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Project Report: 2004 Rapid Assessment Survey for Exotic Species in San Francisco Bay. SFEI Contribution No. 451. San Francisco Estuary Institute: Oakland, Ca.
2005. Project Report for the Southern California Exotics Expedition 2000: A Rapid Assessment Survey of Exotic Species in Sheltered Coastal Waters. Appendix C in:. . California Department of Fish and Game, Office of Oil Spill Prevention and Response, Sacramento CA.
2001. Project Report for the Southern California Exotics Expedition 2000 A Rapid Assessment Survey of Exotic Species in Sheltered Coastal Waters. SFEI Contribution No. 384. San Francisco Estuary Institute: Oakland.
2002. (284.28 KB)Project: Statistical Design, Analysis and Guidance on the Pajaro and Lower Peninsula Watershed Assessments. TASK 3: GRTS Survey Designs and Sample Draws Memorandum – Pajaro and Lower Peninsula Watersheds. SFEI Contribution No. 763.
2015. (641.94 KB)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)Protocol for Accessing and Sampling Archived Sediments from the San Francisco Estuary RMP for Trace Substances. SFEI Contribution No. 119. San Francisco Estuary Institute.
. 2000. (197.08 KB) 2001.
The Pulse of the Bay 2019: Pollutant Pathways. SFEI Contribution No. 954. San Francisco Estuary Institute: Richmond, CA.
. 2019. (21.42 MB)The Pulse of the Bay: The 25th Anniversary of the RMP. SFEI Contribution No. 841. San Francisco Estuary Institute: Richmond, CA.
. 2017. (15.72 MB)The Pulse of the Delta: Linking Science & Management through Regional Monitoring. Aquatic Science Center: Richmond, CA.
. 2012. (17.41 MB)The Pulse of the Delta: Monitoring and Managing Water Quality in the Sacramento - San Joaquin Delta. Aquatic Science Center: Oakland, CA.
. 2011. (13.18 MB)The Pulse of the Estuary: Tracking Contamination with the Regional Monitoring Program 1993-1998. SFEI Contribution No. 100. San Francisco Estuary Institute.
2000. (4.21 MB)Pyrethroid Insecticides: An Analysis of Use Patterns, Distributions, Potential Toxicity and Fate in the Sacramento-San Joaquin Delta and Central Valley. SFEI Contribution No. 415. San Francisco Estuary Institute.
2005. (2.99 MB)Pyrethroids, Pyrethrins, and Piperonyl Butoxide in Sediments by High Resolution Gas Chromatography/High Resolution Mass Spectrometry. Journal of Chromatography 7 . SFEI Contribution No. 439.
2006. (120.43 KB)QAPP for environmental monitoring and assessment program West Coast Pilot 2002 Intertidal Assessment: California Intensification. SFEI Contribution No. 234. San Francisco Estuary Institute: Oakland, CA.
2001. (489.07 KB)Quality Assurance in Environmental Analysis Applied to the San Francisco Estuary. SFEI Contribution No. 168. San Francisco Estuary Project: Oakland, CA.
1991. Quality Assurance Project Plan: Investigations of Sources and Effects of Pyrethroid Pesticides in Watersheds of the San Francisco Bay Estuary. San Francisco Estuary Institute: Oakland.
2007. (1.07 MB)Quantification of Hydroxylated Polybrominated Diphenyl Ethers (OH-BDEs), Triclosan, and Related Compounds in Freshwater and Coastal Systems. PLOS ONE . SFEI Contribution No. 765.
2015. Hydroxylated polybrominated diphenyl ethers (OH-BDEs) are a new class of contaminants of emerging concern, but the relative roles of natural and anthropogenic sources remain uncertain. Polybrominated diphenyl ethers (PBDEs) are used as brominated flame retardants, and they are a potential source of OH-BDEs via oxidative transformations. OH-BDEs are also natural products in marine systems. In this study, OH-BDEs were measured in water and sediment of freshwater and coastal systems along with the anthropogenic wastewater-marker compound triclosan and its photoproduct dioxin, 2,8-dichlorodibenzo-p-dioxin. The 6-OH-BDE 47 congener and its brominated dioxin (1,3,7-tribromodibenzo-p-dioxin) photoproduct were the only OH-BDE and brominated dioxin detected in surface sediments from San Francisco Bay, the anthropogenically impacted coastal site, where levels increased along a north-south gradient. Triclosan, 6-OH-BDE 47, 6-OH-BDE 90, 6-OH-BDE 99, and (only once) 6’-OH-BDE 100 were detected in two sediment cores from San Francisco Bay. The occurrence of 6-OH-BDE 47 and 1,3,7-tribromodibenzo-p-dioxin sediments in Point Reyes National Seashore, a marine system with limited anthropogenic impact, was generally lower than in San Francisco Bay surface sediments. OH-BDEs were not detected in freshwater lakes. The spatial and temporal trends of triclosan, 2,8-dichlorodibenzo-p-dioxin, OH-BDEs, and brominated dioxins observed in this study suggest that the dominant source of OH-BDEs in these systems is likely natural production, but their occurrence may be enhanced in San Francisco Bay by anthropogenic activities.
Quantitative Determination of Pyrethroids, Pyrethrins, and Piperonyl Butoxide in Surface Water by High Resolution Gas Chromatography/High Resolution Mass Spectrometry. Journal of Agricultural and Food Chemistry . SFEI Contribution No. 441.
2006. (49.15 KB) 2007.
Quaternary Ammonium Compounds: A Chemical Class of Emerging Concern. Environmental Science & Technology 57 (20).
2023. (3.53 MB)Quaternary ammonium compounds (QACs), a large class of chemicals that includes high production volume substances, have been used for decades as antimicrobials, preservatives, and antistatic agents and for other functions in cleaning, disinfecting, personal care products, and durable consumer goods. QAC use has accelerated in response to the COVID-19 pandemic and the banning of 19 antimicrobials from several personal care products by the US Food and Drug Administration in 2016. Studies conducted before and after the onset of the pandemic indicate increased human exposure to QACs. Environmental releases of these chemicals have also increased. Emerging information on adverse environmental and human health impacts of QACs is motivating a reconsideration of the risks and benefits across the life cycle of their production, use, and disposal. This work presents a critical review of the literature and scientific perspective developed by a multidisciplinary, multi-institutional team of authors from academia, governmental, and nonprofit organizations. The review evaluates currently available information on the ecological and human health profile of QACs and identifies multiple areas of potential concern. Adverse ecological effects include acute and chronic toxicity to susceptible aquatic organisms, with concentrations of some QACs approaching levels of concern. Suspected or known adverse health outcomes include dermal and respiratory effects, developmental and reproductive toxicity, disruption of metabolic function such as lipid homeostasis, and impairment of mitochondrial function. QACs’ role in antimicrobial resistance has also been demonstrated. In the US regulatory system, how a QAC is managed depends on how it is used, for example in pesticides or personal care products. This can result in the same QACs receiving different degrees of scrutiny depending on the use and the agency regulating it. Further, the US Environmental Protection Agency’s current method of grouping QACs based on structure, first proposed in 1988, is insufficient to address the wide range of QAC chemistries, potential toxicities, and exposure scenarios. Consequently, exposures to common mixtures of QACs and from multiple sources remain largely unassessed. Some restrictions on the use of QACs have been implemented in the US and elsewhere, primarily focused on personal care products. Assessing the risks posed by QACs is hampered by their vast structural diversity and a lack of quantitative data on exposure and toxicity for the majority of these compounds. This review identifies important data gaps and provides research and policy recommendations for preserving the utility of QAC chemistries while also seeking to limit adverse environmental and human health effects.
Rapid Assessment Channel Survey for Exotic Species in San Francisco Bay - November 2005. SFEI Contribution No. 454. San Francisco Estuary Institute: Oakland, CA. p 7.
2005. (132.82 KB)Rapid Assessment Shore Survey for Exotic Species in San Francisco Bay - May 2004. SFEI Contribution No. 453. San Francisco Estuary Institute: Oakland, CA. p 32.
2005. (686.62 KB)Rapid Assessment Survey for Exotic Organisms in Southern California Bays and Harbors, and Abundance in Port and Non-port Areas. Biological Invasions Volume 7, 995 - 1002 . SFEI Contribution No. 423.
2005. (228.57 KB)A Rapid Assessment Survey of Exotic Species in Sheltered Coastal Waters. SFEI Contribution No. 508.
2002. Rapid Assessment Survey of nonindigenous species in coastal Massachusetts. In: Abstracts, Second International Conf. on Marine Bioinvasions, April 9-11, 2001, New Orleans LA..
2001. A Rapid Assessment Survey of Nonindigenous Species in the Shallow Waters of Puget Sound. SFEI Contribution No. 223.
1998. (107.92 KB)Rapid Assessment Survey of the presence of marine invasive species along the coast of Massachusetts (abstract). New England Estuarine Research Society Abstracts, Spring Meeting, May 31-June 3, 2001.
2001. Recalculating the Tule Factor. A report for The Bay Institute of San Francisco: Sausalito, CA.
1988. Recommendations for a Bioaccumulation Monitoring and Human Health Risk Reduction Program for California. SFEI Contribution No. 545.
2008. (3.03 MB)Recommendations for a Modeling Framework to Answer Nutrient Management Questions in the Sacramento-San Joaquin Delta. Central Valley Regional Water Quality Control Board: Rancho Cordova, CA.
2016. (542.21 KB)Recommendations for Improvement of RMP Sediment Monitoring. San Francisco Estuary Institute: Richmond, CA.
1999. (104.89 KB)Recommended Best Practices for Collecting, Analyzing, and Reporting Microplastics in Environmental Media: Lessons Learned from Comprehensive Monitoring of San Francisco Bay. Journal of Hazardous Materials . SFEI Contribution No. 1023.
2020. Microplastics are ubiquitous and persistent contaminants in the ocean and a pervasive and preventable threat to the health of marine ecosystems. Microplastics come in a wide variety of shapes, sizes, and plastic types, each with unique physical and chemical properties and toxicological impacts. Understanding the magnitude of the microplastic problem and determining the highest priorities for mitigation require accurate measures of microplastic occurrence in the environment and identification of likely sources. The field of microplastic pollution is in its infancy, and there are not yet widely accepted standards for sample collection, laboratory analyses, quality assurance/quality control (QA/QC), or reporting of microplastics in environmental samples. Based on a comprehensive assessment of microplastics in San Francisco Bay water, sediment, fish, bivalves, stormwater, and wastewater effluent, we developed recommended best practices for collecting, analyzing, and reporting microplastics in environmental media. We recommend factors to consider in microplastic study design, particularly in regard to site selection and sampling methods. We also highlight the need for standard QA/QC practices such as collection of field and laboratory blanks, use of methods beyond microscopy to identify particle composition, and standardized reporting practices, including suggested vocabulary for particle classification.
Reconnecting Riverside with its River: Integrating Historical and Urban Ecology for a Healthier Future. SFEI Contribution No. 1133. San Francisco Estuary Institute: Richmond, Ca.
2023. (65.92 MB) (8.46 MB)Recovery strategies for the California clapper rail (Rallus longirostris obsoletus) in the heavily urbanized San Francisco estuarine ecosystem. Landscape and Urban Planning 38, 229-243 . SFEI Contribution No. 207.
1997. Re-design Process of the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP) Status & Trends Monitoring Component for Water and Sediment. SFEI Contribution No. 507. San Francisco Estuary Institute: Oakland, CA.
2005. (1.72 MB)Re-design Process of the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP). SFEI Contribution No. 109. San Francisco Estuary Institute: Oakland, CA.
2004. (1.72 MB)Reducing methylmercury accumulation in the food webs of San Francisco Bay and its local watersheds. Environmental Research 119, 3-26.
2012. (1.32 MB)Reducing Methylmercury Accumulation in the Food Webs of San Francisco Bay and Its Local Watersheds. SFEI Contribution No. 707. San Francisco Estuary Institute: Richmond, CA.
2014. (1.87 MB)Re-evaluation of the Floating Percentile Method for Deriving Dredged Sediment Screening Guidelines. SFEI Contribution No. 1143. San Francisco Estuary Institute: Richmond, California.
2023. (3.4 MB)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.
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. (12.17 MB)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. (2.85 MB)A Regional Mass Balance of Methylmercury in San Francisco Bay, California, USA. Environmental Toxicology and Chemistry . SFEI Contribution No. 619.
2010. (306.73 KB) (275.24 KB)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. (122.62 KB)The Regional Monitoring Program for Water Quality in San Francisco Bay, California, USA: Science in support of managing water quality. Regional Studies in Marine Science 4.
2016. The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is a novel partnership between regulatory agencies and the regulated community to provide the scientific foundation to manage water quality in the largest Pacific estuary in the Americas. The RMP monitors water quality, sediment quality and bioaccumulation of priority pollutants in fish, bivalves and birds. To improve monitoring measurements or the interpretation of data, the RMP also regularly funds special studies. The success of the RMP stems from collaborative governance, clear objectives, and long-term institutional and monetary commitments. Over the past 22 years, high quality data and special studies from the RMP have guided dozens of important decisions about Bay water quality management. Moreover, the governing structure and the collaborative nature of the RMP have created an environment that allowed it to stay relevant as new issues emerged. With diverse participation, a foundation in scientific principles and a continual commitment to adaptation, the RMP is a model water quality monitoring program. This paper describes the characteristics of the RMP that have allowed it to grow and adapt over two decades and some of the ways in which it has influenced water quality management decisions for this important ecosystem.
The Regional Monitoring Program: Science in Support of Managing Water Quality in San Francisco Bay. SFEI Contribution No. 435.
2006. (239.75 KB)Regional monitoring programs in the United States: Synthesis of four case studies from Pacific, Atlantic, and Gulf Coasts. Regional Studies in Marine Science 4.
2016. Water quality monitoring is a cornerstone of environmental protection and ambient monitoring provides managers with the critical data they need to take informed action. Unlike site-specific monitoring that is at the heart of regulatory permit compliance, regional monitoring can provide an integrated, holistic view of the environment, allowing managers to obtain a more complete picture of natural variability and cumulative impacts, and more effectively prioritize management actions. By reviewing four long-standing regional monitoring programs that cover portions of all three coasts in the United States–Chesapeake Bay, Tampa Bay, Southern California Bight, and San Francisco Bay–important insights can be gleaned about the benefits that regional monitoring provides to managers. These insights include the underlying reasons that make regional monitoring programs successful, the challenges to maintain relevance and viability in the face of ever-changing technology, competing demands and shifting management priorities. The lessons learned can help other managers achieve similar successes as they seek to establish and reinvigorate their own monitoring programs.
Regional Watershed Modeling and Trends Implementation Plan. SFEI Contribution No. 943. San Francisco Estuary Institute: Richmond, CA.
2019. (2.25 MB)Regional Watershed Spreadsheet Model (RWSM) Year 5 Progress Report. SFEI Contribution No. 788.
2016. (1.82 MB)Regional Watershed Spreadsheet Model (RWSM): Year 6 Progress Report. SFEI Contribution No. 811. San Francisco Estuary Institute: Richmond, CA.
2017. (1.79 MB) 2008.
The regulation of biological pollution: Preventing exotic species invasions from ballast water discharged into California coastal waters. Golden Gate University Law Review 30, 787-883 . SFEI Contribution No. 336.
2000. (395.66 KB)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. (22.59 MB)Relationship Between Sediment Toxicity and Contamination in San Francisco Bay (Abstract). Marine Environmental Research 285-309 . SFEI Contribution No. 332.
1999. 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. 2008.
Relationships Between Sediment Toxicity and Contamination in San Francisco Bay. Marine Environmental Research 48, 285-309 . SFEI Contribution No. 27.
1999. Relative effects of fluvial processes and historical land use on channel morphology in three sub-basins, Napa River basin, California, USA. IAHS, International Association of Hydrological Sciences 288.
2004. (117.55 KB)Relative sensitivities of toxicity test protocols with the amphipods Eohaustorius estuarius and Ampelisca abdita. Ecotoxicology and Environmental Safety 69 (1), 24-31.
2007. The release of pest species by marine aquaculture: lessons from a South African parasite introduced into California waters. Invasions in Aquatic Ecosystems: Impacts on Restoration and Potential for Control, Proceedings of a Workshop, April 25, 1998, 9-13.
2002. (89.75 KB)Remote Sensing Recommendations for Tidal Wetland Indicators. SFEI Contribution No. 1047. San Francisco Estuary Institute: Richmond. CA. p 31.
2021. (412.32 KB)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.
Removal efficiencies of a bioretention system for trace metals, PCBs, PAHs, and dioxins in a semiarid environment. Journal of Environmental Engineering.
2014. Re-Oaking North Bay. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.
2020. (20.51 MB) (1.83 MB)