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2021
Yee, D. 2021. 2019 RMP Data Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.

This memo provides a high-level summary of the quality assurance assessment for data reported by the RMP.  In 2019, fish tissue samples were collected from nine Bay/Delta areas and three additional wetland/slough areas for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). General descriptions of the sample collection methods are provided 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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2021. 2020-21 RMP North Bay Selenium Study. SFEI Contribution No. 1052. San Francisco Estuary Institute: Richmond, CA.

This report details activities associated with the Regional Monitoring Program North Bay Selenium Study in 2020 and 2021. The study was designed to monitor two sites for selenium (Se) in water and clam tissue six times annually between June and February. Due to the COVID pandemic, however, four sample collection events were completed. This report outlines the sampling activities, personnel, and site locations monitored for the project.

 

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Foley, M. 2021. 2021 RMP Multi-Year Plan . SFEI Contribution No. 1027. San Francisco Estuary Institute: Richmond, CA.
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Spotswood, E.; Beller, E. E.; Grossinger, R. M.; Grenier, L.; Heller, N.; Aronson, M. 2021. The biological deserts fallacy: Cities in their landscapes contribute more than we think to regional biodiversity. BioScience 71 (2) . SFEI Contribution No. 1031.

Cities are both embedded within and ecologically linked to their surrounding landscapes. Although urbanization poses a substantial threat to biodiversity, cities also support many species, some of which have larger populations, faster growth rates, and higher productivity in cities than outside of them. Despite this fact, surprisingly little attention has been paid to the potentially beneficial links between cities and their surroundings.

We identify five pathways by which cities can benefit regional ecosystems by releasing species from threats in the larger landscape, increasing regional habitat heterogeneity and genetic diversity, acting as migratory stopovers, preadapting species to climate change, and enhancing public engagement and environmental stewardship. Increasing recognition of these pathways could help cities identify effective strategies for supporting regional biodiversity conservation and could provide a science-based platform for incorporating biodiversity alongside other urban greening goals.

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Panlasigui, S.; Spotswood, E.; Beller, E.; Grossinger, R. 2021. Biophilia beyond the Building: Applying the Tools of Urban Biodiversity Planning to Create Biophilic Cities. Sustainability 13 (5).

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

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Moore, S.; Hale, T.; Weisberg, S. B.; Flores, L.; Kauhanen, P. 2021. California Trash Monitoring Methods and Assessments Playbook. SFEI Contribution No. 1025. San Francisco Estuary Institute: Richmond, Calif.

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.

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Lowe, S.; Pearce, S.; Kauhanen, P.; Collins, J.; Titus, D. 2021. Coyote Creek Watershed Reassessment 2020: 10-Year Reassessment of the Ecological Condition of Streams Applying the California Rapid Assessment Method, Santa Clara County, California. SFEI Contribution No. 1043. San Francisco Estuary Institute: Richmond. CA. p 131.

This report describes the amount and distribution of aquatic resources in the Coyote Creek watershed, Santa Clara County, California, and presents the first reassessment of stream ecosystem conditions using a watershed approach and the California Rapid Assessment Method (CRAM). Field work was conducted in 2020, ten years after the baseline watershed assessment completed in 2010.

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SFEI. 2021. Ecotone levees and wildlife connectivity: A technical update to the Adaptation Atlas. SFEI Contribution No. 1037. San Francisco Estuary Institute: Richmond, CA.
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Moore, S.; Hale, T.; Weisberg, S. B.; Flores, L.; Kauhanen, P. 2021. Field Testing Report: California Trash Monitoring Methods. SFEI Contribution No. 1026. San Francisco Estuary Institute: Richmond, Calif.

Trash has received renewed focus in recent years as policy makers, public agencies, environmental organizations, and community groups have taken many steps towards trash quantification and management across California. The range of management actions is matched by the diversity of monitoring approaches, designed to determine key attributes associated with trash pollution on California’s lands and in its waterways.

This report describes the field testing associated with a project designed to validate the accuracy, precision, and practicality of several trash monitoring methods, practiced across the state. Additionally, the project measured the efficacy of a novel monitoring method designed to detect trash via remote sensing and machine learning. Readers will find details about each respective method -- the specific approach to
landscape characterization, the qualitative or quantitative measures undertaken, the team-based quality assurance for data collection -- as well as the approach that the testing team adopted to ensure efficient, accurate, and useful validation of the methods.

Because the validation efforts integrated multiple methods, using multiple teams at a selection of common sites, the field testing report yields useful statistical information not only about each method individually, but about the comparability of the results. The report illustrates the
correlation factor associated with different forms of trash metrics, associated with different methods practiced on the same assessment sites. The results illustrated a generally high degree of correlation among different methods, which promises opportunities to compare results meaningfully across methods.

Furthermore, this field testing report provides quantitative measures to illustrate the repeatability of each method, the differences and insights yielded by assessment site sizing criteria varying among methods, the transferability / teach-ability of each method among trash monitoring practitioners, and how the degrees of accuracy might aid programs in performing mass balance analysis of known sources
to trash detected in a given site.

Regarding innovation, the project team leveraged multiple on-the-ground methods and special testing scenarios to compare conventional and novel (aerial) assessments to measure the relative accuracy and precision of this emergent technology that might address some of the resource constraints that currently limit the broader or more frequent deployment of conventional trash assessment methods. The analyses captured in this field testing report offer specific quantitative measures of the accuracy (bias), precision (repeatability), practicality and cost associated with each method. This information is subsequently used to inform a companion summary analysis found in the Trash Monitoring Playbook, which is designed to evaluate the applicability of the monitoring methods to address classes of
monitoring questions.

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Dusterhoff, S.; Shaw, S.; McKnight, K. 2021. Flood Control Channel Classification Scheme for the San Francisco Bay Region. Josh Collins, Ed.. San Francisco Bay Region Flood Control Channel Classification . SFEI Contribution No. 1046. San Francisco Estuary Institute: Richmond, CA.
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Chang, D.; Richardot, W.; Miller, E.; Dodder, N.; Sedlak, M.; Hoh, E.; Sutton, R. 2021. Framework for nontargeted investigation of contaminants released by wildfires into stormwater runoff: Case study in the northern San Francisco Bay area. Integrated Environmental Assessment and Management . SFEI Contribution No. 1044.

Wildfires can be extremely destructive to communities and ecosystems. However, the full scope of the ecological damage is often hard to assess, in part due to limited information on the types of chemicals introduced to affected landscapes and waterways. The objective of this study was to establish a sampling, analytical, and interpretive framework to effectively identify and monitor contaminants of emerging concern in environmental water samples impacted by wildfire runoff. A nontargeted analysis consisting of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC/TOF-MS) was conducted on stormwater samples from watersheds in the City of Santa Rosa and Sonoma and Napa Counties, USA, after the three most destructive fires during the October 2017 Northern California firestorm. Chemicals potentially related to wildfires were selected from the thousands of chromatographic features detected through a screening method that compared samples from fire-impacted sites versus unburned reference sites. This screening led to high confidence identifications of 76 potentially fire-related compounds. Authentic standards were available for 48 of these analytes, and 46 were confirmed by matching mass spectra and GC × GC retention times. Of these 46 compounds, 37 had known commercial and industrial uses as intermediates or ingredients in plastics, personal care products, pesticides, and as food additives. Nine compounds had no known uses or sources and may be oxidation products resulting from burning of natural or anthropogenic materials. Preliminary examination of potential toxicity associated with the 46 compounds, conducted via online databases and literature review, indicated limited data availability. Regional comparison suggested that more structural damage may yield a greater number of unique, potentially wildfire-related compounds. We recommend further study of post-wildfire runoff using the framework described here, which includes hypothesis-driven site selection and nontargeted analysis, to uncover potentially significant stormwater contaminants not routinely monitored after wildfires and inform risk assessment. 

Zi, T.; Kauhanen, P.; Whipple, A.; Mckee, L. 2021. Green Stormwater Infrastructure Planning-level Analysis for Livermore-Amador Valley. SFEI Contribution No. 1063. San Francisco Estuary Institute: Richmond, Calif.

Report CoverThis effort is intended to provide planning-level regional guidance for placement of green stormwater infrastructure (GSI) in Livermore-Amador Valley. This work identifies potential GSI locations and quantifies contaminant load and stormwater runoff volume reduction benefits through the application of GreenPlan-IT, a planning tool developed by the San Francisco Estuary Institute and regional partners. Ultimately, the urban greening analysis presented in this report is intended to help enhance stream and watershed resilience, reduce peak flows, and improve water quality.

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Zhu, X.; Munno, K.; Grbic, J.; Werbowski, L. M.; Bikker, J.; Ho, A.; Guo, E.; Sedlak, M.; Sutton, R.; Box, C.; et al. 2021. Holistic Assessment of Microplastics and Other Anthropogenic Microdebris in an Urban Bay Sheds Light on Their Sources and Fate. Environmental Science and Technology Water . SFEI Contribution No. 1060.

The physical and chemical properties of microplastics and their environmental distributions may provide clues about their sources and inform their fate. We demonstrate the value of extensive monitoring of microplastics in an urban bay, San Francisco Bay. Surface water, fish, sediment, stormwater runoff, and treated wastewater were sampled across the bay and adjacent national marine sanctuaries (NMS). We found microplastics and other anthropogenic microdebris (“microdebris”) in all sample types. Concentrations were higher in the bay than in the NMS, and within the bay, concentrations were higher during the wet season than during the dry season. The fate of microdebris varied depending on their morphologies and densities: fibers were dominant in fish, black rubbery fragments were common in sediment, as were fibers, while buoyant fragments and fibers were widely observed in surface waters. Notably, we found large amounts of black rubbery fragments, an emerging contaminant, in stormwater. Moreover, stormwater was a significant pathway of microdebris, with concentrations roughly 140 times greater than those found in wastewater, which was dominated by fibers. Overall, we demonstrate the value of multimatrix regional monitoring to evaluate the sources and fate of microplastics, which can inform effective mitigation for other urban bays around the world.

 

Spotswood, E.; Benjamin, M.; Stoneburner, L.; Wheeler, M. 2021. Nature inequity and higher COVID-19 case rates in less green neighbourhoods in the United States. Nature Sustainability 4 (10).

Nature inequity and higher COVID-19 case rates in less green neighbourhoods in the United StatesUrban nature—such as greenness and parks—can alleviate distress and provide space for safe recreation during the COVID-19 pandemic. However, nature is often less available in low-income populations and communities of colour—the same communities hardest hit by COVID-19. In analyses of two datasets, we quantified inequity in greenness and park proximity across all urbanized areas in the United States and linked greenness and park access to COVID-19 case rates for ZIP codes in 17 states. Areas with majority persons of colour had both higher case rates and less greenness. Furthermore, when controlling for sociodemographic variables, an increase of 0.1 in the Normalized Difference Vegetation Index was associated with a 4.1% decrease in COVID-19 incidence rates (95% confidence interval: 0.9–6.8%). Across the United States, block groups with lower-income and majority persons of colour are less green and have fewer parks. Our results demonstrate that the communities most impacted by COVID-19 also have the least nature nearby. Given that urban nature is associated with both human health and biodiversity, these results have far-reaching implications both during and beyond the pandemic.

Related data: https://www.sfei.org/data/nature-equity-covid-2021

 

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Davis, J.; Buzby, N. 2021. PCBs in Shiner Surfperch in Priority Margin Areas of San Francisco Bay. SFEI Contribution No. 1054.

Conceptual models developed for selected San Francisco Bay margin areas (referred to as priority margin units, or PMUs) have identified shiner surfperch as a crucial indicator of PCB impairment, due to their explicit inclusion as an indicator species in the PCBs TMDL, importance as a popular sport fish species, tendency to accumulate high PCB concentrations, site fidelity, and other factors. The conceptual models recommend periodic monitoring of shiner surfperch to track trends in the PMUs, and as the ultimate indicator of progress in reduction of impairment. The objectives of this study were to 1) establish baselines for long-term monitoring of PCB concentrations in shiner surfperch in four PMUs, and 2) understand local spatial variation in shiner PCB concentrations to support optimization of the long-term sampling design. This study also provided valuable information on the presence of shiner surfperch and other species in the PMUs. 

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Gilbreath, A.; McKee, L.; Hunt, J. 2021. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2020. SFEI Contribution No. 1061. San Francisco Estuary Institute: Richmond, CA.

The San Francisco Bay polychlorinated biphenyl (PCB) and mercury (Hg) total maximum daily loads (TMDLs) call for implementation of control measures to reduce PCB and Hg loads entering the Bay via stormwater. In 2009, the San Francisco Bay Regional Water Quality Control Board (Regional Water Board) issued the first Municipal Regional Stormwater Permit (MRP). This MRP contained a provision aimed at improving information on stormwater pollutant loads in selected watersheds (Provision C.8.) and piloted a number of management techniques to reduce PCB and Hg loading to the Bay from smaller urbanized tributaries (Provisions C.11. and C.12.). To address C8, a previously developed fixed station loads monitoring technique was refined that incorporated turbidity and stage sensors recording at 5-15 minute intervals with the collection of velocity and water samples using both manual and auto sampling techniques to compute loads. In 2015, the Regional Water Board issued the second iteration of the MRP. “MRP 2.0” placed an increased focus on identifying those watersheds, source areas, and source properties that are potentially the most polluted and are therefore most likely to be cost-effective areas for addressing load-reduction requirements.

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Kauhanen, P.; Lowe, S. 2021. Remote Sensing Recommendations for Tidal Wetland Indicators. SFEI Contribution No. 1047. San Francisco Estuary Institute: Richmond. CA. p 31.

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.

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Davis, J.; Foley, M.; Askevold, R.; Chelsky, A.; Dusterhoff, S.; Gilbreath, A.; Lin, D.; Yee, D.; Senn, D.; Sutton, R. 2021. RMP Update 2021. SFEI Contribution No. 1057.

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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Zi, T.; Mckee, L.; Yee, D.; Foley, M. 2021. San Francisco Bay Regional Watershed Modeling Progress Report, Phase 1. SFEI Contribution No. 1038. San Francisco Estuary Institute: Richmond, CA.
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Ellisor, D.; Buzby, N.; Weaver, M.; Foley, M.; Pugh, R. 2021. The San Francisco Estuary Institute Collection at the NIST Biorepository. NIST Interagency/Internal Report (NISTIR) - 8370. SFEI Contribution No. 1039. National Institute of Standards and Technology: Gaithersburg, MD.

The National Institute of Standards and Technology (NIST) has been collaborating with the San Francisco Bay Estuary Institute (SFEI) since 2009, providing biobanking services at the NIST Biorepository in Charleston, South Carolina in support of their ongoing water quality monitoring program, the Regional Monitoring Program for Water Quality in the San Francisco Bay (RMP). Specimens (bivalve tissue, bird egg contents, fish tissue and sediment) are collected and processed by SFEI-partnering institutions according to their established protocols and shipped to the NIST Biorepository for archival. This report outlines NIST's role in the project, describes collection and processing protocols developed by SFEI and their collaborators, details shipping and archival procedures employed by biorepository staff and provides an inventory of the collection maintained by NIST from 2009 to 2020.

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Dusterhoff, S.; McKnight, K.; Grenier, L.; Kauffman, N. 2021. Sediment for Survival: A Strategy for the Resilience of Bay Wetlands in the Lower San Francisco Estuary. SFEI Contribution No. 1015. San Francisco Estuary Institute: Richmond, CA.

The resilience of San Francisco Bay shore habitats, such as tidal marshes and mudflats, is essential to all who live in the Bay Area. Tidal marshes and tidal flats (also known as mudflats) are key components of the shore habitats, collectively called baylands, which protect billions of dollars of bay-front housing and infrastructure (including neighborhoods, business parks, highways, sewage treatment plants, and landfills). They purify the Bay’s water, support endangered wildlife, nurture fisheries, and provide people access to nature within the urban environment. Bay Area residents showed their commitment to restoring these critical habitats when they voted for a property tax to pay for large-scale tidal marsh restoration. However, climate change poses a great threat, because there may not be enough natural sediment supply for tidal marshes and mudflats to gain elevation fast enough to keep pace with sea-level rise.

This report analyses current data and climate projections to determine how much natural sediment may be available for tidal marshes and mudflats and how much supplemental sediment may be needed under different future scenarios. These sediment supply and demand estimates are combined with scientific knowledge of natural physical and biological processes to offer a strategy for sediment delivery that will allow these wetlands to survive a changing climate and provide benefits to people and nature for many decades to come. The approach developed in this report may also be useful beyond San Francisco Bay because shoreline protection, flood risk-management, and looming sediment deficits are common issues facing coastal communities around the world.

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Mendez, M.; Lin, D.; Sutton, R. 2021. Study of Per- and Polyfluoroalkyl Substances in Bay Area POTWs: Phase 1, Sampling and Analysis Plan. SFEI Contribution No. 1020. San Francisco Estuary Institute: Richmond, CA.
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Miller, E.; Sedlak, M.; Sutton, R.; Chang, D.; Dodder, N.; Hoh, E. 2021. Summary for Managers: Non-targeted Analysis of Stormwater Runoff following the 2017 Northern San Francisco Bay Area Wildfires. SFEI Contribution No. 1045. San Francisco Estuary Institute: Richmond, CA.

Urban-wildland interfaces in the western US are increasingly threatened by the growing number and intensity of wildfires, potentially changing the type of contaminants released into the landscape as more urban structures are burned. In October 2017, the Tubbs, Nuns, and Atlas wildfires devastated communities in Northern California (Figure 1), burning over 8,500 buildings and 210,000 acres of land in the span of 24 days (California Department of Forestry and Fire Protection 2017). Together, these wildfires were the most destructive and costliest fires in the history of California at that time (California Department of Forestry and Fire Protection 2019). 

Post-wildfire monitoring efforts in impacted watersheds typically focus on a few well-established water quality and chemistry concerns (McKee et al. 2018). Few studies go beyond these limited targeted analyses and attempt to identify the multitude of other fire-related compounds that are released from or form as the result of combustion of residential, commercial, and industrial structures in urban-wildland interfaces. Some of these unidentified compounds may be toxic to aquatic ecosystems or human health, and may pose risks to wildlife or in water bodies that act as drinking water supplies to nearby communities.  

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Moran, K.; Miller, E.; Mendez, M.; Moore, S.; Gilbreath, A.; Sutton, R.; Lin, D. 2021. A Synthesis of Microplastic Sources and Pathways to Urban Runoff. SFEI Contribution No. 1049. San Francisco Estuary Institute: Richmond, CA.

California Senate Bill 1263 (2018) tasks the Ocean Protection Council (OPC) with leading statewide efforts to address microplastic pollution, and requires the OPC to adopt and implement a Statewide Microplastics Strategy related to microplastic materials that pose an emerging concern for ocean health. Key questions remain about the sources and pathways of microplastics, particularly to urban runoff, to inform an effective statewide microplastics management strategy. The OPC funded this work to inform these microplastics efforts. The purpose of this project was to build conceptual models that synthesize and integrate our current understanding of microplastic sources and pathways to urban runoff in order to provide future research priorities that will inform how best to mitigate microplastic pollution. Specifically, we developed conceptual models for cigarette butts and associated cellulose acetate fibers (Section 2), fibers other than cellulose acetate (Section 3), single-use plastic foodware and related microplastics (Section 4), and tire particles (Section 5), which were prioritized based on findings from the recent urban stormwater monitoring of microplastics in the San Francisco Bay region. Conceptual models specific to each of these particle types are valuable tools to refine source identification and elucidate potential source-specific data gaps and management options.

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

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


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

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

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Zi, T.; Whipple, A.; Kauhanen, P.; Spotswood, E.; Grenier, L.; Grossinger, R.; Askevold, R. 2021. Trees and Hydrology in Urban Landscapes. SFEI Contribution No. 1034. San Francisco Estuary Institute: Richmond, CA.

Effective implementation of urban greening strategies is needed to address legacies of landscape change and environmental degradation, ongoing development pressures, and the urgency of the climate crisis. With limited space and resources, these challenges will not be met through single-issue or individual-sector management and planning. Increasingly, local governments, regulatory agencies, and other urban planning organizations in the San Francisco Bay Area are expanding upon the holistic, portfolio-based, and multi-benefit approaches.

This effort, presented in the Trees and Hydrology in Urban Landscapes report, seeks to build links between stormwater management and urban ecological improvements by evaluating how complementary urban greening activities, including green stormwater infrastructure (GSI) and urban tree canopy, can be integrated and improved to reduce runoff and contaminant loads in stormwater systems. This work expands the capacity for evaluating engineered GSI and non-engineered urban greening within a modeling and analysis framework, with a primary focus on evaluating the hydrologic benefit of urban trees. Insights can inform stormwater management policy and planning. 

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Werbowski, L. M.; Gilbreath, A.; Munno, K.; Zhu, X.; Grbic, J.; Wu, T.; Sutton, R.; Sedlak, M.; Deshpande, A. D.; Rochman, C. M. 2021. Urban Stormwater Runoff: A Major Pathway for Anthropogenic Particles, Black Rubbery Fragments, and Other Types of Microplastics to Urban Receiving Waters. Environmental Science and Technology Water . SFEI Contribution No. 1040.

Stormwater runoff has been suggested to be a significant pathway of microplastics to aquatic habitats; yet, few studies have quantified microplastics in stormwater. Here, we quantify and characterize urban stormwater runoff from 12 watersheds surrounding San Francisco Bay for anthropogenic debris, including microplastics. Depth-integrated samples were collected during wet weather events. All stormwater runoff contained anthropogenic microparticles, including microplastics, with concentrations ranging from 1.1 to 24.6 particles/L. These concentrations are much higher than those in wastewater treatment plant effluent, suggesting urban stormwater runoff is a major source of anthropogenic debris, including microplastics, to aquatic habitats. Fibers and black rubbery fragments (potentially tire and road wear particles) were the most frequently occurring morphologies, comprising ∼85% of all particles across all samples. This suggests that mitigation strategies for stormwater should be prioritized. As a case study, we sampled stormwater from the inlet and outlet of a rain garden during three storm events to measure how effectively rain gardens capture microplastics and prevent it from contaminating aquatic ecosystems. We found that the rain garden successfully removed 96% of anthropogenic debris on average and 100% of black rubbery fragments, suggesting rain gardens should be further explored as a mitigation strategy for microplastic pollution.

Iknayan, K.; Wheeler, M.; Safran, S. M.; Young, J. S.; Spotswood, E. 2021. What makes urban parks good for California quail? Evaluating park suitability, species persistence, and the potential for reintroduction into a large urban national park. Journal of Applied Ecology.

  1. Preserving and restoring wildlife in urban areas benefits both urban ecosystems and the well-being of urban residents. While urban wildlife conservation is a rapidly developing field, the majority of conservation research has been performed in wildland areas. Understanding the applicability of wildland science to urban populations and the relative importance of factors limiting species persistence are of critical importance to identifying prescriptive management strategies for restoring wildlife to urban parks.
  2. We evaluated how habitat fragmentation, habitat quality and mortality threats influence species occupancy and persistence in urban parks. We chose California quail Callipepla californica as a representative species with potential to respond to urban conservation. We used publicly available eBird data to construct occupancy models of quail in urban parks across their native range, and present an application using focal parks interested in exploring quail reintroduction.
  3. Urban parks had a 0.23 ± 0.02 probability of quail occupancy, with greater occupancy in larger parks that were less isolated from potential source populations, had higher shrub cover and had lower impervious cover. Less isolated parks had higher colonization rates, while larger parks had lower extinction rates. These results align with findings across urban ecology showing greater biodiversity in larger and more highly connected habitat patches.
  4. A case study highlighted that interventions to increase effective park size and improve connectivity would be most influential for two highly urban focal parks, while changes to internal land cover would have a relatively small impact. Low joint extinction probability in the parks (0.010 ± 0.013) indicated reintroduced populations could persist for some time.
  5. Synthesis and applications. We show how eBird data can be harnessed to evaluate the responsiveness of wildlife to urban parks of variable size, connectivity and habitat quality, highlighting what management actions are most needed. Using California quail as an example, we found park size, park isolation and presence of coyotes are all important drivers of whether quail can colonize and persist in parks. Our results suggest reintroducing quail to parks could be successful provided parks are large enough to support quail, and management actions are taken to enhance regional connectivity or periodic assisted colonization is used to supplement local populations.
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2020
2020. 2019-20 RMP North Bay Selenium Study. 2019-20 RMP North Bay Selenium Study. SFEI Contribution No. 1051. San Francisco Estuary Institute: Richmond, CA.

This report details activities associated with the Regional Monitoring Program North Bay Selenium Study. The  study was designed to monitor two sites for selenium (Se) in clam tissues and water six times between June  2019 and February 2020. This report outlines the sampling activities, personnel, and site locations monitored for  the project. 

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Franz, A.; Salop, P. 2020. 2019 Bay RMP Water Cruise Plan. SFEI Contribution No. 971. San Francisco Estuary Institute: Richmond, CA.
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Buzby, N.; Yee, D.; Salop, P.; Foley, M. 2020. 2019 RMP North Bay Selenium Monitoring Sampling and Analysis Plan. SFEI Contribution No. 969. San Francisco Estuary Institute: Richmond, CA.

The goal of monitoring for selenium in the North Bay tissue and water is to identify leading indicators of change to allow prompt management response to signs of increasing impairment. At the 2016 technical workshop, participants reached a consensus that monitoring sturgeon, clams, and water are all needed to answer management questions. Recommendations for long-term monitoring of these three matrices are detailed in the North Bay Monitoring Design document (Grieb et al. 2018). The purpose of this Sampling and Analysis Plan is to clearly document the sampling design, methods, and responsibilities; and to facilitate coordination among project partners.

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Buzby, N.; Yee, D.; Foley, M.; David, J.; Sigala, M.; Bonnema, A. 2020. 2019 Sport Fish Monitoring Sampling and Analysis Plan. SFEI Contribution No. 970. San Francisco Estuary Institute: Richmond, CA.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) monitors concentrations of contaminants in fish tissue as indicators of bioaccumulation of contaminants in the Bay. In 2019, the RMP will conduct its eighth round of sport fish monitoring by collecting sport fish samples from various locations in the Bay as a part of routine Status and Trends Monitoring. Add-ons to the routine Status and Trends sport fish monitoring design will include archiving for microplastics and fipronil, as well as additional collections of shiner surfperch in Priority Margin Unit areas (PMUs).

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2020. 2020 Bay RMP Detailed Workplan and Budget. SFEI Contribution No. 980. San Francisco Estuary Institute: Richmond, CA.
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Miller, E.; Mendez, M.; Shimabuku, I.; Buzby, N.; Sutton, R. 2020. Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations 2020 Update. SFEI Contribution No. 1007. San Francisco Estuary Institute: Richmond, CA.

This 2020 CEC Strategy Update is a brief summary document that describes the addition of recently monitored CECs to the tiered risk-based framework. Reviews of findings relevant to San Francisco Bay are provided, as is a discussion of the role of environmental persistence in classifying CECs within the framework. The Strategy is a living document that guides RMP special studies on CECs, assuring continued focus on the issues of highest priority to protecting the health of the Bay. A key focus of the Strategy is a tiered risk-based framework that guides future monitoring proposals. The Strategy also features a multi-year plan indicating potential future research priorities.

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Lowe, S. 2020. Coyote Creek Watershed Reassessment 2020 Ambient Stream Condition Survey Design and Monitoring Plan: A Review of the Original 2010 Survey Design and Development of the 2020 Reassessment Strategy. Pearce, S., Ed.; Titus, D., Tran.. SFEI Contribution No. 1055. San Francisco Estuary Institute: Richmond. CA. p 18.

This technical report describes the ten-year ambient stream condition reassessment survey design and monitoring plan (or strategy) for the Coyote Creek watershed. Because the reassessment employed (and modified) the 2010 sample draw, essential background information about the original 2010 probability-based survey design, sample draw, and field assessment outcomes were provided.

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Heberger, M.; Sutton, R.; Buzby, N.; Sun, J.; Lin, D.; Mendez, M.; Hladik, M.; Orlando, J.; Sanders, C.; Furlong, E. 2020. Current-Use Pesticides, Fragrance Ingredients, and Other Emerging Contaminants in San Francisco Bay Margin Sediment and Water. SFEI Contribution No. 934. San Francisco Estuary Institute: Richmond, CA.

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) has recently focused attention on better characterization of contaminants in nearshore “margin” areas of San Francisco Bay. The margins of the Lower South Bay are mudflats and shallow regions that receive direct discharges of stormwater and wastewater; as a result, they may have higher levels of urban contaminants than the open Bay. In the summer of 2017, the RMP collected samples of margin
sediment in the South and Lower South Bay for analysis of legacy contaminants. The study described here leveraged that sampling effort by adding monitoring of sediment and water for two additional sets of emerging contaminants: 1) current-use pesticides; and 2) fragrance ingredients including the polycyclic musk galaxolide, as well as a range of other commonly detected emerging contaminants linked to toxicity concerns such as endocrine disruption.

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Vaughn, L. Smith; Safran, S.; Robinson, A.; Whipple, A.; Richey, A.; Grenier, L.; Cloern, J.; Andrews, S.; Boyer, K.; Drexler, J.; et al. 2020. Delta Landscapes Primary Production: Past, Present, Future. SFEI Contribution No. 988.

This report describes the Delta Landscapes Primary Production project, which quantifies how landscape change in the Delta has altered the quantity and character of primary production. Combining historical and modern maps with simple models of production for five dominant plant and algae groups, we estimate primary production across the hydrologically connected Delta. We evaluate changes in primary production over time (between the early 1800s and early 2000s), between wet and dry years, and with future targets for landscape-scale restoration. For managers in the Delta, restoring historical patterns of primary productivity is a means to better support native fish and other wildlife. To better equip decision makers in managing for improved primary production, this study offers historical context and the best available science on the relative production value of habitat types and their configurations. 

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Foley, M.; Christian, E.; Goeden, B.; Ross, B. 2020. Expert review of the sediment screening guidelines for the beneficial reuse of dredged material in San Francisco Bay. SFEI Contribution No. 978. San Francisco Estuary Institute: Richmond, CA.

The beneficial reuse of dredged sediment is one strategy in a broader portfolio that is being developed for San Francisco Bay to help marshes adapt to rising sea level. Dredged sediment is currently being used in restoration projects around the Bay, but additional sediment is needed to meet the demand. The guidelines for determining if sediment is appropriate for beneficial reuse were developed twenty years ago. As part of assessing the role of dredged sediment in Bay restoration and adaptation strategies, the Regional Monitoring Program for Water Quality (RMP) and stakeholders recognized the need to revisit the beneficial reuse guidelines for dredged sediment. In September 2019, the RMP convened a workshop that included four technical experts to review the beneficial reuse guidelines. The experts were asked to answer three questions: 1) Are the current screening guidelines appropriate for beneficial reuse? 2) Is the current screening process appropriate and adequate? If not, what are your recommendations for improving it? and 3) How should bioaccumulation potential be addressed for the beneficial reuse of sediment? Based on the discussion of these three questions, six recommendations emerged from the workshop.

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Hung, C.; Klasios, N.; Zhu, X.; Sedlak, M.; Sutton, R. 2020. Methods Matter: Methods for Sampling Microplastic and Other Anthropogenic Particles and Their Implications for Monitoring and Ecological Risk Assessment. Integrated Environmental Assessment and Management 16 (6) . SFEI Contribution No. 1014.

To inform mitigation strategies and understand how microplastics affect wildlife, research is focused on understanding the sources, pathways, and occurrence of microplastics in the environment and in wildlife. Microplastics research entails counting and characterizing microplastics in nature, which is a labor‐intensive process, particularly given the range of particle sizes and morphologies present within this diverse class of contaminants. Thus, it is crucial to determine appropriate sampling methods that best capture the types and quantities of microplastics relevant to inform the questions and objectives at hand. It is also critical to follow protocols with strict quality assurance and quality control (QA/QC) measures so that results reflect accurate estimates of microplastic contamination. Here, we assess different sampling procedures and QA/QC strategies to inform best practices for future environmental monitoring and assessments of exposure. We compare microplastic abundance and characteristics in surface‐water samples collected using different methods (i.e., manta and bulk water) at the same sites, as well as duplicate samples for each method taken at the same site and approximate time. Samples were collected from 9 sampling sites within San Francisco Bay, California, USA, using 3 different sampling methods: 1) manta trawl (manta), 2) 1‐L grab (grab), and 3) 10‐L bulk water filtered in situ (pump). Bulk water sampling methods (both grab and pump) captured more microplastics within the smaller size range (<335 μm), most of which were fibers. Manta samples captured a greater diversity of morphologies but underestimated smaller‐sized particles. Inspection of pump samples revealed high numbers of particles from procedural contamination, stressing the need for robust QA/QC, including sampling and analyzing laboratory blanks, field blanks, and duplicates. Choosing the appropriate sampling method, combined with rigorous, standardized QA/QC practices, is essential for the future of microplastics research in marine and freshwater ecosystems.

Miller, E.; Klasios, N.; Lin, D.; Sedlak, M.; Sutton, R.; Rochman, C. 2020. Microparticles, Microplastics, and PAHs in Bivalves in San Francisco Bay. SFEI Contribution No. 976. San Francisco Estuary Institute: Richmond, CA.

California mussels (Mytilus californianus and hybrid Mytilus galloprovincialis / Mytilus trossulus) and Asian clams (Corbicula fluminea) were collected at multiple sites in San Francisco Bay. Mussels from a reference area with minimal urban influence were also deployed in cages for 90 days at multiple sites within the Bay prior to collection.Mussels from the reference time zero site, Bodega Head, had some of the lowest microparticle levels found in this study, along with resident clams from the San Joaquin and Sacramento Rivers and mussels transplanted to Pinole Point. The highest concentrations of microparticles were in mussels transplanted to Redwood Creek and Coyote Creek. The results of this study and current literature indicate that bivalves may not be good status and trends indicators of microplastic concentrations in the Bay unless the interest is in human health exposure via contaminated bivalve consumption.

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Soberón, F. Sánchez; Sutton, R.; Sedlak, M.; Yee, D.; Schuhmacher, M.; Park, J. - S. 2020. Multi-box mass balance model of PFOA and PFOS in different regions of San Francisco Bay. Chemosphere 252 . SFEI Contribution No. 986.

We present a model to predict the long-term distribution and concentrations of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) in estuaries comprising multiple intercommunicated sub-embayments. To that end, a mass balance model including rate constants and time-varying water inputs was designed to calculate levels of these compounds in water and sediment for every sub-embayment. Subsequently, outflows and tidal water exchanges were used to interconnect the different regions of the estuary. To calculate plausible risks to population, outputs of the model were used as inputs in a previously designed model to simulate concentrations of PFOA and PFOS in a sport fish species (Cymatogaster aggregata). The performance of the model was evaluated by applying it to the specific case of San Francisco Bay, (California, USA), using 2009 sediment and water sampled concentrations of PFOA and PFOS in North, Central and South regions. Concentrations of these compounds in the Bay displayed exponential decreasing trends, but with different shapes depending on region, compound, and compartment assessed. Nearly stable PFOA concentrations were reached after 50 years, while PFOS needed close to 500 years to stabilize in sediment and fish. Afterwards, concentrations stabilize between 4 and 23 pg/g in sediment, between 0.02 and 44 pg/L in water, and between 7 and 104 pg/g wet weight in fish, depending on compound and region. South Bay had the greatest final concentrations of pollutants, regardless of compartment. Fish consumption is safe for most scenarios, but due to model uncertainty, limitations in monthly intake could be established for North and South Bay catches.

Buzby, N.; Lin, D.; Sutton, R. 2020. Neonicotinoids and Their Degradates in San Francisco Bay Water. SFEI Contribution No. 1002. San Francisco Estuary Institute: Richmond, CA.

In the summer of 2017, open Bay water samples were collected during the RMP Status and Trends Water Cruise. Samples were analyzed for 19 neonicotinoids and metabolites. The only neonicotinoid detected was imidacloprid, an active ingredient used in both urban and agricultural applications. Imidacloprid was detected at a single site above the method detection limits (2.2-2.6 ng/L) in Lower South Bay at a level of 4.2 ng/L. This value is within the range of concentrations found in a separate RMP study in water samples collected from the South and Lower South Bay margins in 2017. Imidacloprid was detected at 3 of 12 of the margin sites at levels between 3.9 and 11 ng/L; no other neonicotinoids were detected. Of note, these RMP studies appear to represent the first evaluation of ambient neonicotinoid concentrations in an estuarine environment in the nation.

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Sun, J.; Sutton, R.; Ferguson, L.; Overdahl, K. 2020. New San Francisco Bay Contaminants Emerge. SFEI Contribution No. 931. San Francisco Estuary Institute: Richmond, CA.

In 2016, the RMP launched a novel investigation to detect new or unexpected contaminants in Bay waters, as well as treated sewage (or wastewater) discharged to the Bay. This study used non-targeted analysis, a powerful tool that provides a broad, open-ended view of thousands of synthetic and naturally-derived chemicals simultaneously. We identified hundreds of contaminants, and the results have opened our eyes to urban stormwater runoff as an important pathway for emerging contaminants to enter the Bay.

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Gilbreath, A.; Hunt, J.; Mckee, L. 2020. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015 - 2019. SFEI Contribution No. 987. San Francisco Estuary Institute: Richmond, CA.

Reconnaissance monitoring for water years 2015, 2016, 2017, 2018 and 2019 was completed with funding provided by the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). This report is designed to be updated each year until completion of the study. At least one additional water year (2020) is underway. An earlier draft of this report was prepared for the Bay Area Stormwater Management Agencies Association (BASMAA) in support of materials submitted on or before March 31st 2020 in compliance with the Municipal Regional Stormwater Permit (MRP) Order No. R2-2015-0049.

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Miller, E.; Sedlak, M.; Lin, D.; Box, C.; Holleman, C.; Rochman, C. M.; Sutton, R. 2020. 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.

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.

Baumgarten, S.; Grossinger, R.; Bazo, M.; Benjamin, M. 2020. Re-Oaking North Bay. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.
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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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Kauhanen, P.; Lowe, S. 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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