing practices, with a particular focus on contaminants like TDCPP and TPhP that were found at levels comparable to thresholds for aquatic toxicity.
Characterization of Sediment Contamination in Central Bay Margin Areas. SFEI Contribution No. 829. San Francisco Estuary Institute: Richmond, CA.
2017. (2.89 MB)Characterization of Sediment Contamination in South Bay Margin Areas. SFEI Contribution No. 962. San Francisco Estuary Institute: Richmond, CA.
2019. (6.05 MB)The Bay margins (i.e., mudflats and adjacent shallow areas of the Bay) are important habitats where there is high potential for wildlife to be exposed to contaminants. However, until recently, these areas had not been routinely sampled by the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) due to logistical considerations. In 2015, the RMP conducted a spatially-distributed characterization of surface sediment contamination and ancillary characteristics within the RMP-defined Central San Francisco Bay margin areas. This was repeated in 2017 within South Bay, which for this report refers to the area collectively encompassing Upper South Bay (usually just called the “South Bay” segment in the Bay RMP, “Upper” added here to distinguish from the combined area), Lower South Bay, and “Extreme” Lower South Bay (previously named “Southern Sloughs”) margin areas.
Ambient margins data in South Bay provide a context against which the severity of contamination at specific sites can be compared. The baseline data could also be useful in setting targets and tracking improvements in watershed loads and their nearfield receiving waters, or for appropriate assessment of re-use or disposal of dredged sediment. These spatially distributed data also provide improved estimates of mean concentrations and contaminant inventories in margins. Based on data from this study, contamination in the margin areas accounts for 35% of PCB mass in the upper 15 cm of surface sediments in South Bay, which is approximately proportional to the relative area of the margin (34% of the region). In contrast, margins only contain 30% of the mercury mass in South Bay, somewhat less than their proportional area.
Characterization Studies of a Thyroid Endocrine-disrupted Condition in Wild Fishes of San Francisco Bay. SFEI Contribution No. 644. SFEI: Oakland. p 64.
2010. (431.23 KB) (431.23 KB) (1.37 MB)Characterizing and quantifying nutrient sources, sinks and transformations in the Delta: synthesis, modeling, and recommendations for monitoring. SFEI Contribution No. 785. San Francisco Estuary Institute: Richmond, CA.
2015. (2.39 MB) (101.95 KB) (2.58 MB) (1.52 MB) (115.37 KB) (8.97 MB) (36.31 MB)Characterizing vectors of marine invasions. In Marine Bioinvasions: Ecology, Conservation and Management Perspectives. . Marine Bioinvasions: Ecology, Conservation and Management Perspectives. Springer: Heidelberg, Germany.
2006. Charter: Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI Contribution No. 1184. San Francisco Estuary Institute: Richmond, CA.
2022. (890.58 KB)This Charter describes the purpose and function of the Regional Monitoring Program for Water
Quality in San Francisco Bay (RMP). Established in 1993, the RMP is a collaborative effort
between the San Francisco Estuary Institute, the California Regional Water Quality Control
Board, San Francisco Bay Region, and the regulated discharger community.
Charter: Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI Contribution No. 750. San Francisco Estuary Institute: Richmond, Calif.
2015. (554.31 KB)The overarching goal of the RMP is to collect data and communicate information about water quality in San Francisco Bay in support of management decisions. The RMP was created in 1993 through Regional Board Resolution No. 92-043 that directed the Executive Officer to implement a Regional Monitoring Plan in collaboration with permitted dischargers pursuant to California Water Code, Sections 13267, 13383, 13268, and 13385. The goal was to replace individual receiving water monitoring requirements for dischargers with a comprehensive Regional Monitoring Program.
The Program is guided by a Memorandum of Understanding (MOU) between the Regional Board and SFEI, first approved in 1996 and amended at various times since (see Appendix C of this Charter). Section VIII of the MOU states the roles and responsibilities of the Regional Board and SFEI in the implementation of the Program. Participating dischargers pay fees to the Program to comply with discharge permit requirements. The cost allocation schedule for Participants is described in Appendix B. The RMP provides an open forum for a wide range of Participant Groups and other Interested Parties to discuss contaminant issues, prioritize science needs, and monitor potential impacts of discharges on the Bay.
In support of the overarching goal described above, the following guiding principles define the intentions and expectations of RMP Participants. Implementation of the RMP will:
- Develop sound scientific information on water quality in the Bay;
- Prioritize funding decisions through collaborative discussions;
- Conduct decision-making in a transparent manner that consistently represents the diversity of RMP Participant interests;
- Utilize external science advisors for guidance and peer review;
- Maintain and make publicly available the data collected by the Program;
- Enhance public awareness and support by regularly communicating the status and trends of water quality in the Bay; and
- Coordinate with other monitoring and scientific studies in the Bay-Delta region to ensure efficiency.
Charter: Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI Contribution No. 844. San Francisco Estuary Institute : Richmond, CA.
2017. (1.68 MB)Chemistry and Fate of Triazolopyrimidine Sulfonamide Herbicides. Reviews of Environmental Contamination & Toxicology.
2007. 1991.
Chinook Salmon Habitat Quantification Tool: User Guide (Version 1.0). Prepared for American Rivers. Funded by the Natural Resources Conservation Service Conservation Innovation Grant (#69-3A75-17-40), Water Foundation and Environmental Defense Fund. A report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 953. San Francisco Estuary Institute: Richmond, CA.
2019. (5.78 MB) (31.36 MB)The Salmon Habitat Quantification Tool provides systematic, transparent, and consistent accounting of the spatial extent, temporal variability, and quality of salmon habitat on the landscape. It is part of the multi-species assessment of the Central Valley Habitat Exchange (CVHE, www.cvhe.org). The suitability criteria applied in the tool were established by Stillwater Sciences and the Technical Advisory Committee (TAC), and the Chinook salmon HQT habitat evaluation and User Guide development was led by American Rivers and the San Francisco Estuary Institute. The approach uses commonly-applied concepts for evaluating suitable habitat based on modeling, with methods adapted from the hydrospatial analysis approach developed by Alison Whipple (2018).
Chlorinated Hydrocarbons in the San Francisco Estuary and its Watershed. In Draft Chapter in Spies, R.B. (ed.). Contaminants and Toxicity in the Sacramento-San Joaquin Delta, Its Cathchment, and the San Francisco Estuary - A CALFED White Paper. Applied Marine Sciences, Livermore, CA.. Draft Chapter in Spies, R.B. (ed.). Contaminants and Toxicity in the Sacramento-San Joaquin Delta, Its Cathchment, and the San Francisco Estuary - A CALFED White Paper. Applied Marine Sciences, Livermore, CA.
2000. Chromium in San Francisco Bay: inorganic speciation, distribution, and geochemical processes, University of California: Santa Cruz.
1994. Chromium speciation in San Francisco Bay: Superposition of geochemical processes causes complex spatial distribution of inorganic species. Marine Chemistry 49, 189-200 . SFEI Contribution No. 183.
1995. CISNet San Pablo Bay Network of Environmental Stress Indicators; Benthic Microfauna. SFEI Contribution No. 299. San Francisco Estuary Institute: Oakland, CA.
2003. Cisnet Technical Report: Contaminant Accumulation In Eggs of Double-Crested Cormorants and Song Sparrows In San Pablo Bay. SFEI Contribution No. 412. San Francisco Estuary Institute.
2004. (633.82 KB)Cisnet Technical Report: Contaminant Accumulation in Forage Fish. SFEI Contribution No. 413. San Francisco Estuary Institute.
2004. (639.71 KB)Closing in on unidentified contaminants. pp p. 18-19 . SFEI Contribution No. 274.
2000. The Cloudwater Chemistry of Iron and Copper at Great Dun Fell, U.K. Atmospheric Environment 31 (16), 2515-2526.
1997. (1.35 MB) 2009.
CMARP Phase III Technical Support: Highlighting Monitoring Activities and Recommendations for Addressing Shortfalls and Improving Monitoring Coordination in the Delta-Suisun Bay Planning Area. SFEI Contribution No. 565. Department of Fish and Game, Central Valley Bay-Delta Branch, Ecosystem Restoration Program.
. 2008. The colonial ascidian Didemnum sp. A: Current distribution, basic biology, and potential threat to marine communities of the northeast and west coasts of North America. Journal of Experimental Marine Biology and Ecology 99-108.
2007. (472.34 KB)Comparable levels of trace metal contamination in two semi-enclosed embayments: San Diego Bay and South San Francisco Bay. Environmental Science and Technology 27, 1934-1936 . SFEI Contribution No. 173.
1993. 2013.
Comparison of Methods to Map California Riparian Areas. . SFEI Contribution No. 522.
2006. (13.1 MB)Comparison of sediment supply to San Francisco Bay from watersheds draining the Bay Area and the Central Valley of California. Marine Geology Special Issue: A multi-discipline approach for understanding sediment transport and geomorphic evolution in an estuarine-coastal system.
2013. Competitive equilibration techniques for determining transition metal speciation in natural waters: Evaluation using model data. Analytica Chimica Acta 343, 161-181 . SFEI Contribution No. 211.
1997. The concentration and load of PCBs, OC pesticides, and mercury associated with suspended sediments in the lower Guadalupe River, San Jose, California. A Technical Report of the Regional Watershed Program. SFEI Contribution No. 86. San Francisco Estuary Institute: Oakland, CA.
2004. (1.66 MB)Concentrations and loads of mercury, PCBs, and OC pesticides in the lower Guadalupe River, San Jose,California: Water Years 2003 and 2004. SFEI Contribution No. 409. San Francisco Estuary Institute. p 80.
2005. (1.61 MB)Concentrations and Loads of Mercury, PCBs and PBDEs in the Lower Guadalupe River, San Jose, California: Water Years 2003, 2004, and 2005. SFEI Contribution No. 424. San Francisco Estuary Institute: Oakland.
2006. (11.98 MB)Concentrations and Loads of Mercury Species in the Guadalupe River, San Jose, California: Water Year 2010. San Francisco Estuary Institute: Oakland.
2010. (3.34 MB)Concentrations and loads of PCBs, dioxins, PAHs, PBDEs, OC pesticides and pyrethroids during storm and low flow conditions in a small urban semi-arid watershed. Science of the Total Environment 526, 251-261 . SFEI Contribution No. 650.
2015. Urban runoff has been identified in water quality policy documents for San Francisco Bay as a large and potentially controllable source of pollutants. In response, concentrations of suspended sediments and a range of trace organic pollutants were intensively measured in dry weather and storm flow runoff from a 100% urban watershed. Flow in this highly urban watershed responded very quickly to rainfall and varied widely resulting in rapid changes of turbidity, suspended sediments and pollutant concentrations. Concentrations of each organic pollutant class were within similar ranges reported in other studies of urban runoff, however comparison was limited for several of the pollutants given information scarcity. Consistently among PCBs, PBDEs, and PAHs, the more hydrophobic congeners were transported in larger proportions during storm flows relative to low flows. Loads for Water Years 2007-2010 were estimated using regression with turbidity during the monitored months and a flow weighted mean concentration for unmonitored dry season months. More than 91% of the loads for every pollutant measured were transported during storm events, along with 87% of the total discharge. While this dataset fills an important local data gap for highly urban watersheds of San Francisco Bay, the methods, the uniqueness of the analyte list, and the resulting interpretations have applicability for managing pollutant loads in urban watersheds in other parts of the world.
Concentrations and Loads of Trace Contaminants in a Small Urban Tributary, San Francisco Bay, California. SFEI Contribution No. 650. SFEI: Richmond, CA. p 40.
2012. (1.25 MB)