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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.2018. (4.09 MB)
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).
Microbial Water Quality at Minimally Human-Impacted Reference Beaches in Northern California. SFEI Contribution No. 858. San Francisco Estuary Institute : Richmond, CA.2018. (3.87 MB)
Non-Targeted Analysis of Water-Soluble Compounds Highlights Overlooked Contaminants and Pathways (Coming Soon). SFEI Contribution No. 905. San Francisco Estuary Institute: Richmond, CA.2018.
North Bay Mercury Biosentinel Project: 2016 - 2017. SFEI Contribution No. 868.2018. (1.59 MB)
North Bay Selenium Monitoring Design. SFEI Contribution No. 921. San Francisco Estuary Institute : Richmond, CA.2018. (2.08 MB)
Observational Study of Sycamore Regeneration at two sites in Santa Clara County after the 2016-2017 Water Year. SFEI Contribution No. 874.2018. (8.44 MB)
Per and Polyfluoroalkyl Substances (PFAS) in San Francisco Bay: Synthesis and Strategy. SFEI Contribution No. 867. San Francisco Estuary Institute : Richmond, CA.2018. (3.2 MB)
Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.2018. (121.7 MB) (43.68 MB)
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.
Pollutants of Concern Reconnaissance Monitoring Water Years 2015, 2016, and 2017. SFEI Contribution No. 840. San Francisco Estuary Institute: Richmond, CA.2018. (5.55 MB)
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 40.2018. (68.63 MB) (20.14 MB)
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.
Resilient Landscape Vision for Upper Penitencia Creek. SFEI Contribution No. 894. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.2018. (67.6 MB) (11.75 MB)
RMP Small Tributaries Loading Strategy: Modeling and Trends Strategy 2018. SFEI Contribution No. 886. San Francisco Estuary Institute : Richmond, CA.2018. (1.3 MB)
Screening of Pharmaceuticals in San Francisco Bay Wastewater. SFEI Contribution No. 910. San Francisco Estuary Institute : Richmond, CA.2018. (1.06 MB)
Sediment Supply to San Francisco Bay. SFEI Contribution No. 842. San Francisco Estuary Institute : Richmond, CA.2018. (1.74 MB)
Selenium in Muscle Plugs of White Sturgeon from North San Francisco Bay, 2015-2017. SFEI Contribution No. 929. San Francisco Estuary Institute : Richmond, CA.2018. (2.24 MB)
Selenium in White Sturgeon from North San Francisco Bay: The 2015-2017 Sturgeon Derby Study - (Coming Soon). SFEI Contribution No. 897. San Francisco Estuary Institute : Richmond, CA.2018.
Statistical Methods Development and Sampling Design Optimization to Support Trends Analysis for Loads of Polychlorinated Biphenyls from the Guadalupe River in San Jose, California, USA. SFEI Contribution No. 876. Applied Marine Sciences: Livermore, CA.2018. (1.76 MB)
Status & Trends Monitoring Design: 2018 Update. San Francisco Estuary Institute : Richmond, CA.2018. (1.13 MB)
Support for Sediment Bioaccumulation Evaluation: Toxicity Reference Values for the San Francisco Bay. SFEI Contribution No. 916. San Francisco Estuary Institute : Richmond, CA.2018. (317.14 KB)
Sycamore Alluvial Woodland Planting Guide. SFEI Contribution No. 901.2018. (1.22 MB)
Translating Science-Based Restoration Strategies into Spatially-Explicit Restoration Opportunities in the Delta (2018 Bay-Delta Science Conference Presentation).2018. (3.78 MB)
In a previous report titled “A Delta Renewed” we offered a collection of guidelines for science-based ecological restoration in the Sacramento-San Joaquin Delta that emphasized restoring or emulating natural processes, anticipating future changes associated with climate change, establishing appropriate configurations of habitat types at the landscape scale, and utilizing a variety multi-benefit management strategies. In this talk, we present on our recent work to support regional restoration planning efforts by developing a repeatable process for using these guidelines to identify spatially-explicit restoration opportunities. The process is largely GIS-based and utilizes spatial data on existing land cover and conservation status, habitat configuration (including patch sizes and distances), surface elevations (including depth of subsidence), and future changes in tidal elevations associated with sea-level rise. By distilling generalized guidelines into spatially-explicit opportunities, we hope to provide a practical tool for incorporating science into planning. To that end, these new methods are currently being piloted through planning efforts focused on the Central Delta Corridor and the McCormack Williamson Tract, and are also being used to assist with the quantification of ecological restoration potential in the Delta Plan Ecosystem Amendment.
Presentation recording: available here.
2016 RMP Bird Egg Samples Quality Assurance Report. San Francisco Estuary Institute: Richmond, CA.2017. (332.09 KB)
2016 RMP Bivalve Samples Quality Assurance Report. San Francisco Estuary Institute : Richmond, CA.2017. (284.38 KB)
2017 Margins Microplastics Cruise Report. SFEI Contribution No. 848. Coastal Conservancy & Research: Moss Landing, CA.2017. (1.95 MB)
2017 Margins Sediment Cruise Plan. SFEI Contribution No. 847. San Francisco Estuary Institute : Richmond, CA.2017. (919.33 KB)
2017 Quality Assurance Program Plan for the Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI Contribution No. 828. San Francisco Estuary Institute: Richmond, CA.2017. (4.26 MB)
2017 RMP Detailed Workplan and Budget. San Francisco Estuary Institute: Richmond, CA.. 2017. (2.27 MB)
2017 RMP Multi-Year Plan. San Francisco Estuary Institute: Richmond, CA.. 2017. (2.14 MB)
2017 RMP Water Cruise Plan. SFEI Contribution No. 845. San Francisco Estuary Institute : Richmond, CA.2017. (3.63 MB)
2017 RMP Water Cruise Report. SFEI Contribution No. 846. Applied Marine Sciences: Livermore, CA.2017. (1.16 MB)
2018 RMP Detailed Workplan and Budget. San Francisco Estuary Institute : Richmond, CA.2017. (390.05 KB)
Annotated Bibliography for Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project.. 2017. (769.62 KB)
One component of the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project is this annotated bibliography of existing scientific literature pertaining to California sycamore ecology. This annotated bibliography is a product of an extensive review into documents, mapping efforts, and personal communications, and presents sources that have been determined to be relevant to understanding the factors that influence California sycamore health and regeneration in central California. The annotated bibliography is divided into the following sections by topic: General Ecology; Historical and Present Distribution; Restoration Ecology and Management; Wildlife Ecology; Geomorphology; Hydrology and Soils; and Health and Regeneration. Each item is briefly summarized and its relevance to the project is described. References that fall under multiple categories are cross-referenced within the document. Similarly, key words are indicated or each reference to highlight various subtopics affecting California sycamore ecology.
Applied Aquatic Science: A Business Plan for EcoAtlas. San Francisco Estuary Institue: Richmond, CA.2017. (1.69 MB) (323.4 KB) (214.45 KB)
The following plan is intended to ensure the continued vitality of the toolset. The plan’s success will depend upon the continued collaboration of the public agencies that have supported the toolset thus far, but it must also integrate principles of resilience as it accounts for the tensions that arise as organizations move in different strategic directions.
Assessing the Impact of Periodic Dredging on Macroinvertebrate-Prey Availability for Benthic Foraging Fishes: Final Study Plan and Preliminary Pilot Study Results. SFEI Contribution No. 833. U.S. Geological Survey: Vallejo, CA.2017. (1.88 MB)
Changing Channels: Regional Information for Developing Multi-benefit Flood Control Channels at the Bay Interface. Flood Control 2.0. SFEI Contribution No. 801. San Francisco Estuary Institute: Richmond, CA.2017. (62.69 MB) (23.02 MB)
Over the past 200 years, many of the channels that drain to San Francisco Bay have been modified for land reclamation and flood management. The local agencies that oversee these channels are seeking new management approaches that provide multiple benefits and promote landscape resilience. This includes channel redesign to improve natural sediment transport to downstream bayland habitats and beneficial re-use of dredged sediment for building and sustaining baylands as sea level continues to rise under a changing climate. Flood Control 2.0 is a regional project that was created to help develop innovative approaches for integrating habitat improvement and resilience into flood risk management at the Bay interface. Through a series of technical, economic, and regulatory analyses, the project addresses some of the major elements associated with multi-benefit channel design and management at the Bay interface and provides critical information that can be used by the management and restoration communities to develop long-term solutions that benefit people and wildlife.
This Flood Control 2.0 report provides a regional analysis of morphologic change and sediment dynamics in flood control channels at the Bay interface, and multi-benefit management concepts aimed at bringing habitat restoration into flood risk management. The findings presented here are built on a synthesis of historical and contemporary data that included input from Flood Control 2.0 project scientists, project partners, and science advisors. The results and recommendations, summarized below, will help operationalize many of the recommendations put forth in the Baylands Ecosystem Habitat Goals Science Update (Goals Project 2015) and support better alignment of management and restoration communities on multi-benefit bayland management approaches.
Characterization of Sediment Contamination in Central Bay Margin Areas. SFEI Contribution No. 829. San Francisco Estuary Institute: Richmond, CA.2017. (2.89 MB)
Charter: Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI Contribution No. 844. San Francisco Estuary Institute : Richmond, CA.2017. (1.68 MB)
Conceptual Model to Support PCB Management and Monitoring in the Emeryville Crescent Priority Margin Unit. SFEI Contribution No. 824. San Francisco Estuary Institute: Richmond, CA.2017. (3.08 MB)
Conceptual Model to Support PCB Management and Monitoring in the San Leandro Bay Priority Margin Unit: Phase I. SFEI Contribution No. 830. San Francisco Estuary Institute: Richmond, CA.2017. (14.6 MB)
Contaminant Concentrations in Sport Fish from San Francisco Bay, 2014. SFEI Contribution No. 806.2017. (1.42 MB)
Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations. 2017 Revision. SFEI Contribution No. 815. San Francisco Estuary Institute: Richmond, CA.2017. (5.51 MB)
Delta Landscapes: A Delta Renewed User Guide. SFEI Contribution No. 854.2017. (28.86 MB)
A Delta Renewed User Guide aims to increase the accessibility of the technical findings in A Delta Renewed for easier application to restoration and conservation efforts across the Delta. The recommendations in A Delta Renewed focus on landscape-scale ecological guidance. We present three examples of how the information in A Delta Renewed might be used to address different management and restoration questions. Because of the complexity of the Delta system, this guide does not address all possible questions and does not replace the need for detailed, site-specific data and expertise. Rather, it shows how the information in A Delta Renewed might provide a common foundation for restoration planning.
The User Guide was written for a broad audience, including restoration practitioners, landowners, and local, state and federal agencies. The guide provides a step-by-step path through A Delta Renewed; a user is walked through how to apply the findings of the report via a series of steps to address each of the three restoration and management questions. This process is intended to help the user access regionally-specific recommendations and strategies to plan and manage future Delta landscapes that can support desired ecological functions over the long term.
The goal of A Delta Renewed and this guide is not to recreate the Delta of the past. Rather, the objective is to understand how we can re-establish or mimic important natural processes and patterns within this altered system to support desirable ecological functions (such as healthy native fish populations, a productive food web, and support for endangered species), now and into the future.
Delta Landscapes Executive Summary. SFEI Contribution No. 853.2017. (23.99 MB)
Demonstration of a Watershed Approach to Wetland Restoration Planning for Load Reductions: A Pilot Demonstration Project Using GreenPlan-IT in the Santa Rosa Plain, Sonoma County, California. SFEI Contribution No. 996. San Francisco Estuary Institute: Richmond. CA.. 2017. (761.48 KB) (420.02 KB) (1.29 MB) (1.67 MB) (2.09 MB)
This summary memorandum presents technical recommendations to the 401 Certification and Waste Discharge Program (401 Program) of the State Water Resources Control Board (State Board) for a coherent, scientifically sound, repeatable, watershed approach to wetland restoration site evaluation, compliance monitoring and assessment, and Tracking. The recommendations are drawn from the previous four memoranda produced for the Pilot Demonstration Project (Project) that address the following subjects: project work plan and information flow diagram; scientific literature review; landscape scenario planning (to map and prioritize restoration opportunities); and a framework for a watershed-approach to evaluate and report the capacity of a wetland restoration site to protect wetland beneficial uses.
This Project focused on a sub-watershed of the Santa Rosa Plain, in Sonoma County, California. The area was chosen for the Project for three reasons: (1) it is integral to an existing nutrient TMDL and therefore is supported relatively well with hydrological and nutrient data; (2) the historical and existing wetlands and streams of the area were mapped recently in sufficient detail to inform landscape planning; and (3) implementation of the TMDL will involve wetland restoration to reduce downstream nutrient loads, and therefore the Project may help implement the TMDL.
The primary overall purpose of this Project was to explore how numerical simulation and statistical modeling could be combined with existing wetland assessment and reporting tools to create a coherent, watershed-based approach to wetland beneficial use protection. Any relevance to the existing nutrient TMDL for the demonstration area is an intentional, but secondary benefit of this Project.
The effects of kaolin clay on the amphipod Eohaustorius estuarius: Part Two. SFEI Contribution No. 822.2017. (1.43 MB)
Estuary-wide Data Repository for Delta Environmental Data to Understand a California Estuary Poster (2017).2017. (894.14 KB)
From Sediment to Top Predators: Broad Exposure of Polyhalogenated Carbazoles in San Francisco Bay (U.S.A.). Environmental Science and Technology 51, 2038-2046.2017.
The present study provides the first comprehensive investigation of polyhalogenated carbazoles (PHCZ) contamination in an aquatic ecosystem. PHCZs have been found in soil and aquatic sediment from several different regions, but knowledge of their bioaccumulation and trophodynamics is extremely scarce. This work investigated a suite of 11 PHCZ congeners in San Francisco Bay (United States) sediment and organisms, including bivalves (n = 6 composites), sport fish (n = 12 composites), harbor seal blubber (n = 18), and bird eggs (n = 8 composites). The most detectable congeners included 3,6-dichlorocarbazole (36-CCZ), 3,6-dibromocarbazole (36-BCZ), 1,3,6-tribromocarbazole (136-BCZ), 1,3,6,8-tetrabromocarbazole (1368-BCZ), and 1,8-dibromo-3,6-dichlorocarbazole (18-B-36-CCZ). The median concentrations of ΣPHCZs were 9.3 ng/g dry weight in sediment and ranged from 33.7 to 164 ng/g lipid weight in various species. Biomagnification was observed from fish to harbor seal and was mainly driven by chlorinated carbazoles, particularly 36-CCZ. Congener compositions of PHCZs differed among species, suggesting that individual congeners may be subject to different bioaccumulation or metabolism in species occupying various trophic levels in the studied aquatic system. Toxic equivalent (TEQ) values of PHCZs were determined based on their relative effect potencies (REP) compared to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The median TEQ was 1.2 pg TEQ/g dry weight in sediment and 4.8 – 19.5 pg TEQ/g lipid weight in biological tissues. Our study demonstrated the broad exposure of PHCZs in San Francisco Bay and their characteristics of bioaccumulation and biomagnification along with dioxin-like effects. These findings raise the need for additional research to better elucidate their sources, environmental behavior, and fate in global environments.
Historical Ecology and Landscape Change in the Central Laguna de Santa Rosa. SFEI Contribution No. 820. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.2017. (94.51 MB) (39.07 MB)
This study synthesizes a diverse array of data to examine the ecological patterns, ecosystem functions, and hydrology that characterized a central portion of the Laguna de Santa Rosa during the mid-19th century, and to analyze landscape changes over the past 150 years. The primary purpose of this study was to help guide restoration actions and other measures aimed at reducing nutrient loads within this portion of the Laguna de Santa Rosa watershed.
Linkage of In Vitro Assay Results With In Vivo End Points, Phases 1 and 2. SFEI Contribution No. 823.2017. (14.2 MB)
Long-term variation in concentrations and mass loads in a semi-arid watershed influenced by historic mercury mining and urban pollutant sources. Science of The Total Environment 605-606, 482-497 . SFEI Contribution No. 831.2017.
Lower Peninsula Watershed Condition Assessment 2016: Southwest San Francisco Bay, Santa Clara County, San Francisquito to Stevens Creeks. Technical memorandum prepared for the Santa Clara Valley Water District. . SFEI Contribution No. 809. San Francisco Estuary Institute: Richmond. p 53.2017. (5.17 MB)
Microplastic Monitoring and Science Strategy for San Francisco Bay. SFEI Contribution No. 798. San Francisco Estuary Institute: Richmond, Calif.2017. (17.38 MB)
MS4 2009 Permit Monitoring Results (2010-2015) Summary of Sonoma County Water Agency’s Data for two Sites in Santa Rosa Creek. SFEI Contribution No. 832. San Francisco Estuary Institute: Richmond. CA. p 35.2017. (1.43 MB)
This memo summarizes the Sonoma County Water Agency's 2009 receiving water monthly monitoring results for the North Coast Regional Water Quality Control Board's NPDES Permit No. R1-2009-0050. The data were compiled, formatted and uploaded to SFEI’s Regional Data Center and are availble through CEDEN (https://ceden.waterboards.ca.gov/AdvancedQueryTool) under the Program Name "Russian River MS4 Program" and Project Names "2009 5 year Permit for RR_MS4 Program SCWA" and "2009 5 year Permit for RR_MS4 Program CSR". The memo summarizes field measures and water chemistry, bacteria, and toxiciity results from two receving waters sites in Santa Rosa Creek downstream (C1-SRC-D) and upstream of the City of Santa Rosa.
This memo was funded by a Suplemental Environmental Project (SEP) settlement of an enforcement action by the North Coast Regional Water Quality Control Board against the County of Sonoma. 2016.
Nutrient Management Strategy Science Program. SFEI Contribution No. 879. San Francisco Estuary Institute: Richmond, CA.2017. (49.7 MB)
Passage of fiproles and imidacloprid from urban pest control uses through wastewater treatment plants in northern California. Environmental Toxicology and Chemistry 36, 1473-1482 . SFEI Contribution No. 783.2017.
Urban pest control insecticides, specifically fipronil and its four major degradates (fipronil sulfone, sulfide, desulfinyl, and amide) and imidacloprid, were monitored during drought conditions in eight San Francisco Bay wastewater treatment plants (WWTPs). In influent and effluent, ubiquitous detections were obtained in units of ng/L for fipronil (13-88), fipronil sulfone (1-28), fipronil sulfide (1-5) and imidacloprid (58-306). In influent, 100% of imidacloprid and 62 ± 9% of total fiproles (fipronil and degradates) were present in the dissolved state, with the balance being bound to filter-removable particulates. Targeted insecticides persisted during wastewater treatment, regardless of treatment technology utilized (imidacloprid: 93 ± 17%; total fiproles: 65 ± 11%), with partitioning into sludge (3.7-151.1 μg/kg dry weight as fipronil) accounting for minor losses of total fiproles entering WWTPs. The load of total fiproles was fairly consistent across the facilities but fiprole speciation varied. This first regional study on fiprole and imidacloprid occurrences in raw and treated California sewage revealed ubiquity and marked persistence to conventional treatment of both phenylpyrazole and neonicotinoid compounds. Flea and tick control agents for pets are identified as potential sources of pesticides in sewage meriting further investigation and inclusion in chemical-specific risk assessments.
Per- and polyfluoroalkyl substances (PFAS) in San Francisco Bay wildlife: Temporal trends, exposure pathways, and notable presence of precursor compounds. Chemosphere 185, 1217-1226 . SFEI Contribution No. 839.2017.
Pilot Study of Contaminants of Emerging Concern (CECs) in the Russian River Watershed: Lessons Learned. SFEI Contribution No. 852. San Francisco Estuary Institute: Richmond, CA.2017. (796.56 KB)
Pollutants of Concern Monitoring: A low-intensity, budget conscious stormwater sampling method to identify highly polluted areas for potential management action .2017. (1.92 MB)
Pollutants of concern reconnaissance monitoring final progress report, water years 2015 and 2016. SFEI Contribution No. 817.2017. (4.01 MB)
The Pulse of the Bay: The 25th Anniversary of the RMP. SFEI Contribution No. 841. San Francisco Estuary Institute: Richmond, CA.. 2017. (15.72 MB)
Regional Watershed Spreadsheet Model (RWSM): Year 6 Progress Report. SFEI Contribution No. 811. San Francisco Estuary Institute: Richmond, CA.2017. (1.79 MB)
Re-Oaking Silicon Valley: Building Vibrant Cities with Nature. SFEI Contribution No. 825. San Francisco Estuary Institute: Richmond, CA.2017. (65.64 MB) (31.88 MB)
In this report, we investigate how re-integrating components of oak woodlands into developed landscapes — “re-oaking” — can provide an array of valuable functions for both wildlife and people. Re-oaking can increase the biodiversity and ecological resilience of urban ecosystems, improve critical urban forest functions such as shade and carbon storage, and enhance the capacity of cities to adapt to a changing climate. We focus on Silicon Valley, where oak woodland replacement by agriculture and urbanization tells a story that has occurred in many other cities in California. We highlight how the history and ecology of the Silicon Valley landscape can be used as a guide to plan more ecologically-resilient cities in the Bay Area, within the region and elsewhere in California. We see re-oaking as part of, and not a substitute for, the important and broader oak woodland conservation efforts taking place throughout the state.
RMP Field Sampling Report 2016. SFEI Contribution No. 826. San Francisco Estuary Institute: Richmond, CA.2017. (1.08 MB)
Sampling and Analysis Plan for Microplastic Monitoring in San Francisco Bay and Adjacent National Marine Sanctuaries. SFEI Contribution No. 819. San Francisco Estuary Institute: Richmond, CA.2017. (5 MB)
San Francisco Bay California Toxics Rule Priority Pollutant Ambient Water Monitoring Report. SFEI Contribution No. 814. San Francisco Estuary Institute: Richmond.2017. (1.92 MB)
San Francisco Bay Interim Model Validation Report. SFEI Contribution No. 850. San Francisco Estuary Institute: Richmond, CA.2017. (34.98 MB)
San Leandro Bay PCB Study Data Report. SFEI Contribution No. 855. San Francisco Estuary Institute: Richmond, CA.2017. (3.39 MB)
Selenium in White Sturgeon Tissues: 2015 Sturgeon Derby. SFEI Contribution No. 834.2017. (1.85 MB)
Summary of Workshop on Monitoring for Acidification Threats in West Coast Estuaries: A San Francisco Bay Case Study.2017. (2.04 MB)
Sycamore Alluvial Woodland: Habitat Mapping and Regeneration Study. SFEI Contribution No. 816.2017. (53.95 MB) (21.31 MB)
This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and natural settings. Using an array of ecological and geomorphic field analyses, we discuss site characteristics favorable to SAW health and regeneration, make recommendations for restoration and management, and identify next steps. Findings from this study will contribute to the acquisition, restoration, and improved management of SAW as part of the Santa Clara Valley Habitat Plan (VHP).
Tijuana River Valley Historical Ecology Investigation. Prepared for the State Coastal Conservancy. A Report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 760. San Francisco Estuary Institute - Aquatic Science Center : Richmond, CA. p 230.2017. (232.2 MB) (73.63 MB)
The Tijuana River Valley Historical Ecology Investigation addresses a regional data gap by reconstructing the landscape and ecosystem characteristics of the river valley prior to the major modifications of the late 19th and 20th centuries. The research presented here, funded by the California State Coastal Conservancy, supplies foundational information at the regional and system scale about how the Tijuana Estuary, River, and valley looked and functioned in the recent past, as well as how they have changed over time. The ultimate goal of this study is to provide a new tool and framework that, in combination with contemporary research and future projections, can support and guide ongoing restoration design, planning, and management efforts in the valley.
Water and Suspended-Sediment Flux Measurements at the Golden Gate, 2016-2017. SFEI Contribution No. 856.2017. (2.41 MB)
Water Column Selenium Concentrations in the San Francisco Bay-Delta: Recent Data and Recommendations for Future Monitoring. SFEI Contribution No. 836.2017. (2.56 MB)
A Watershed Approach to Restoration and Mitigation Planning, Monitoring, and Assessment Based on the Wetland and Riparian Area Monitoring Plan (WRAMP): Addendum to the Upper Pajaro River Watershed Assessment 2015. SFEI Contribution No. 818. San Francisco Estuary Institute: Richmond. CA. p 30.2017. (2 MB)
This report demonstrates a possible watershed-based approach to evaluating mitigation sites using the California Rapid Assessment Method (CRAM). The Santa Clara Valley Water District (Valley Water) is leading the Llagas Creek Flood Control Project in the upper Pajaro River watershed, Santa Clara County, CA. Mitigation for the Project involves enhancing riverine wetlands on-site (within the flood control channel) and restoring riverine wetlands and enhancing depressional wetlands at Lake Silveira, in the Llagas Creek watershed. Valley Water is incorporating CRAM into its planning and assessment of mitigation efforts and Valley Water's Priority D.5 Project's Pajaro River Watershed ambient stream condition survey (2015) provided the watershed context for evaluating project conditions against the general ecological conditions of streams within the watershed - employing CRAM. This WRAMP demonstration compared pre-project ecological condition assessments (employing CRAM) from the project's impact and mitigation sites to ambient watershed conditions and estimated the amount of ecological lift expected in the future as a result of the planned mitigation and restoration efforts.
2015 Annual Monitoring Report. SFEI Contribution No. 775. San Francisco Estuary Institute: Richmond, CA.. 2016. (3.28 MB)
2016 Quality Assurance Program Plan for the Regional Monitoring Program for Water Quality in San Francisco Bay.2016. (3.1 MB)
2016 Regional Monitoring Program Update. SFEI Contribution No. 790. San Francisco Estuary Institute: Richmond, CA.. 2016. (6.27 MB)
2016 RMP Detailed Workplan and Budget. San Francisco Estuary Institue: Richmond, CA.. 2016. (1.73 MB)
2016 RMP Multi-Year Plan. San Francisco Estuary Institute: Richmond, CA.. 2016. (5.57 MB)
2016 RMP Sturgeon Derby Study Sampling & Analysis Plan. San Francisco Estuary Institute : Richmond, CA.. 2016. (250.62 KB)
2016 Updated ambient concentrations of toxic chemicals in San Francisco Bay area sediments. San Francisco Estuary Institute: Richmond, CA.2016. (3.1 MB)
California Wetland and Riparian Area Protection Policy. Technical Advisory Team. Technical Memorandum No. 5: Stream Definition (Final Draft). SFEI Contribution No. 1001.. 2016. (816.97 KB)
Contaminant Concentrations in Eggs of Double-crested Cormorants and Forster's Terns from San Francisco Bay: 2002-2012. SFEI Contribution No. 736.2016. (1.42 MB)
A Delta Renewed: A Guide to Science-Based Ecological Restoration in the Sacramento-San Joaquin Delta. Delta Landscapes Project. Prepared for the California Department of Fish and Wildlife and Ecosystem Restoration Program. A Report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 799. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.2016. (121.28 MB) (17.67 MB)
This report offers guidance for creating and maintaining landscapes in the Sacramento-San Joaquin Delta that support desired ecological functions, while retaining the overall agricultural character and water-supply service of the region. Based on extensive research into how the Delta functioned historically, how it has changed, and how it is likely to evolve, we discuss where and how to re-establish the dynamic natural processes that can sustain native Delta habitats and wildlife into the future. The approach, building on work others have piloted and championed, is to restore or emulate natural processes where possible, establish an appropriate mosaic of habitat types at the landscape scale, use multi-benefit management strategies to increase support for native species in agricultural and urban areas, and allow the Delta to adapt to future uncertainties of climate change, levee failure, and human population growth. With this approach, it will be critical to integrate ecological improvements with the human landscape: a robust agricultural economy, water infrastructure and diversions, and urbanized areas. Strategic restoration that builds on the history and ecology of the region can contribute to the strong sense of place and recreational value of the Delta.
Printed copies of the report are available for purchase.
EcoAtlas: Enhancing Regional Capacity for Habitat Restoration Project Tracking, Assessment and Reporting.. 2016. (6.61 MB)
2016. EcoAtlas - Lake Tahoe Environmental Improvement Program: Tool Integration White Paper. SFEI Contribution No. 800.(703.29 KB)
Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary: Phase II Technical Memorandum. SFEI Contribution No. 786.2016. (955.14 KB)
The physical and ecological environment of the upper San Francisco Estuary has been profoundly altered since the early 1800s. Recent efforts have utilized maps of the upper estuary’s historical habitat types to infer associated changes in desired ecosystem processes and functions. The work presented in this memo builds on these previous efforts, but utilizes a new tool for evaluating change over time: a 3D hydrodynamic model of the pre-development estuary. This model was constructed by Resource Management Associates (RMA) using a new digital elevation model of the pre-development upper estuary generated by SFEI and UC Davis (UCD) and “natural” boundary flows calculated by the California Department of Water Resources (CDWR).
Once completed and calibrated, the pre-development model was paired with a similar model of the contemporary system in order to analyze hydrodynamic changes in the upper estuary. These analyses are presented in a technical memorandum published by RMA (2015). This memorandum takes these analyses and considers the ecological implications of modeled changes (see the “Results” section). Hydrodynamic analyses include analyzing changes in tidal prism, isohaline positions, low-salinity zone habitat, channel velocity, and source water distribution.
In addition to describing the ecological implications of modeled hydrodynamic changes, this memorandum summarizes major ongoing questions about estuarine hydrodynamics that might be explored using these models, including changes in water residence time, temperature, transport pathways, and the connectivity of aquatic and semi-aquatic habitats. Understanding changes in these and other factors would greatly improve our understanding of the desirable ecosystem functions provided by the historical system and, as a result, improve our ability to recover these functions now and into the future.