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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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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. San Francisco Estuary Institute: Richmond, CA.

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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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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Wu, J.; Kauhanen, P.; Lowe, S.; Pearce, S.; Josh Collins. 2017. 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.

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.

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Cloern, J. E.; Cole, B. E.; Jassby, A. D. 1997. The design of sampling transects for characterizing water quality in estuaries. Estuarine, Coastal and Shelf Science 45, 285-302 . SFEI Contribution No. 23.
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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. 2002. Dispersal Ecology. Blackwell Publishing: Oxford.
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Flegal, A. R.; Sanudo-Wilhelmy, S. A.; Rivera-Duarte, I. 1996. Distribution of Colloidal trace metals in the San Francisco Bay estuary. Geochimica et Cosmochimica Acta 60, 4933-4944 . SFEI Contribution No. 194.
Grossinger, R. M. 2001. Documenting Local Landscape Change: The Bay Area Historical Ecology Project. In The Historical Ecology Handbook: A Restorationist's Guide to Reference Ecosystems.. Egan, D., Howell, E., Eds.. The Historical Ecology Handbook: A Restorationist's Guide to Reference Ecosystems. Island Press: Washington D.C.
Grossinger, R. M. 2005. Documenting Local Landscape Change: The Bay Area Historical Ecology Project. In The HISTORICAL ECOLOGY HANDBOOK: A Restorationist's Guide to Reference Ecosystems. Egan, D., Howell, E. A., Trans.. The HISTORICAL ECOLOGY HANDBOOK: A Restorationist's Guide to Reference Ecosystems. Island Press.
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.
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.
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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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Askevold, R. A.; Whipple, A.; Grossinger, R. M.; Stanford, B.; Salomon, M. N. 2011. East Contra Costa Historical Ecology Study GIS data, GIS data produced for the East Contra Costa County Historical Ecology Study.
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Panlasigui, S.; Baumgarten, S.; Spotswood, E. 2021. E-Bikes and Open Space: The Current State of Research and Management Recommendations. SFEI Contribution No. 1064. San Francisco Estuary Institute: Richmond, 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.
Baumgarten, S. A. 2022. Ecological Horticulture at the Presidio. Lee, V., Bazo, M., Spotswood, E., Eds.. SFEI Contribution No. 1080. San Francisco Estuary Institute: Richmond, Ca.

The Presidio of San Francisco—the nation’s largest urban national park—is located in an area of exceptional ecological diversity. Historically, many different habitat types thrived in the mix of windswept dunes, riparian forests, and curious dwarf oak woodlands that characterized this landscape. Many of these habitat types are rare today (and some were even rare in the region historically), and together they harbor a host of unique plants and animals.

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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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San Francisco Estuary Institute. 2023. Ecology for Health: Design Guidance for Fostering Human Health and Biodiversity in Cities. Funded by the Robert Wood Johnson Foundation. SFEI Contribution No. 1130. San Francisco Estuary Institute: Richmond, CA.

Ecology for HealthGreenspaces provide crucial nature contact for urban residents. When we have greater access and exposure to nature in the places where we live, work, learn, and play, we tend to experience better human health outcomes. Urban parks, trees, and vegetation encourage physical activity, reduce anxiety and depression, support social cohesion by providing gathering spaces, and are associated with reduced mortality and improved overall health.

While traditionally biodiversity conservation has focused on large open spaces, cities can also play a key role in supporting biodiversity. Many of the world’s major cities developed in biodiversity hotspots due to historical settlement patterns dependent on natural resources. Thus cities contain vital remnant habitat as well as globally important native and endangered species that rely on urban greenspaces.

As urbanization increases, cities around the world are developing and implementing plans to better integrate nature within urban settings. Many of these plans emphasize the importance of urban greening in providing multiple, substantial benefits such as biodiversity conservation, stormwater management, human health and well-being improvements, climate resilience, and more. However not all greenspaces are created equal in their biodiversity support and human health provision.

The goal of this document is to provide science-based guidance for designing urban spaces that foster both human health and urban biodiversity. Anyone making decisions about land use and urban design in cities across the world can benefit from the recommendations in this document (including community organizations, local non-profits, local leaders and policy makers, city planners, urban designers, landscape architects, engineers, gardeners/horticulturists/arborists, residents, and landowners). However, the majority of the document is specifically aimed at supporting designers and planners who work at the planning, site, and detailed design scales such as landscape architects, civil engineers, and urban designers. As noted in more detail in the limitations section below, this document synthesizes global research and design strategies while strongly informed by our experience as scientists and designers in California’s San Francisco Bay Area.

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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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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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Sommers, F.; Mudrock, E.; Labenia, J.; Baldwin, D. 2016. Effects of salinity on olfactory toxicity and behavioral responses of juvenile salmonids from copper. Aquatic Toxicology 175.

Dissolved copper is one of the more pervasive and toxic constituents of stormwater runoff and is commonly found in stream, estuary, and coastal marine habitats of juvenile salmon. While stormwater runoff does not usually carry copper concentrations high enough to result in acute lethality, they are of concern because sublethal concentrations of copper exposure have been shown to both impair olfactory function and alter behavior in various species in freshwater. To compare these results to other environments that salmon are likely to encounter, experiments were conducted to evaluate the effects of salinity on the impairment of olfactory function and avoidance of copper. Copper concentrations well within the range of those found in urban watersheds, have been shown to diminish or eliminate the olfactory response to the amino acid, l-serine in freshwater using electro-olfactogram (EOG) techniques. The olfactory responses of both freshwater-phase and seawater-phase coho and seawater-phase Chinook salmon, were tested in freshwater or seawater, depending on phase, and freshwater-phase coho at an intermediate salinity of 10‰. Both 10‰ salinity and full strength seawater protected against the effects of 50μg copper/L. In addition to impairing olfactory response, copper has also been shown to alter salmon behavior by causing an avoidance response. To determine whether copper will cause avoidance behavior at different salinities, experiments were conducted using a multi-chambered experimental tank. The circular tank was divided into six segments by water currents so that copper could be contained within one segment yet fish could move freely between them. The presence of individual fish in each of the segments was counted before and after introduction of dissolved copper (<20μg/L) to one of the segments in both freshwater and seawater. To address whether use of preferred habitat is altered by the presence of copper, experiments were also conducted with a submerged structural element. The presence of sub-lethal levels of dissolved copper altered the behavior of juvenile Chinook salmon by inducing an avoidance response in both freshwater and seawater. While increased salinity is protective against loss of olfactory function from dissolved copper, avoidance could potentially affect behaviors beneficial to growth, survival and reproductive success.

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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.
Whipple, A.; Robinson, A.; Safran, S. M. 2022. ELEVATION AND OPPORTUNITY IN THE DELTA: Restoring the right thing in the right place. SFEI Contribution No. 1082. San Francisco Estuary Institute: Richmond, Ca.

 

A future Sacramento-San Joaquin Delta and Suisun Marsh (“Delta” herein) that supports healthy ecosystems and native species, while also meeting flood risk reduction, water supply, water quality, carbon sequestration, economic, and cultural objectives, requires that appropriate restoration and management actions be taken in the right place at the right time. Geographic setting affects the potential opportunities available—not all actions are suitable everywhere. Physical factors determining what types of activities are appropriate now and in the future include a site’s elevation, degree of tidal and fluvial influence, salinity, soil type, and local effects of climate change, which all vary spatially across the Delta. While there has been considerable progress over the last several decades, continued acceleration of the pace and scale of enhancement actions appropriate to landscape position is needed. Understanding the physical template is necessary for developing strategies that move beyond opportunistic restoration, support resilience over time, and have the potential to connect and magnify benefits across the larger landscape.

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Oros, D. R. 2005. Emerging Contaminants: Endocrine Disrupting Chemicals (EDCs). RMP Regional Monitoring News, San Francisco Estuary Regional Monitoring Program for Trace Substances 10, p.1-11 . SFEI Contribution No. 502.
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