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Robinson, A.; Beagle, J.; Safran, S. M.; McKnight, K.; Grenier, J. Letitia; Askevold, R. A. 2017. Delta Landscapes: A Delta Renewed User Guide. SFEI Contribution No. 854.

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.

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Jabusch, T. W.; Bernstein, B. 2010. Delta Regional Monitoring Program. Aquatic Science Center: Oakland, CA.
Jabusch, T.; Trowbridge, P.; Heberger, M.; Orlando, J.; De Parsia, M.; Stillway, M. 2018. Delta Regional Monitoring Program Annual Monitoring Report for Fiscal Year 2015–16: Pesticides and Toxicity. SFEI Contribution No. 864. Aquatic Science Center: Richmond, CA.

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

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

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

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

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

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

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

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

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Robinson, A.; Safran, S. M.; Beagle, J.; Grenier, J. Letitia; Grossinger, R. M.; Spotswood, E.; Dusterhoff, S. D.; Richey, A. 2016. 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.

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.

 

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Gunther, A.; Thompson, B. 2004. Development of Environmental Indicators of the Condition of San Francisco Estuary. SFEI Contribution No. 113. San Francisco Estuary Institute: Oakland.
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Connor, M.; Yee, D.; Davis, J. A.; Werme, C. 2004. Dioxins in San Francisco Bay: Conceptual Model/Impairment Assessment. SFEI Contribution No. 309. San Francisco Estuary Institute: Oakland. p 60.
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Cohen, A. N.; McGann, M.; Sloan, D. 1996. Documenting the intorduction of estuarine foraminifers: a San Francisco Bay Study. Ann. Mtg., Geological Society of America, Denver, CO, Oct. 1996 (abstract).
Smith, R.; Riege, L. 1996. DOD Sediment Criteria Project Ambient Analysis Draft Interim Report. SFEI Contribution No. 9. San Francisco Regional Water Quality Control Board: Oakland, CA.
Foley, M. 2019. DRAFT - 2020 RMP Multi-Year Plan. SFEI Contribution No. 959. San Francisco Estuary Institute: Richmond, CA.
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Collins, J. N.; Sutula, M.; Stein, E. 2003. DRAFT California Rapid Assessment (CRAM) Verification Approach. SFEI Contribution No. 283. San Francisco Estuary Institute: Oakland, CA. p p. 9.
Collins, J. N. 2003. Draft Guidelines for Developing the CRAM Metrics. SFEI Contribution No. 284. San Francisco Estuary Institute: Oakland, CA. p 2.
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Oram, J. J.; Leatherbarrow, J. E.; Davis, J. A. 2005. DRAFT REPORT: A Model of Long-Term PCB Fate and Transport in San Francisco Bay, CA. SFEI Contribution No. 388. San Francisco Estuary Institute: Oakland, CA.
Oram, J. J.; Melwani, A. R. 2006. Dredging Impacts on Food-Web Bioaccumulation of DDTs in San Francisco Bay, CA. SFEI Contribution No. 418. San Francisco Estuary Institute: Oakland, CA.
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Bigelow, P.; Pearce, S.; McKee, L. J. . 2009. Dry Creek Watershed Sediment Source Reconnaissance Technical Memorandum. SFEI Contribution No. 595. San Francisco Estuary Institute: Oakland,Ca.
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Davis, J. A. 1986. Ecological guidelines for the use of natural wetlands for municipal wastewater management in North Carolina. SFEI Contribution No. 134. Division of Environmental Management, North Carolina Department of Natural Resources and Community Development: Raleigh, NC.
Safran, S. M.; Grenier, J. Letitia; Grossinger, R. M. 2016. Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary: Phase II Technical Memorandum. SFEI Contribution No. 786.

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.

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Anderson, B.; Phillips, B.; Voorhees, J. 2015. The Effects of Kaolin Clay on the Amphipod Eohaustorius estuarius. SFEI Contribution No. 755. Department of Environmental Toxicology, University of California, Davis: Davis, CA.

Several lines of evidence from the Regional Monitoring Program and other studies have suggested that sediment grain size characteristics influence amphipod (Eohaustorius estuarius) survival in 10 day toxicity tests.  Two workshops were convened to address the influence of non-contaminant factors on amphipod toxicity tests, and the current project was prioritized based on the recommendations of experts participating in these workshops.  The study was designed to investigate the effects of kaolin clay on amphipod survival since this is the dominant clay type in Francisco Estuary sediments.  In these experiments reference sand was spiked with increasing concentrations of kaolin to determine whether there was a dose-based relationship between amphipod mortality and increasing concentrations of this type of clay. Wild-caught E. estuarius were collected from Beaver Creek Beach (Oregon) and supplied by Northwest Aquatic Sciences. The initial experiment did not demonstrate a dose-response relationship: E. estuarius survival in all concentrations from 10% to 100% kaolin was lower than in the sand control, and survival in the clay spiked sand was also highly variable.  This experiment exposed a mixture of amphipod size classes representative of those typically provided by the amphipod supplier.  Reasoning that variable response to clay was related to variable tolerances by the different amphipod size classes, a follow-up experiment was conducted to investigate this relationship.  Amphipods were separated into small, medium and large size classes and these were exposed to 100% kaolin.  These results showed survival in 100% clay was 86%, 82% and 66% by small, medium and large amphipods, respectively.  To further investigate size-related responses to clay, small, medium and large amphipods were exposed to concentrations of sand spiked with clay from 0 to 100%.  The results of this experiment showed that smaller amphipods tolerated high clay concentrations better than larger animals, but there was not a strict monotonic dose-response relationship.  Conclusions based on this experiment were constrained by an inability to sort amphipods into three distinct size classes, because there were not enough of the largest animals present at the Oregon collection site.  In addition, grain size analysis of the sand spiked clay suggested that the clay tended to flocculate in the treatments above 70% kaolin.  This experiment was repeated when three distinct size classes were present in December 2014.  The results of this experiment also showed that smaller amphipods tolerated high kaolin better than larger amphipods.  As in the previous experiment, there was not a monotonic response to clay, especially at the higher kaolin concentrations, and the grain size analysis also showed flocculation occurred in the highest clay treatments.  Despite these inconsistencies, the results of this experiment suggest that tolerance of E. estuarius to clay varies with amphipod size.  Average survival was 81%, 79%, and 65% for small, medium and large amphipods, respectively in concentrations > 50% clay.  Possible mechanisms for size specific clay effects on this amphipod species include lower survival related to reduced energy reserves in larger animals, inhibition of gill function, and inhibition of feeding and locomotion through clogging of amphipod setae.  The results suggest that use of smaller amphipods in routine monitoring of high clay sediments will reduce the influence of this factor on test results.  Additional experiments with high clay reference site sediments from San Francisco Bay are recommended to confirm the size related response with field sediments.

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Clark, S.; Bailey, H. C.; Davis, J. A. 1995. The Effects of Toxic Contaminants in Waters of the San Francisco Bay and Delta. SFEI Contribution No. 184. Prepared for Bay/Delta Oversight Council: Sacramento, CA. p 125 pp.
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Hale, T.; Azimi-Gaylon, S.; Fong, S.; Goodwin, P.; Isaac, G.; Osti, A.; Shilling, F.; Slawecki, T.; Steinberg, S.; Tompkins, M.; et al. 2015. Enhancing the Vision for Managing California's Environmental Information. SFEI Contribution No. 792. Delta Stewardship Council: Sacramento, CA.

The Environmental Data Summit, convened under the auspices of the Delta Stewardship Council’s Delta Science Program in June 2014, witnessed remarkable participation from experts across California, the nation, and even the world. Summit attendees from the public, private, federal, and non-profit sectors shared their views regarding the urgent needs and proposed solutions for California’s data-sharing and data-integration challenges, especially pertaining to the subject of environmental resource management in the era of “big data.” After all, this is a time when our data sources are growing in number, size, and complexity. Yet our ability to manage and analyze such data in service of effective decision-making lags far behind our demonstrated needs.

In its review of the sustainability of water and environmental management in the California Bay-Delta, the National Research Council (NRC) found that “only a synthetic, integrated, analytical approach to understanding the effects of suites of environmental factors (stressors) on the ecosystem and its components is likely to provide important insights that can lead to enhancement of the Delta and its species” (National Research Council 2012). The present “silos of data” have resulted in separate and compartmentalized science, impeding our ability to make informed decisions. While resolving data integration challenges will not, by itself, produce better science or better natural resource outcomes, progress in this area will provide a strong foundation for decision-making. Various mandates ranging from the California Water Action Plan to the President’s executive order demanding federal open data policies demonstrate the consensus on the merits of modern data sharing at the scale and function needed to meet today’s challenges.

This white paper emerges from the Summit as an instrument to help identify such opportunities to enhance California’s cross-jurisdictional data management. As a resource to policymakers, agency leadership, data managers, and others, this paper articulates some key challenges as well as proven solutions that, with careful and thoughtful coordination, can be implemented to overcome those obstacles. Primarily featured are tools that complement the State’s current investments in technology, recognizing that success depends upon broad and motivated participation from all levels of the public agency domain. Executive Summary

This document describes examples, practices, and recommendations that focus on California’s Delta as an opportune example likely to yield meaningful initial results in the face of pressing challenges. Once proven in the Delta, however, this paper’s recommended innovations would conceivably be applied statewide in subsequent phases.

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Cohen, A. N. 1996. Environmental Review and Mitigation of a Water Supply Project in California. A report for the Japanese Ministry of Construction, Tokyo.
Salop, P.; Gunther, A.; Bell, D.; Cotsifas, J.; Gold, J.; Ogle, S. 2002. Episodic Ambient Water Toxicity in the San Francisco Estuary. SFEI Contribution No. 51. San Francisco Estuary Institute: Oakland, CA.
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Stevens, D. 2002. Estimation of Means, Totals, and Distribution Functions from Probability Survey Data. SFEI Contribution No. 110. San Francisco Estuary Institute: Oakland, CA.
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Denslow, N.; Kroll, K.; Mehinto, A.; Maruya, K. 2018. Estrogen Receptor In Vitro Assay Linkage Studies. SFEI Contribution No. 888. San Francisco Estuary Institute : Richmond, CA.
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Aquatic Habitat Institute. 1990. Estuarine Data Index: A Guide to Bay-Delta Research and Monitoring Programs, Volume I. SFEI Contribution No. 157. Aquatic Habitat Institute: RIchmond, CA. p 395.
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Aquatic Habitat Institute. 1990. Estuarine Index: A Guide to Bay-Delta Research and Monitoring Programs: Volume I. Association of Bay Area Governments Urban Runoff Studies, Association of Bay Area Governments Environmental Protection Agency. p 395.
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Hoenicke, R.; Leatherbarrow, J. E. 2000. The Estuary Interface Pilot Study: 1998 Progress Report. SFEI Contribution No. 49. San Francisco Estuary Institute.
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Gunther, A. J.; Davis, J. A. 1998. An evaluation of bioaccumulation monitoring with transplanted bivalves in the RMP. SFEI Contribution No. 322. San Francisco Estuary Institute: Richmond, CA. pp 187-200.
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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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O'Connor, J. M. 1991. Evaluation of Turbidity and Turbidity Related Effects on the Biota of the San Francisco Bay-Delta Estuary. SFEI Contribution No. 169. San Francisco Estuary Institute: Richmond, CA. p 84.
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Collins, J. N. 2002. Executive Summary 2002 (Wetlands Science Program). SFEI Contribution No. 250. San Francisco Estuary Institute. p 4.
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Phillips, A. 1988. Executive Summary of the Monitoring of Toxic Contaminants in the San Francisco Bay-Delta: A Crtical Review. SFEI Contribution No. 151. San Francisco Estuary Institue: Richmond, CA. p 14.
Phillips, D. J. H. 1987. Executive Summary of Toxic Contaminats in the San Francisco Bay - Delta and Their Possible Biological Effects. SFEI Contribution No. 139. San Francisco Estuary Institute: Richmond, CA. p 15.
Collins, J. N. 2002. Executive Summary: SFEI Component of the Integrated Regional Wetlands Monitoring Pilot Project. SFEI Contribution No. 251. San Francisco Estuary Institute. p 2.
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Cohen, A. N. 2004. An Exotic Species Detection Program for Puget Sound. SFEI Contribution No. 380. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 2004. An Exotic Species Detection Program for the Lower Columbia River Estuary. SFEI Contribution No. 381. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 2004. An Exotic Species Detection Program for Tillamook Bay. SFEI Contribution No. 379. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 1998. The exotic species threat to California's coastal resources. SFEI Contribution No. 386. American Society of Civil Engineers: Reston, VA. pp 1418-1426.
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Cohen, A. N. 1999. Extent and impacts of ballast water invasions. SFEI Contribution No. 326. West Coast Ballast Outreach Project: Davis, CA. Vol. 1, pp 2-3.
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Novick, E.; Senn, D. B. 2014. External Nutrient Loads to San Francisco Bay. SFEI Contribution No. 704. San Francisco Estuary Institute: Richmond, CA. p 98.
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Shimabuku, I.; Pearce, S.; Trowbridge, P.; Franz, A.; Yee, D.; Salop, P. 2018. Field Operations Manual for the Regional Monitoring Program. SFEI Contribution No. 902. San Francisco Estuary Institute: Richmond, CA.
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Salop, P.; Bell, D.; Gold, J. 1999. Field Sampling Manual for the RMP for Trace Substances (version 1, January 1999). SFEI Contribution No. 324. San Francisco Estuary Institute: Richmond, CA.
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Collins, J. N. 2001. Final Draft Master List of NIS Plant Species. SFEI Contribution No. 366. San Francisco Estuary Institute.
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Collins, J. N.; Grosso, C. 2004. First Annual Report of the Montezuma Wetlands Restoration Project Technical Review Team. SFEI Contribution No. 102. San Francisco Estuary Institute: Oakland, CA.
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