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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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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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David, N.; Gluchowski, D. C.; Leatherbarrow, J. E.; Yee, D.; McKee, L. J. . 2015. Estimation of Contaminant Loads from the Sacramento-San Joaquin River Delta to San Francisco Bay. Water Environment Research 87 (4), 334-346.

Contaminant concentrations from the Sacramento-San Joaquin River watershed were determined in water samples mainly during flood flows in an ongoing effort to describe contaminant loads entering San Francisco Bay, CA, USA. Calculated PCB and total mercury loads during the 6-year observation period ranged between 3.9 and 19 kg/yr and 61 and 410 kg/yr, respectively. Long-term average PCB loads were estimated at 7.7 kg/yr and total mercury loads were estimated at 200 kg/yr. Also monitored were PAHs, PBDEs (two years of data), and dioxins/furans (one year of data) with average loads of 392, 11, and 0.15/0.014 (OCDD/OCDF) kg/yr, respectively. Organochlorine pesticide loads were estimated at 9.9 kg/yr (DDT), 1.6 kg/yr (chlordane), and 2.2 kg/yr (dieldrin). Selenium loads were estimated at 16 300 kg/yr. With the exception of selenium, all average contaminant loads described in the present study were close to or below regulatory load allocations established for North San Francisco Bay.

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Yarnell, S. M.; Petts, G. E.; Schmidt, J. C.; Whipple, A.; Beller, E. E.; Dahm, C. N.; Goodwin, P.; Viers, J. H. 2015. Functional Flows in Modified Riverscapes: Hydrographs, Habitats and Opportunities. BioScience.

Building on previous environmental flow discussions and a growing recognition that hydrogeomorphic processes are inherent in the ecological functionality and biodiversity of riverscapes, we propose a functional-flows approach to managing heavily modified rivers. The approach focuses on retaining specific process-based components of the hydrograph, or functional flows, rather than attempting to mimic the full natural flow regime. Key functional components include wet-season initiation flows, peak magnitude flows, recession flows, dry-season low flows, and interannual variability. We illustrate the importance of each key functional flow using examples from western US rivers with seasonably predictable flow regimes. To maximize the functionality of these flows, connectivity to morphologically diverse overbank areas must be enhanced in both space and time, and consideration must be given to the sediment-transport regime. Finally, we provide guiding principles for developing functional flows or incorporating functional flows into existing environmental flow frameworks.

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Wu, J.; Kauhanen, P.; Mckee, L. 2015. GreenPlan-IT Toolkit Demonstration Report. SFEI Contribution No. 958. San Francisco Estuary Institute: Richmond, CA.

GreenPlan-IT is a planning level tool that was developed by SFEP and SFEI with support and oversight from BASMAA to provide Bay Area municipalities with the ability to evaluate multiple management alternatives using green infrastructure for addressing stormwater issues in urban watersheds. GreenPlan-IT combines sound science and engineering principles with GIS analysis and optimization techniques to support the cost-effective selection and placement of Green Infrastructure (GI) at a watershed scale.  Tool outputs can be used to develop quantitatively-derived watershed master plans to guide future GI implementation for improving water quality in the San Francisco Bay and its tributary watersheds.

This report provides an overview of the GreenPlan-IT Tool and demonstrates its utility and power through two pilot studies which is summarized in this report as a case study. The pilot studies with the City of San Mateo and the City of San Jose explored the use of GreenPlan-IT for identifying feasible and optimal GI locations for mitigation of stormwater runoff. They are provided here to give the reader an overview of the user application process from start to finish, including problem formulation, data collection, GIS analysis, establishing a baseline condition, GI representation, and the optimization process. Through the pilot study application process the general steps and recommendations for how GreenPlan-IT can be applied and interpreted are presented.

Wu, J.; Kauhanen, P.; Mckee, L. 2015. GreenPlan-IT Toolkit User Guide. SFEI Contribution No. 958. San Francisco Estuary Institute: Richmond, CA.

Structurally, the GreenPlan-IT is comprised of three components: (a) a GIS-based Site Locator Tool to identify potential GI sites; (b) a Modeling Tool that quantifies anticipated watershed-scale runoff and pollutant load reduction from GI sites; and (c) an Optimization Tool that uses a cost-benefit analysis to identify the best combinations of GI types and number of sites within a watershed for achieving flow and/or load reduction goals. The three tool components were designed as standalone modules to provide flexibility and their interaction is either through data exchange, or serving as a subroutine to another tool. This user manual addresses each of the tools separately, though they are designed to complement each other.

Beller, E. E.; Robinson, A.; Grossinger, R. M.; Grenier, J. Letitia. 2015. Landscape Resilience Framework: Operationalizing Ecological Resilience at the Landscape Scale. SFEI Contribution No. 752. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
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Baumgarten, S.; Beller, E. E.; Grossinger, R. M.; Askevold, R. A. 2015. Mt. Wanda Historical Ecology Investigation. SFEI Contribution No. 743. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 51.
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Salomon, M.; Baumgarten, S.; Dusterhoff, S. D.; Beller, E. E.; Askevold, R. A. 2015. Novato Creek Baylands Historical Ecology Study. SFEI Contribution No. 740. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.

Project Background

Over the past century and a half, lower Novato Creek and the surrounding tidal wetlands have been heavily modified for flood control and land reclamation purposes. Levees were built in the tidal portion of the mainstem channel beginning in the late 1800s to convey flood flows out to San Pablo Bay more rapidly and to remove surrounding areas from inundation. Following levee construction, the wetlands surrounding the channel were drained and converted to agricultural, residential, and industrial areas. These changes have resulted in a considerable loss of wetland habitat, reduced sediment transport to marshes and the Bay, and an overall decreased resilience of the system to sea level rise.
In addition to tidal wetland modification, land use changes upstream in the Novato Creek watershed have resulted in several challenges for flood control management. Dam construction and increased runoff in the upper watershed have resulted in elevated rates of channel incision, which have increased transport of fine sediment from the upper watershed to lower Novato Creek. Channelization of tributaries and construction of irrigation ditches have likely increased drainage density in the upper watershed, also potentially contributing to increased rates of channel incision and fine sediment production (Collins 1998). Downstream, sediment transport capacity has been reduced by construction of a railroad crossing and loss of tidal prism and channel capacity associated with the diking of the surrounding marsh. As a result of the increased fine sediment supply from the watershed and the loss of sediment transport capacity in lower Novato Creek, sediment aggradation occurs within the channel, which in turn reduces the flood capacity of the channel, necessitating periodic dredging.

Currently, the Marin County Department of Public Works (MCDPW) is coordinating the Novato Watershed Program, which includes Marin County Flood Control and Water Conservation District, Novato Sanitary District, and North Marin Water District. Within lower Novato Creek, the Program is seeking to implement a new approach to flood control that includes redirecting sediment for beneficial use, reducing flood channel maintenance costs, restoring wetland habitat, and enhancing resilience to sea level rise. Included as part of this goal is the re-establishment of historical physical processes that existed before major channel modification, which in turn will re-establish historical ecological functions and help to create a tidal landscape that is resilient to increasing sea level.

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Grossinger, R. M.; Dusterhoff, S. D.; Doehring, C.; Salomon, M.; Askevold, R. A. 2015. Novato Creek Baylands Vision: Integrating ecological functions and flood protection within a climate-resilient landscape. SFEI Contribution No. 764.

This report explores the potential for integrating ecological functions into flood risk management on lower Novato Creek. It presents an initial vision of how ecological elements could contribute to flood protection, based on a broad scale analysis and a one day workshop of local and regional experts. The Vision is not intended to be implemented as is, but rather adapted and applied through future projects and analysis. Other actions (e.g., floodwater detention basins) may also need to be implemented in the interim to meet flood risk objectives.

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Kerrigan, J. F.; Engstrom, D. R.; Yee, D.; Sueper, C.; Erickson, P. R.; Grandbois, M.; McNeill, K.; Arnold, W. A. 2015. Quantification of Hydroxylated Polybrominated Diphenyl Ethers (OH-BDEs), Triclosan, and Related Compounds in Freshwater and Coastal Systems. PLOS ONE . SFEI Contribution No. 765.

Hydroxylated polybrominated diphenyl ethers (OH-BDEs) are a new class of contaminants of emerging concern, but the relative roles of natural and anthropogenic sources remain uncertain. Polybrominated diphenyl ethers (PBDEs) are used as brominated flame retardants, and they are a potential source of OH-BDEs via oxidative transformations. OH-BDEs are also natural products in marine systems. In this study, OH-BDEs were measured in water and sediment of freshwater and coastal systems along with the anthropogenic wastewater-marker compound triclosan and its photoproduct dioxin, 2,8-dichlorodibenzo-p-dioxin. The 6-OH-BDE 47 congener and its brominated dioxin (1,3,7-tribromodibenzo-p-dioxin) photoproduct were the only OH-BDE and brominated dioxin detected in surface sediments from San Francisco Bay, the anthropogenically impacted coastal site, where levels increased along a north-south gradient. Triclosan, 6-OH-BDE 47, 6-OH-BDE 90, 6-OH-BDE 99, and (only once) 6’-OH-BDE 100 were detected in two sediment cores from San Francisco Bay. The occurrence of 6-OH-BDE 47 and 1,3,7-tribromodibenzo-p-dioxin sediments in Point Reyes National Seashore, a marine system with limited anthropogenic impact, was generally lower than in San Francisco Bay surface sediments. OH-BDEs were not detected in freshwater lakes. The spatial and temporal trends of triclosan, 2,8-dichlorodibenzo-p-dioxin, OH-BDEs, and brominated dioxins observed in this study suggest that the dominant source of OH-BDEs in these systems is likely natural production, but their occurrence may be enhanced in San Francisco Bay by anthropogenic activities.

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San Francisco Estuary Institute. 2015. RipZET: The Riparian Zone Estimation Tool version 2.0. San Francisco Estuary Institute: Richmond, CA.
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San Francisco Estuary Institute. 2015. RipZET User's Manual v1.0. San Francisco Estuary Institute: Richmond, CA.
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Beagle, J.; Salomon, M.; Grossinger, R. M.; Baumgarten, S.; Askevold, R. A. 2015. Shifting Shores: Marsh Expansion and Retreat in San Pablo Bay. SFEI Contribution No. 751.

As sea level rise accelerates, our shores will be increasingly vulnerable to erosion. Particular concern centers around the potential loss of San Francisco Bay’s much-valued tidal marshes, which provide natural flood protection to our shorelines, habitat for native wildlife, and many other ecosystem services. Addressing this concern, this study is the first systematic analysis of the rates of marsh retreat and expansion over time for San Pablo Bay, located in the northern part of San Francisco Bay.

Key findings:
• Over the past two decades, more of the marshes in San Pablo Bay have expanded (35% by length) than retreated (6%).
• Some areas have been expanding for over 150 years.
• Some marsh edges that appear to be retreating are in fact expanding rapidly at rates of up to 8 m/yr.
• Marsh edge change may be a useful indicator of resilience, identifying favorable sites for marsh persistence.
• These data can provide a foundation for understanding drivers of marsh edge expansion and retreat such as wind direction, wave energy, watershed sediment supply, and mudflat shape.
• This understanding of system dynamics will help inform management decisions about marsh restoration and protection.
• This study provides a baseline and method for tracking marsh edge response to current and future conditions, particularly anticipated changes in sea level, wave energy, and sediment supply.

Recommended next steps:
• This pilot study for San Pablo Bay marshes should be extended to other marshes in San Francisco Bay.
• These initial marsh expansion and retreat findings should be further analyzed and interpreted to improve our understanding of system drivers and identify management responses.
• A program for repeated assessment should be developed to identify and track changes in shoreline position, a leading indicator of the likelihood marsh survival.

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Safran, S. M. 2015. The Tijuana River Valley: An Ecological Look into the Past.

Hot springs in the Tijuana River? Antelope by the beach? Zip-lines over the international border?
Come find out what the Tijuana River Valley looked like in the not-so-distant past and how the river, estuary, and surrounding areas have changed over the past two centuries. Hear how researchers “recreated” the historical landscape and how this information helps us to better plan for the future.

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Applied Marine Sciences. 2014. 2013 RMP Water Cruise Plan. Applied Marine Sciences: Livermore, CA.
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Davis, J. A. 2014. 2014 Regional Monitoring Program Update. SFEI Contribution No. 728. San Francisco Estuary Institute: Richmond, CA.
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Lowe, S.; Robinson, A.; Frontiera, P.; Cayce, K.; Collins, J. N. 2014. Creating Landscape Profiles of Aquatic Resource Abundance, Diversity and Condition. SFEI Contribution No. 725. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 21.
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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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Dusterhoff, S. D.; Doehring, C.; Shusterman, G. 2014. How Creeks Meet the Bay: Changing Interfaces (Interactive web map).

San Francisco Bay’s connections to local creeks are integral to its health. These fluvial-tidal (F-T) interfaces are the points of delivery for freshwater, sediment, contaminants, and nutrients. The ways in which the F-T interface has changed affect flooding dynamics, ecosystem functioning, and resilience to a changing climate. As the historical baylands have been altered, the majority of contemporary F-T interface types have changed leading to additional F-T interface types within the present-day landscape. Illustrations of each F-T interface type and methods for classification are available here

This project is part of Flood Control 2.0. For further information please visit this project page

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SFEI; Safran, S. M. 2014. Natural Flow Hydrodynamic Modeling Technology Support Phase 1 Technical Memorandum.

This technical memorandum summarizes the work to date carried out by the San Francisco Estuary Institute (SFEI) to generate a bathymetric-topographic digital elevation model (DEM) of the historical Sacramento-San Joaquin Delta (representative of early 1800s conditions). The historical DEM described in this document is an interim/draft product completed for Phase I of the Bay-Delta Natural Flow Hydrodynamics and Salinity Transport modeling project. It is expected that the product and methods described here will be refined during a second phase of the project.

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Robinson, A.; Slotton, D. G.; Lowe, S.; Davis, J. A. 2014. North Bay Mercury Biosentinel Project (December 2014 Report). SFEI Contribution No. 738. San Francisco Estuary Institute: Richmond, CA.
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Beller, E. E.; Baumgarten, S.; Grossinger, R. M.; Longcore, T.; Stein, E. D.; Dark, S.; Dusterhoff, S. D. 2014. Northern San Diego County Lagoons Historical Ecology Investigation. SFEI Contribution No. 722. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 215.
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Grosso, C.; Hale, A.; Williams, M.; May, M. 2014. Online 401: From Pilot to Production. San Francisco Estuary Institute: Richmond, CA.
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Sutton, R.; Sedlak, M.; Davis, J. A. 2014. Polybrominated Diphenyl Ethers (PBDEs) in San Francisco Bay: A Summary of Occurrence and Trends. SFEI Contribution No. 713. San Francisco Estuary Institute: Richmond, CA. p 62.
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Collins, J. N.; Lowe, S.; Pearce, S.; Roberts, C. 2014. Santa Rosa Plain Wetlands Profile: A Demonstration of the CaliforniaWetland and Riparian Area Monitoring Plan. SFEI Contribution No. 726. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 46.
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Senn, D. B.; Novick, E. 2014. Suisun Bay Ammonium Synthesis. SFEI Contribution No. 706. San Francisco Estuary Institute: Richmond, CA. p 191.
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Stein, E. D.; Cayce, K.; Salomon, M. N.; Bram, D. L.; De Mello, D.; Grossinger, R. M.; Dark, S. 2014. Wetlands of the Southern California Coast: Historical Extent and Change Over Time. SFEI Contribution No. 720. Southern California Coastal watershed Research Project (SCCWRP), San Francisco Estuary Institute (SFEI), CSU Northridge Center for Geographical Studies: Costa Mesa, Richmond, Northridge.
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