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2020
Richey, A.; Dusterhoff, S. D.; Baumgarten, S. A.; Clark, E.; Benjamin, M.; Shaw, S.; Askevold, R. A.; McKnight, K. 2020. Restoration Vision for the Laguna de Santa Rosa. SFEI Contribution No. 983. SFEI: Richmond, CA.

 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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Davis, J.; Foley, M.; Askevold, R.; Buzby, N.; Chelsky, A.; Dusterhoff, S.; Gilbreath, A.; Lin, D.; Miller, E.; Senn, D.; et al. 2020. RMP Update 2020. SFEI Contribution No. 1008.

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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Brander, S. M.; Renick, V. C.; Foley, M. M.; Steele, C.; Woo, M.; Lusher, A.; Carr, S.; Helm, P.; Box, C.; Cherniak, S.; et al. 2020. Sampling and Quality Assurance and Quality Control: A Guide for Scientists Investigating the Occurrence of Microplastics Across Matrices. Applied Spectroscopy 74 (9) . SFEI Contribution No. 1012.

Plastic pollution is a defining environmental contaminant and is considered to be one of the greatest environmental threats of the Anthropocene, with its presence documented across aquatic and terrestrial ecosystems. The majority of this plastic debris falls into the micro (1 lm–5 mm) or nano (1–1000 nm) size range and comes from primary and secondary sources. Its small size makes it cumbersome to isolate and analyze reproducibly, and its ubiquitous distribution creates numerous challenges when controlling for background contamination across matrices (e.g., sediment, tissue, water, air). Although research on microplastics represents a relatively nascent subfield, burgeoning interest in questions surrounding the fate and effects of these debris items creates a pressing need for harmonized sampling protocols and quality control approaches. For results across laboratories to be reproducible and comparable, it is imperative that guidelines based on vetted protocols be readily available to research groups, many of which are either new to plastics research or, as with any new subfield, have arrived at current approaches through a process of trial-and-error rather than in consultation with the greater scientific community. The goals of this manuscript are to (i) outline the steps necessary to conduct general as
well as matrix-specific quality assurance and quality control based on sample type and associated constraints, (ii) briefly review current findings across matrices, and (iii) provide guidance for the design of sampling regimes. Specific attention is paid to the source of microplastic pollution as well as the pathway by which contamination occurs, with details provided regarding each step in the process from generating appropriate questions to sampling design and collection.

Lowe, S. 2020. Santa Clara County Five Watersheds Assessment: A Synthesis of Ecological Data Collection and Analysis Conducted by Valley Water. Pearce, S., Salomon, M., Collins, J., Titus, D., Eds.. SFEI Contribution No. 963. San Francisco Estuary Institute: Richmond. CA. p 71.

This report synthesizes the baseline assessments for Santa Clara County’s five watersheds to present similarities, differences, and compare ecological condition in streams across watersheds and their subregions, San Francisco Bay-Delta ecoregion, and statewide based on CRAM. It also interprets the assessment results and comparisons to identify risks to stream conditions, and opportunities for stream stewardship. Project D5’s baseline assessments establish a monitoring and assessment framework for evaluating the performance of Valley Water’s programs, projects, maintenance activities, and on-the-ground stewardship actions.

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Mckee, L.; Lowe, J.; Dusterhoff, S.; Foley, M.; Shaw, S. 2020. Sediment Monitoring and Modeling Strategy. Sediment Monitoring and Modeling Strategy. SFEI Contribution No. 1016. San Francisco Estuary Institute: Richmond, CA.
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McKnight, K.; Lowe, J.; Plane, E. 2020. Special Study on Bulk Density. SFEI Contribution No. 975. San Francisco Estuary Institute: Richmond, CA. p 43.

Sediment bulk density is the total mass of mineral and organic sediment within a defined volume. It is a key variable in many research questions pertaining to Bay sediment studies but one that is often poorly quantified and can be misinterpreted. The motivation for this report comes from a recommendation by Schoellhamer et al. (2018) to compile more accurate estimates of bulk density of Bay sediments to convert between volume and mass with a higher level of certainty. Through funding and guidance from the Bay Regional Monitoring Program Sediment Work Group, this report is a first step towards compiling the available data on sediment bulk densities across Bay habitats and along salinity gradients to provide better information for resource managers and others working on sediment-related issues. This report discusses the need to know the bulk density of Bay soils to convert between sediment mass and soil volume; clarifies general definitions and common points of confusion related to sediment bulk density; compiles primary sources of bulk density measurements, secondary sources of bulk density estimates, and standard engineering estimates of bulk density for different habitats in San Francisco Bay; and, provides a database where practitioners can track, analyze, and share bulk density measurements.
 

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Grossinger, R. M.; Wheeler, M.; Spotswood, E.; Ndayishimiye, E.; Carbone, G.; Galt, R. 2020. Sports and urban biodiversity. . SFEI Contribution No. 1028.

SFEI collaborated with the International Union for the Conservation of Nature (IUCN) and the International Olympic Committee (IOC) to create a guide to incorporating nature into urban sports, from the development of Olympic cities to the design and management of the many sport fields throughout the urban landscape. We applied the Urban Biodiversity Framework developed in Making Nature’s City to the world of sports, with case studies drawn from international sport federations, Olympic cities, and individual sport teams and venues around the world. The guide is part of IUCN’s ongoing collaboration with IOC to develop best practices around biodiversity for the sporting industry.

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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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Livsey, D. N.; Downing-Kunz, M. A.; Schoellhamer, D. H.; Manning, A. J. 2020. Suspended Sediment Flux in the San Francisco Estuary: Part I—Changes in the Vertical Distribution of Suspended Sediment and Bias in Estuarine Sediment Flux Measurements. Estuaries and Coasts . SFEI Contribution No. 990.

In this study, we investigate how changes in the vertical distribution of suspended sediment affect continuous suspended sediment flux measurements at a location in the San Francisco Estuary. Current methods for measuring continuous suspended sediment flux estimates relate continuous estimates of suspended-sediment concentration (SSC) measured at-a-point (SSCpt) to discrete cross-section measurements of depth-averaged, velocity-weighted SSC (SSCxs). Regressions that compute SSCxs from continuous estimates of SSCpt require that the slope between SSCpt and SSCxs, controlled by the vertical distribution of SSC, is fixed. However, in tidal systems with suspended cohesive sediment, factors that control the vertical SSC profile—vertical turbulent mixing and downward settling of suspended sediment mediated by flocculation of cohesive sediment—constantly vary through each tide and may exhibit systematic differences between flood and ebb tides (tidal asymmetries in water velocity or particle size). We account for changes in the vertical SSC profile on estimates of SSCxs using time series of the Rouse number of the Rouse-Vanoni-Ippen equation combined with optical turbidity measurements, a surrogate for SSCpt, to predict SSCxs from 2009 to 2011 and 2013. Time series of the Rouse number were estimated by fitting the Rouse-Vanoni-Ippen equation to SSC estimated from optical-turbidity measurements taken at two elevations in the water column. When accounting for changes in the vertical SSC profile, changes in not only the magnitude but also the direction of cumulative sediment-flux measurements were observed. For example, at a mid-depth sensor, sediment flux estimates changed from − 319 kt (± 65 kt, negative indicating net seaward transport) to 482 kt (± 140 kt, positive indicating net landward transport) for 2009–2011 and from − 388 kt (± 140 kt) to 1869 kt (± 406 kt) for 2013–2016. At the study location, estimation of SSCxs solely from SSCpt resulted in sediment flux values that were underestimates on flood tides and overestimates on ebb tides. This asymmetry is driven by covariance between water velocity and particle settling velocity (Ws) with larger Ws on flood compared to ebb tides. Results of this study indicate that suspended-sediment-flux measurements estimated from point estimates of SSC may be biased if systematic changes in the vertical distribution of SSC are unaccounted for.

Rochman, C. M.; Munno, K.; Box, C.; Cummins, A.; Zhu, X.; Sutton, R. 2020. Think Global, Act Local: Local Knowledge Is Critical to Inform Positive Change When It Comes to Microplastics. Environmental Science & Technology . SFEI Contribution No. 1024.

Microplastic contamination in the marine environment is a global issue. Across the world, policies at the national and international level are needed to facilitate the scale of change needed to tackle this significant problem. However, sources and patterns of plastic contamination vary around the world, and the most pressing actions differ from one location to another. Therefore, local policies are a critical part of the solution; recognizing local sources will enable mitigations with measurable impacts. Here, we highlight how investigating the contamination comprehensively in one location can inform relevant mitigation strategies that can be transferred globally. We examine the San Francisco Bay in California, USA—the largest estuary on the West Coast of the Americas, and home to over 7 million people. The local contamination of microplastics in surface water, sediments, and fish from this urban bay is reportedly higher than many places studied to date.(1) This example demonstrates the value of local monitoring in identifying sources, informing local mitigation strategies and developing an array of solutions to stem the multifaceted tide of plastic pollution entering our global oceans.

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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2019
Yee, D. 2019. 2018 RMP Sediment Data Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.

In 2018, sediment samples were collected from 27 stations (7 historical sites, with the rest from the GRTS random draw panels) for the Regional Monitoring Program for Water Quality in San Francisco Bay. The details of the cruise and sample collection methods are described in the RMP Quality Assurance Program Plan, cruise plans, cruise reports, and field sampling reports. These documents are available from the SFEI website (http://www.sfei.org/content/status-and-trends-monitoring-documents).

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Yee, D. 2019. 2018 RMP Tissue Data Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.

In 2018, bivalve tissue samples were collected from six Bay/Delta stations and a reference site for the Regional Monitoring Program for Water Quality in San Francisco Bay. Bird egg tissue samples were collected from two sites for cormorants, and four sites for terns. General descriptions of the sample collection methods are provided in the RMP Quality Assurance Program Plan, cruise plans, cruise reports, and sampling reports. These documents are available from the SFEI website (http://www.sfei.org/content/status-and-trends-monitoring-documents)

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Foley, M. 2019. 2019 Bay RMP Multi-Year Plan. SFEI Contribution No. 940. San Francisco Estuary Institute: Richmond, CA.
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Sigala, M. 2019. 2019 RMP Contaminant Concentrations in San Francisco Bay Sportfish Cruise Report. SFEI Contribution No. 968. Marine Pollution Studies Laboratory, Moss Landing Marine Laboratories: Moss Landing, CA.

This report contains information on the spring and summer field sampling efforts conducted by the Marine Pollution Studies Laboratory at Moss Landing Marine Labs (MPSL-MLML). The purpose of this field effort was to collect sportfish for an eighth season of data (in support of 1994, 1997, 2000, 2003, 2006, 2009, and 2014 surveys) in the ongoing study of Contamination in San Francisco Bay Sportfish. The work was contracted through the San Francisco Estuary Institute (SFEI) for the Regional Monitoring Program (RMP) for Water Quality. 

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Salop, P.; Herrmann, C. 2019. 2019 RMP Water Cruise Report. SFEI Contribution No. 967. Applied Marine Sciences: Livermore, CA.

This report details activities associated with the annual Regional Monitoring Program for Water Quality in the San Francisco Estuary (RMP) water cruise. The RMP water sampling program was redesigned in 2002 to adopt a randomized sampling design at thirty-one sites in place of the twenty-six “spine of the Estuary” stations sampled previously. In 2007, the number of sites was decreased to twenty-two stations and it remains as such for 2019.

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Foley, M. 2019. 2020 RMP Multi-Year Plan. SFEI Contribution No. 959. San Francisco Estuary Institute: Richmond, CA.
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Sutton, R.; Chen, D.; Sun, J.; Greig, D. J.; Wu, Y. 2019. 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.

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.

Yee, D.; Wong, A.; Buzby, N. 2019. Characterization of Sediment Contamination in South Bay Margin Areas. SFEI Contribution No. 962. San Francisco Estuary Institute: Richmond, CA.

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.

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Whipple, A.; Grantham, T.; Desanker, G.; Hunt, L.; Merrill, A.; Hackenjos, B.; Askevold, R. A. 2019. 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.

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).

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Yee, D.; Gilbreath, A. N.; McKee, L. J. .; Davis, J. A. 2019. Conceptual Model to Support PCB Management and Monitoring in the San Leandro Bay Priority Margin Unit - Final Report. SFEI Contribution No. 928. San Francisco Estuary Institute: Richmond, CA.

The goal of RMP PCB special studies over the next few years is to inform the review and possible revision of the PCB TMDL and the reissuance of the Municipal Regional Permit for Stormwater, both of which are tentatively scheduled to occur in 2020. Conceptual model development for a set of four representative priority margin units will provide a foundation for establishing an effective and efficient monitoring plan to track responses to load reductions, and will also help guide planning of management actions. The Emeryville Crescent was the first PMU to be studied in 2015-2016. The San Leandro Bay PMU is second (2016-2018), Steinberger Slough in San Carlos is third (2018), and Richmond Harbor will be fourth (2018-2019).

This document is Phase Three of a report on the conceptual model for San Leandro Bay. A Phase One report (Yee et al. 2017) presented analyses of watershed loading, initial retention, and long-term fate, including results of sediment sampling in 2016. A Phase Two data report (Davis et al. 2017) documented the methods, quality assurance, and all of the results of the 2016 field study. This Phase Three report is the final report that incorporates all of the results of the 2016 field study, and includes additional discussion of the potential influence of contaminated sites in the
watershed, the results of passive sampling by Stanford researchers and a comparative analysis of long-term fate in San Leandro Bay and the Emeryville Crescent, a section on bioaccumulation, and a concluding section with answers to the management questions that were the impetus for the work.

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Yee, D.; Wong, A. 2019. Evaluation of PCB Concentrations, Masses, and Movement from Dredged Areas in San Francisco Bay. SFEI Contribution No. 938. San Francisco Estuary Institute: Richmond, CA.
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Spotswood, E.; Grossinger, R.; Hagerty, S.; Bazo, M.; Benjamin, M.; Beller, E.; Grenier, L.; Askevold, R. A. 2019. Making Nature's City. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.

Cities will face many challenges over the coming decades, from adapting to a changing climate to accommodating rapid population growth. A related suite of challenges threatens global biodiversity, resulting in many species facing extinction. While urban planners and conservationists have long treated these issues as distinct, there is growing evidence that cities not only harbor a significant fraction of the world’s biodiversity, but also that they can also be made more livable and resilient for people, plants, and animals through nature-friendly urban design. 

Urban ecological science can provide a powerful tool to guide cities towards more biodiversity-friendly design. However, current research remains scattered across thousands of journal articles and is largely inaccessible to practitioners. Our report Making Nature’s City addresses these issues, synthesizing global research to develop a science-based approach for supporting nature in cities. 

Using the framework outlined in the report, urban designers and local residents can work together to connect, improve, and expand upon city greenspaces to better support biodiversity while making cities better places to live. As we envision healthier and more resilient cities, Making Nature’s City provides practical guidance for the many actors who together will shape the nature of cities.

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Sedlak, M.; Sutton, R.; Miller, L.; Lin, D. 2019. Microplastic Strategy Update. SFEI Contribution No. 951. San Francisco Estuary Institute: Richmond, CA.

Based on the detection of microplastics in San Francisco Bay surface water and Bay Area wastewater effluent in 2015, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) convened a Microplastic Workgroup (MPWG) in 2016 to discuss the issue, identify management information needs and management questions (MQs), and prioritize studies to provide information to answer these management questions. The MPWG meets annually to review on-going microplastic projects and to conduct strategic long-term planning in response to new information in this rapidly evolving field.


In this nascent field with new findings published almost daily, the Strategy is designed to be a living document that is updated periodically. This Strategy Update includes a short summary of recent findings from the San Francisco Bay Microplastics Project - a major monitoring effort in the Bay - and an updated multi-year plan based on the newly acquired knowledge and current management needs.

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Gilbreath, A.; McKee, L.; Shimabuku, I.; Lin, D.; Werbowski, L. M.; Zhu, X.; Grbic, J.; Rochman, C. 2019. Multi-year water quality performance and mass accumulation of PCBs, mercury, methylmercury, copper and microplastics in a bioretention rain garden. Journal of Sustainable Water in the Built Environment 5 (4) . SFEI Contribution No. 872.

A multiyear water quality performance study of a bioretention rain garden located along a major urban transit corridor east of San Francisco Bay was conducted to assess the efficacy of bioretention rain gardens to remove pollutants. Based on data collected in three years between 2012 and 2017, polychlorinated biphenyls (PCBs) and suspended sediment concentrations (SSCs) were reduced (>90%), whereas total mercury (Hg), methylmercury (MeHg), and copper (Cu) were moderately captured (37%, 49%, and 68% concentration reduction, respectively). Anthropogenic microparticles including microplastics were retained by the bioretention rain garden, decreasing in concentration from 1.6 particles/L to 0.16 particles/L. Based on subsampling at 50- and 150-mm intervals in soil cores from two areas of the unit, PCBs, Hg, and MeHg were all present at the highest concentrations in the upper 100 mm in the surface media layers. Based on residential screening concentrations, the surface media layer near the inlet would need to be removed and replaced annually, whereas the rest of the unit would need replacement every 8 years. The results of this study support the use of bioretention in the San Francisco Bay Area as one management option for meeting load reductions required by San Francisco Bay total maximum daily loads, and provide useful data for supporting decisions about media replacement and overall maintenance schedules.

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Sutton, R.; Xie, Y.; Moran, K. D.; Teerlink, J. 2019. Occurrence and Sources of Pesticides to Urban Wastewater and the Environment. In Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management. Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management. American Chemical Society: Washington, DC. pp 63-88.

Municipal wastewater has not been extensively examined as a pathway by which pesticides contaminate surface water, particularly relative to the well-recognized pathways of agricultural and urban runoff. A state-of-the-science review of the occurrence and fate of current-use pesticides in wastewater, both before and after treatment, indicates this pathway is significant and should not be overlooked. A comprehensive conceptual model is presented to establish all relevant pesticide-use patterns with the potential for both direct and indirect down-the-drain transport. Review of available studies from the United States indicates 42 pesticides in current use. While pesticides and pesticide degradates have been identified in wastewater, many more have never been examined in this matrix. Conventional wastewater treatment technologies are generally ineffective at removing pesticides from wastewater, with high removal efficiency only observed in the case of highly hydrophobic compounds, such as pyrethroids. Aquatic life reference values can be exceeded in undiluted effluents. For example, seven compounds, including three pyrethroids, carbaryl, fipronil and its sulfone degradate, and imidacloprid, were detected in treated wastewater effluent at levels exceeding U.S. Environmental Protection Agency (US EPA) aquatic life benchmarks for chronic exposure to invertebrates. Pesticides passing through wastewater treatment plants (WWTPs) merit prioritization for additional study to identify sources and appropriate pollution-prevention strategies. Two case studies, diazinon and chlorpyrifos in household pesticide products, and fipronil and imidacloprid in pet flea control products, highlight the importance of identifying neglected sources of environmental contamination via the wastewater pathway. Additional monitoring and modeling studies are needed to inform source control and prevention of undesirable alternative solutions.

Wu, J.; Kauhanen, P.; Hunt, J. A.; Senn, D.; Hale, T.; McKee, L. J. . 2019. Optimal Selection and Placement of Green Infrastructure in Urban Watersheds for PCB Control. Journal of Sustainable Water in the Built Environment 5 (2) . SFEI Contribution No. 729.

San Francisco Bay and its watersheds are polluted by legacy polychlorinated biphenyls (PCBs), resulting in the establishment of a total maximum daily load (TDML) that requires a 90% PCB load reduction from municipal stormwater. Green infrastructure (GI) is a multibenefit solution for stormwater management, potentially addressing the TMDL objectives, but planning and implementing GI cost-effectively to achieve management goals remains a challenge and requires an integrated watershed approach. This study used the nondominated sorting genetic algorithm (NSGA-II) coupled with the Stormwater Management Model (SWMM) to find near-optimal combinations of GIs that maximize PCB load reduction and minimize total relative cost at a watershed scale. The selection and placement of three locally favored GI types (bioretention, infiltration trench, and permeable pavement) were analyzed based on their cost and effectiveness. The results show that between optimal solutions and nonoptimal solutions, the effectiveness in load reduction could vary as much as 30% and the difference in total relative cost could be well over $100 million. Sensitivity analysis of both GI costs and sizing criteria suggest that the assumptions made regarding these parameters greatly influenced the optimal solutions. 

If you register for access to the journal, then you may download the article for free through July 31, 2019.

DOI: 10.1061/JSWBAY.0000876

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Gilbreath, A.; Hunt, J.; Mckee, L. 2019. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2018. SFEI Contribution No. 942. San Francisco Estuary Institute: Richmond, CA.
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Lowe, S.; Kauhanen, P. 2019. Prioritizing Candidate Green Infrastructure Sites within the City of Ukiah: A Demonstration of the Site Locator Tool of GreenPlan-IT. Report prepared for the City of Ukiah Department of Public Works under Supplemental Environmental Project # R1-018-0024. San Francisco Estuary Institute: Richmond. CA.

This report describes the application of GreenPlan-IT’s Site Locator Tool to identify and rank candidate GI installation sites within the City of Ukiah.  The Site Locator Tool is the first (foundational) tool of the GreenPlan-IT toolkit, meaning that the outputs are required inputs for both the Hydrologic Modeling and Optimization tools.   The Site Locator Tool addresses the question: where are the best locations for GI implementation based on local planning priorities? 

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SFEI. 2019. The Pulse of the Bay 2019: Pollutant Pathways. SFEI Contribution No. 954. San Francisco Estuary Institute: Richmond, CA.
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Wu, J.; McKee, L. 2019. Regional Watershed Modeling and Trends Implementation Plan. SFEI Contribution No. 943. San Francisco Estuary Institute: Richmond, CA.
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Box, C.; Cummins, A. 2019. San Francisco Bay Microplastics Project: Science-Supported Solutions and Policy Recommendations. SFEI Contribution No. 955. 5 Gyres: Los Angeles, CA.

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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Beagle, J.; Lowe, J.; McKnight, K.; Safran, S. M.; Tam, L.; Szambelan, S. Jo. 2019. 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.

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.

Printed copies available for purchase from Amazon.

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Sun, J.; Davis, J. A.; Stewart, R.; Palace, V. 2019. Selenium in White Sturgeon from North San Francisco Bay: The 2015-2017 Sturgeon Derby Study. SFEI Contribution No. 897. San Francisco Estuary Institute: Richmond, CA.

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) tissues collected during the 2015-2017 Sturgeon Derby events in North San Francisco Bay. The goal of this study was to investigate the distribution of selenium among sturgeon tissues to inform the toxicological and regulatory interpretation of selenium measured in non-lethally collected tissues, including muscle plugs and fin rays. This technical report provides documentation of the study and presents its major findings.

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Sutton, R.; Lin, D.; Sedlak, M.; Box, C.; Gilbreath, A.; Holleman, R.; Miller, L.; Wong, A.; Munno, K.; Zhu, X.; et al. 2019. Understanding Microplastic Levels, Pathways, and Transport in the San Francisco Bay Region. SFEI Contribution No. 950. San Francisco Estuary Institute: Richmond, CA.

Microplastics (particles less than 5 mm) are ubiquitous and persistent pollutants 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 microplastics problem and determining the highest priorities for mitigation require accurate measures of microplastic occurrence in the environment and identification of likely sources.

To develop critical baseline data and inform solutions, the San Francisco Estuary Institute and the 5 Gyres Institute have completed the first comprehensive regional study of microplastic pollution in a major estuary. This project supported multiple scientific components to develop improved knowledge about and characterization of microparticles and microplastics in San Francisco Bay and adjacent National Marine Sanctuaries, with the following objectives:

  1. Contribute to the development and standardization of sample collection and analysis methodology for microplastic transportation research.
  2. Determine a baseline for future monitoring of microplastics in San Francisco Bay surface water, sediment, and fish, and in ocean waters outside the Golden Gate.
  3. Characterize pathways by which microplastics enter the Bay, including urban stormwater and treated wastewater effluent.
  4. Investigate the contribution of Bay microplastics to the adjacent National Marine Sanctuaries through computer simulations.
  5. Communicate findings to regional stakeholders and the general public through meetings and educational materials.
  6. Facilitate evaluation of policy options for San Francisco Bay, with recommendations on source reduction.

This document presents the findings of this three-year project. A companion document, “San Francisco Bay Microplastics Project: Science-Supported Solutions and Policy Recommendations,” has been developed by 5 Gyres using the findings of this study (Box and Cummins, 2019).

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Hagerty, S.; Spotswood, E.; McKnight, K.; Grossinger, R. M. 2019. 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.
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Lowe, S. 2019. West Valley Watershed Assessment 2018: Baseline Ecological Condition Assessment of Southwest San Francisco Bay Creeks in Santa Clara County; Calabazas, San Tomas Aquino, Saratoga, Sunnyvale East and West. Salomon, M., Pearce, S., Josh Collins, Titus, D., Eds.. SFEI Contribution No. 944. San Francisco Estuary Institute: Richmond.

This report describes baseline information about the amount and distribution of aquatic resources, and evaluates the overall ecological conditions of streams using the California Rapid Assessment Method (CRAM), for the West Valley watershed in Santa Clara County; consisting of Sunnyvale East and West Channels, Calabazas Creek, San Tomas Aquino and Saratoga creeks, and many smaller tributaries.

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King, A. 2019. Wind Over San Francisco Bay and the Sacramento-San Joaquin River Delta: Forcing for Hydrodynamic Models. SFEI Contribution No. 937. San Francisco Estuary Institute: Richmond, CA.
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2018
Yee, D. 2018. 2017 RMP Bay Margins Sediment Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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Yee, D. 2018. 2017 RMP Water Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.
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Trowbridge, P. 2018. 2018 Bay RMP Multi-Year Plan. SFEI Contribution No. 860. San Francisco Estuary Institute : Richmond, CA.
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Salop, P.; Shimabuku, I.; Davis, J.; Franz, A. 2018. 2018 Bivalve Retrieval Cruise Report. SFEI Contribution No. 920. San Francisco Estuary Institute : Richmond, CA.
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Davis, J. 2018. 2018 Regional Monitoring Program Update. SFEI Contribution No. 906. San Francisco Estuary Institute : Richmond, CA.
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Trowbridge, P.; Wong, A.; Davis, J.; Ackerman, J. 2018. 2018 RMP Bird Egg Monitoring Sampling and Analysis Plan. SFEI Contribution No. 891. San Francisco Estuary Institute: Richmond, CA.
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Shimabuku, I.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Bivalve Deployment Cruise Plan. SFEI Contribution No. 892. San Francisco Estuary Institute: Richmond, CA.
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Salop, P. 2018. 2018 RMP Bivalve Deployment Cruise Report. SFEI Contribution No. 903. San Francisco Estuary Institute : Richmond, CA.
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Shimabuku, I.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute: Richmond, CA.
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Shimabuku, I.; Trowbridge, P.; Salop, P.; Franz, A. 2018. 2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute : Richmond, CA.
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Salop, P.; Franz, A. 2018. 2018 RMP Sediment Cruise Report. SFEI Contribution No. 907. San Francisco Estuary Institute : Richmond, CA.
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Franz, A.; Trowbridge, P.; Salop, P. 2018. 2018 RMP Sediment Sampling and Analysis Plan. SFEI Contribution No. 904. San Francisco Estuary Institute: Richmond, CA.
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Lin, D.; Sutton, R. 2018. Alternative Flame Retardants in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 885. San Francisco Estuary Institute : Richmond, CA.
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Jabusch, T.; Trowbridge, P.; Wong, A.; Heberger, M. 2018. Assessment of Nutrient Status and Trends in the Delta in 2001–2016: Effects of drought on ambient concentrations and trends. SFEI Contribution No. 865. Aquatic Science Center: Richmond, CA.

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP). The Program’s first assessment question regarding nutrients is: “How do concentrations of nutrients (and nutrient-associated parameters) vary spatially and temporally?” In this analysis, we confirmed previously reported declining trends in the San Joaquin River for nutrient concentrations at Vernalis and chlorophyll-a concentrations at Buckley Cove and Disappointment Slough. A slight increasing trend for dissolved oxygen at Buckley Cove was also detected which could be confirmation that management actions for the San Joaquin River Dissolved Control Program are having the desired effect. Finally, at stations in Suisun Bay, the Confluence region, and Franks Tract, chlorophyll-a showed modest increasing trends, which were not evident in previous analyses. The new analyses presented in this report and the findings from earlier reports constitute encouraging early progress toward answering the Delta RMP’s assessment questions. Specifically, due to the existence of long-term data sets and synthesis efforts, spatial and temporal trends in the concentrations of nutrients and nutrient-related parameters are reasonably well understood and so are the magnitudes of the most important sources of nutrients from outside the Delta. However, additional synthesis work could be done to understand the factors behind these trends. Large knowledge gaps remain about nutrient sinks, sources, and processes within the Delta. The mechanistic, water quality-hydrodynamic models being developed for the Delta may be able to address these questions in the future.

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Shimabuku, I.; Trowbridge, P.; Sun, J. 2018. Bay 2017 Bay RMP Field Sampling Report. SFEI Contribution No. 849. San Francisco Estuary Institute : Richmond, CA.
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Gilbreath, A.; Pearce, S.; Shimabuku, I.; McKee, L. 2018. Bay Area Green Infrastructure Water Quality Synthesis. SFEI Contribution No. 922. San Francisco Estuary Institute : Richmond, CA.
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Beller, E. E.; Spotswood, E.; Robinson, A.; Anderson, M. G.; Higgs, E. S.; Hobbs, R. J.; Suding, K. N.; Zavaleta, E. S.; Grenier, L.; Grossinger, R. M. 2018. Building Ecological Resilience in Highly Modified Landscapes.

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.

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Yee, D.; Wong, A.; Hetzel, F. 2018. Current Knowledge and Data Needs for Dioxins in San Francisco Bay. SFEI Contribution No. 926. San Francisco Estuary Institute : Richmond, CA.
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Jabusch, T.; Trowbridge, P.; Heberger, M.; Orlando, J.; De Parsia, M.; Stillway, M. 2018. Delta Regional Monitoring Program Annual Monitoring Report for Fiscal Year 2015–16: Pesticides and Toxicity. SFEI Contribution No. 864. Aquatic Science Center: Richmond, CA.

The primary purpose of this report is to document the first year (FY15/16) of pesticide monitoring by the Delta Regional Monitoring Program (Delta RMP). This document reports the results from samples collected monthly from July 2015 through June 2016. The data described in this report are available for download via the California Environmental Data Exchange Network (CEDEN) website.

Pesticide monitoring of the Delta RMP includes chemical analysis and toxicity testing of surface water samples. The parameters analyzed include 154 current use pesticides, dissolved copper, field parameters, and “conventional” parameters (ancillary parameters measured in the laboratory, such as dissolved/particulate organic carbon and hardness). Toxicity tests included an algal species (Selenastrum capricornutum, also known as Raphidocelis subcapitata), an invertebrate (Ceriodaphnia dubia, a daphnid or water flea), and a fish species (Pimephales promelas, fathead minnow). Toxicity testing included the evaluation of acute (survival) and chronic (growth, reproduction, biomass) toxicity endpoints. The surface water samples were collected from 5 fixed sites representing key inflows to the Delta that were visited monthly: Mokelumne River at New Hope Road, Sacramento River at Hood, San Joaquin River at Buckley Cove, San Joaquin River at Vernalis, and Ulatis Creek at Brown Road.

A total of 52 pesticides were detected above method detection limits (MDLs) in water samples (19 fungicides, 17 herbicides, 9 insecticides, 6 degradates, and 1 synergist). A total of 9 pesticides (5 herbicides, 3 insecticides, and 1 degradate) were detected in suspended sediments in 10 of a total of 60 samples collected during the study period. All collected samples contained mixtures of pesticides ranging from 2 to 26 pesticides per sample. From a total of 154 target parameters, 100 compounds were never detected in any of the samples.

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Jabusch, T.; Trowbridge, P.; Heberger, M.; Guerin, M. 2018. Delta Regional Monitoring Program Nutrients Synthesis: Modeling to Assist Identification of Temporal and Spatial Data Gaps for Nutrient Monitoring. SFEI Contribution No. 866. Aquatic Science Center: Richmond, CA.

Nutrient loads are an important water quality management issue in the Sacramento-San Joaquin Delta (Delta) and there is consensus that the current monitoring activities do not collect all the information needed to answer important management questions. The purpose of this report is to use hydrodynamic model outputs to refine recommendations for monitoring nutrients and related conditions in the Delta. Two types of modeling approaches were applied: 1) volumetric water source analysis to evaluate the mix of source waters within each subregion; and 2) particle tracking simulations.The analysis revealed that each Delta subregion has a unique “fingerprint” in terms of how much of its water comes from different sources. Three major recommendations for a future monitoring design were derived from this analysis:

Recommendation #1: The subregions proposed for status and trends monitoring in a previous report should be redrawn to better reflect the mixtures of source waters.

Recommendation #2: Long-term water quality stations are needed in the North Delta, Eastside, and South Delta subregions.

Recommendation #3: Areas with a long-residence time and where mixing of different water sources occurs are potential for nutrient transformation hotspots. High-frequency water quality mapping of these areas has the

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Denslow, N.; Kroll, K.; Mehinto, A.; Maruya, K. 2018. Estrogen Receptor In Vitro Assay Linkage Studies. SFEI Contribution No. 888. San Francisco Estuary Institute : Richmond, CA.
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Shimabuku, I.; Pearce, S.; Trowbridge, P.; Franz, A.; Yee, D.; Salop, P. 2018. Field Operations Manual for the Regional Monitoring Program. SFEI Contribution No. 902. San Francisco Estuary Institute: Richmond, CA.
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Wu, J.; Kauhanen, P.; Hunt, J.; McKee, L. 2018. Green Infrastructure Planning for North Richmond Pump Station Watershed with GreenPlan-IT. SFEI Contribution No. 882. San Francisco Estuary Institute: Richmond, CA.
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Wu, J.; Kauhanen, P.; Hunt, J.; McKee, L. 2018. Green Infrastructure Planning for the City of Oakland with GreenPlan-IT. SFEI Contribution No. 884. San Francisco Estuary Institute : Richmond, CA.
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Wu, J.; Kauhanen, P.; Hunt, J.; McKee, L. 2018. Green Infrastructure Planning for the City of Richmond with GreenPlan-IT. SFEI Contribution No. 883. San Francisco Estuary Institute: Richmond, CA.
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Wu, J.; Kauhanen, P.; Hunt, J.; McKee, L. 2018. Green Infrastructure Planning for the City of Sunnyvale with GreenPlan-IT. SFEI Contribution No. 881. San Francisco Estuary Institute : Richmond, CA.
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Kauhanen, P.; Wu, J.; Hunt, J.; McKee, L. 2018. Green Plan-IT Application Report for the East Bay Corridors Initiative. SFEI Contribution No. 887. San Francisco Estuary Institute: Richmond, CA.
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Hale, T.; Sim, L.; McKee, L. J. 2018. GreenPlan-IT Tracker.

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.

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Jahn, A. 2018. Gut Contents Analysis of Four Fish Species Collected in the San Leandro Bay RMP PCB Study in August 2016. SFEI Contribution No. 900. San Francisco Estuary Institute: Richmond, CA.
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Safran, S. M.; Baumgarten, S. A.; Beller, E. E.; Bram, D. L.; Crooks, J. A.; Dark, S. J.; Grossinger, R. M.; Longcore, T. R.; Lorda, J.; Stein, E. D. 2018. The Historical Ecology of the Tijuana Estuary & River Valley (Restore America's Estuaries 2018 Conference Presentation).

This talk was given at the 2018 Restore America's Estuary Conference in Long Beach, CA as part of a special session titled "Restoration Perspectives from the Tijuana River National Estuarine Research Reserve." It is based on information from the Tijuana River Valley Historical Ecology Investigation, a report published in 2017.


Though many areas of the binational Tijuana River watershed remain relatively undeveloped, land and water use changes over the past 200 years have resulted in significant ecological impacts, particularly in the more urbanized areas of the lower watershed. Drawing upon a diverse set of historical data, we reconstructed the ecological and hydrogeomorphic conditions of the lower Tijuana River valley prior to major Euro-American modification (ca. 1850) and documented major changes in habitat distribution and physical processes over this time. The river corridor, which was historically dominated by riparian scrub, today instead supports dense stands of riparian forest. The valley bottom surrounding the river corridor, which historically supported extensive seasonal wetlands, has largely been converted to drier habitat types and agricultural uses. The estuary, which historically supported large expanses of salt marsh and mudflat as well as seasonally dry salt flats, has retained much of its former extent and character, but has been altered by increased sediment input and other factors. The new information about the historical landscape presented here is relevant to a number of issues scientists and managers are dealing with today, including the conservation of endangered species, the fate of the valley’s riparian habitats after the recent invasion of invasive shot-hole borer beetles, and the effects on groundwater levels on native plant communities. We will also draw from other historical ecology studies conducted in Southern California to illustrate how the information about the past has been utilized to improve the functioning and resilience of nearby coastal ecosystems.

Presentation recording: available here.

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Davis, J. A.; Heim, W. A.; Bonnema, A.; Jakl, B.; Yee, D. 2018. Mercury and Methylmercury in Fish and Water from the Sacramento-San Joaquin Delta: August 2016 – April 2017. SFEI Contribution No. 908. Aquatic Science Center: Richmond, CA.

Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest priority information needs related to implementation of the Sacramento–San Joaquin Delta Estuary Total Maximum Daily Load (TMDL) for Methylmercury (Wood et al. 2010). Two species of sport fish, largemouth bass (Micropterus salmoides) and spotted bass (Micropterus punctulatus), were collected at six sampling locations in August and September 2016. The length-adjusted (350 mm) mean methylmercury (measured as total mercury, which is a routinely used proxy for methylmercury in predator fish) concentration in bass ranged from 0.15 mg/kg or parts per million (ppm) wet weight at Little Potato Slough to 0.61 ppm at the Sacramento River at Freeport. Water samples were collected on four occasions from August 2016 through April 2017. Concentrations of methylmercury in unfiltered water ranged from 0.021 to 0.22 ng/L or parts per trillion. Concentrations of total mercury in unfiltered water ranged from 0.91 to 13 ng/L.

Over 99% of the lab results for this project met the requirements of the Delta RMP Quality Assurance Program Plan, and all data were reportable. This data report presents the methods and results for the first year of monitoring. Historic data from the same or nearby monitoring stations from 1998 to 2011 are also presented to provide context. Monitoring results for both sport fish and water were generally comparable to historic observations.

For the next several years, annual monitoring of sport fish will be conducted to firmly establish baseline concentrations and interannual variation in support of monitoring of long-term trends as an essential performance measure for the TMDL. Monitoring of water will solidify the linkage analysis (the quantitative relationship between methylmercury in water and methylmercury in sport fish) in the TMDL. Water monitoring will also provide data that will be useful in verifying patterns and trends predicted by numerical models of mercury transport and cycling being developed for the Delta and Yolo Bypass by the California Department of Water Resources (DWR).

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Jabusch, T.; Trowbridge, P. 2018. Microbial Water Quality at Minimally Human-Impacted Reference Beaches in Northern California. SFEI Contribution No. 858. San Francisco Estuary Institute : Richmond, CA.
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Sun, J. 2018. Non-Targeted Analysis of Water-Soluble Compounds Highlights Overlooked Contaminants and Pathways (Coming Soon). SFEI Contribution No. 905. San Francisco Estuary Institute: Richmond, CA.
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Grieb, T.; Roy, S.; Rath, J.; Stewart, R.; Sun, J.; Davis, J. A. 2018. North Bay Selenium Monitoring Design. SFEI Contribution No. 921. San Francisco Estuary Institute : Richmond, CA.
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Sedlak, M.; Sutton, R.; Wong, A.; Lin, D. 2018. Per and Polyfluoroalkyl Substances (PFAS) in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 867. San Francisco Estuary Institute : Richmond, CA.
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Baumgarten, S.; Clark, E.; Dusterhoff, S.; Grossinger, R. M.; Askevold, R. A. 2018. Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.

This study reconstructs the historical landscape of the Petaluma River watershed and documents the major landscape changes that have taken place within the watershed over the past two centuries. Prior to Spanish and American settlement of the region, the Petaluma River watershed supported a dynamic and interconnected network of streams, riparian forests, freshwater wetlands, and tidal marshes. These habitats were utilized by a wide range of plant and animal species, including a number of species that are today listed as threatened or endangered such as Ridgway’s Rail, Black Rail, salt marsh harvest mouse, California red-legged frog, Central California Coast steelhead, and soft bird’s beak (CNDDB 2012, SRCD 2015). Agricultural and urban development beginning in the mid-1800s has significantly altered the landscape, degrading habitat for fish and wildlife and contributing to contemporary management challenges such as flooding, pollutant loading, erosion, and sedimentation. While many natural areas and remnant wetlands still exist throughout the watershed—most notably the Petaluma Marsh—their ecological function is in many cases seriously impaired and their long-term fate jeopardized by climate change and other stressors. Multi-benefit wetland restoration strategies, guided by a thorough understanding of landscape history, can simultaneously address a range of chronic management issues while improving the ecological health of the watershed, making it a better place to live for both people and wildlife.

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Gilbreath, A.; Wu, J.; Hunt, J.; McKee, L. 2018. Pollutants of Concern Reconnaissance Monitoring Water Years 2015, 2016, and 2017. SFEI Contribution No. 840. San Francisco Estuary Institute: Richmond, CA.
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McKnight, K.; Dusterhoff, S. D.; Grossinger, R. M.; Askevold, R. A. 2018. 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.

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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Richey, A.; Dusterhoff, S. D.; McKnight, K.; Salomon, M.; Hagerty, S.; Askevold, R. A.; Grossinger, R. M. 2018. Resilient Landscape Vision for Upper Penitencia Creek. SFEI Contribution No. 894. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
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