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Sediment Supply, deposition, and transport in the Flood Control Facilities of Arroyo Mocho and Arroyo Las Positas from 2006-2014. . SFEI Contribution No. 771. San Francisco Estuary Institue: Richmond, CA.
2015. 
Shifting Shores: Marsh Expansion and Retreat in San Pablo Bay. SFEI Contribution No. 751.
2015. EXECUTIVE SUMMARY
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.


The Tijuana River Valley: An Ecological Look into the Past.
2015. 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.

Vision for a Resilient Silicon Valley Landscape. SFEI Contribution No. 753.
. 2015. 
2012 Annual Monitoring Results. San Francisco Estuary Institute: Richmond, CA.
. 2014. 
2013 RMP Water Cruise Plan. Applied Marine Sciences: Livermore, CA.
. 2014. 
2014 Quality Assurance Program Plan for the Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI: Richmond, CA.
2014. 
2014 Regional Monitoring Program Update. SFEI Contribution No. 728. San Francisco Estuary Institute: Richmond, CA.
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.
2014. 
A Delta Transformed: Ecological Functions, Spatial Metrics, and Landscape Change in the Sacramento-San Joaquin Delta. SFEI Contribution No. 729. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
2014. 

Development of Benthic Community Condition Indices – San Francisco Bay. San Francisco Estuary Institute: Richmond, CA.
2014. 
Estimating Regional Pollutant Loads for San Francisco Bay Area Tributaries using the Regional Watershed Spreadsheet Model( RWSM): Year’s 3 and 4 Progress Report. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
2014. 
External Nutrient Loads to San Francisco Bay. SFEI Contribution No. 704. San Francisco Estuary Institute: Richmond, CA. p 98.
2014. 
Futures Past Exploring California landscapes with the San Francisco Estuary Institute. Boom: The Journal of California . pp 4-27.
2014. Historical Changes in Channel Alignment along Lower Laguna de Santa Rosa and Mark West Creek. SFEI: Richmond, CA.
2014. 
How Creeks Meet the Bay: Changing Interfaces (Interactive web map).
2014. 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.
Initial Protocol to Identify and Delineate the Head of Tide Zone in San Francisco Bay Tributaries. SFEI Contribution No. 719. San Francisco Estuary Institute: Richmond, CA.
2014. 
Landscape Scale Management Strategies for Arroyo Mocho and Arroyo Las Positas: Process-Based Approaches for Dynamic, Multi-Benefit Urban Channels. SFEI Contribution No. 714. San Francisco Estuary Institute: Richmond, CA.
2014. 
Linkage of In Vitro Assay Results With In Vivo End Points. San Francisco Estuary Institute: Richmond, CA.
2014. 
Model Development Plan to Support Nutrient Management Decisions in San Francisco Bay. SFEI Contribution No. 705. Richmond, CA.
2014. 
Natural Flow Hydrodynamic Modeling Technology Support Phase 1 Technical Memorandum.
2014. 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.

Newcomb Avenue Green Street (Case Study Site and Technical Reports). SFEI Contribution No. 793.
2014. 

North Bay Mercury Biosentinel Project (December 2014 Report). SFEI Contribution No. 738. San Francisco Estuary Institute: Richmond, CA.
2014. 
Northern San Diego County Lagoons Historical Ecology Investigation. SFEI Contribution No. 722. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 215.
2014. 

Nutrient Moored Sensor Program: Year 1 Progress Update. SFEI: Richmond, CA.
2014. 
Nutrient Stormwater Monitoring Results: WY2012 and WY2013. San Francisco Estuary Institute: Richmond, CA.
2014. 
Online 401: From Pilot to Production. San Francisco Estuary Institute: Richmond, CA.
2014. 
PCBs in San Francisco Bay: Assessment of the Current State of Knowledge and Priority Information Gaps. SFEI Contribution No. 727. SFEI: Richmond, CA.
2014. 
Pollutants of Concern (POC) Loads Monitoring Data Progress Report: Water Years (WYs) 2012 and 2013. SFEI Contribution No. 708. SFEI: Richmond, CA. pp 1-84.
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.
2014. 
Polychlorinated biphenyls in the exterior caulk of San Francisco Bay Area buildings, California, USA. Environment International 66, 38-43.
2014. 
Reducing Methylmercury Accumulation in the Food Webs of San Francisco Bay and Its Local Watersheds. SFEI Contribution No. 707. San Francisco Estuary Institute: Richmond, CA.
2014. 
Removal efficiencies of a bioretention system for trace metals, PCBs, PAHs, and dioxins in a semiarid environment. Journal of Environmental Engineering.
2014. San Francisco Bay Nutrient Management Strategy: Detailed Modeling Workplan for FY15-FY21. San Francisco Estuary Institute: Richmond, CA.
2014. 
San Francisco State University Site 1 Vegetated Infiltration Basin (Case Study Site and Technical Reports). SFEI Contribution No. 794.
2014. 

San Francisco State University Site 3 Basin and Swale System (Case Study Site and Technical Reports). SFEI Contribution No. 795.
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.
2014. 
Suisun Bay Ammonium Synthesis. SFEI Contribution No. 706. San Francisco Estuary Institute: Richmond, CA. p 191.
2014. 
Sunset Circle Vegetated Swale and Infiltration System (Case Study Site and Technical Reports). SFEI Contribution No. 796.
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.
2014. 
2013 Pulse of the Bay: Contaminants of Emerging Concern. San Francisco Estuary Institute : Richmond, CA. p 102.
. 2013. 
Adjustment of the San Francisco estuary and watershed to decreasing sediment supply in the 20th century. Marine Geology 345, 63-71.
2013. Alameda Creek Watershed Historical Ecology Study. San Francisco Estuary Institute: Richmond, CA.
2013. 

Applying Sediment Quality Objective Assessment Protocols to Two San Francisco Bay 303(d)-Listed Sites. Final Report. San Francisco Estuary Institute: Richmond.
2013. 
Applying Sediment Quality Objective Assessments to San Francisco Bay Samples from 2008-2012. San Francisco Estuary Institute and Southern California Coastal Water Research Project: Richmond, CA.
2013. 
An Assessment of the South Bay Historical Tidal-Terrestrial Transition Zone. SFEI Contribution No. 693. San Francisco Estuary Institute: Richmond, CA.
2013. 
Benthic macrofaunal assemblages of the San Francisco Estuary and Delta, USA. Environmental Monitoring Assessment.
2013. 
2013.
Comparison of sediment supply to San Francisco Bay from watersheds draining the Bay Area and the Central Valley of California. Marine Geology Special Issue: A multi-discipline approach for understanding sediment transport and geomorphic evolution in an estuarine-coastal system.
2013. Contaminants in Fish from California Rivers and Streams, 2011. California State Water Resources Control Board: Sacramento, CA.
2013. 





Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations. San Francisco Estuary Institute: Richmond, CA.
2013. 
Contaminants of Emerging Concern in San Francisco Bay: A Summary of Occurrence Data and Identification of Data Gaps. SFEI Contribution No. 698. p 121.
2013. 
Demonstration Watershed Assessment For the Tahoe Basin Using the Wetland & Riparian Area Monitoring Plan. SFEI Contribution No. 703. San Francisco Estuary Institute: Richmond, CA.
2013. 
2013.
Estuary News RMP Insert 2013. Estuary News. San Francisco Estuary Institute: Richmond, CA.
2013. 
Exploring the Traditional Use of Fire in the Coastal Mountains of Central California. Joint Fire Science Program.
2013. 
Landscape Patterns and Processes of the McCormack-Williamson Tract and Surrounding Area: A framework for restoring a resilient and functional landscape. SFEI Contribution No. 674. SFEI-ASC: Richmond, CA.
2013. 
Method validation and reconnaissance of pharmaceuticals, personal care products, and alkylphenols in surface waters, sediments, and mussels in an urban estuary. Environment International 54, 92-99.
2013. 
Pollutants of concern (POC) loads monitoring data progress report, water year (WY) 2012. SFEI: Richmond, CA.
2013. 
Predictors of Mercury Spatial Patterns in San Francisco Bay Forage Fish. Environmental Toxicology and Chemistry 32 (12), 2728-2737.
2013. 
Regional Curves of Hydraulic Geometry for Wadeable Streams In Marin and Sonoma Counties, San Francisco Bay Area. Watershed Sciences Berkeley and Marin County Flood Control District.
2013. 
Riparian Zone Estimation Tool: Hydrologic Connectivity Module Field Plan. San Francisco Estuary Institute: Richmond, CA.
. 2013. 
Seasonal and annual trends in forage fish mercury concentrations, San Francisco Bay. Science of the Total Environment 444, 591-601.
2013. 
Seasonal and annual trends in forage fish mercury concentrations, San Francisco Bay. Science of the Total Environment 444, 591-601.
2013. Seasonal variations in suspended-sediment dynamics in the tidal reach of an estuarine tributary. Marine Geology 345, 314-326.
2013. A sediment budget for the southern reach in San Francisco Bay, CA: Implications for habitat restoration. Marine Geology 345, 281-293.
2013. Sediment transport in the San Francisco Bay Coastal System: An overview. Marine Geology Special Issue: A multi-discipline approach for understanding sediment transport and geomorphic evolution in an estuarine-coastal system.
2013.