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2008.
Analysis of Reference Tidal Channel Plan Form for the Montezuma Wetlands Restoration Project. SFEI Contribution No. 80. San Francisco Estuary Institute: Oakland, CA.
2004. 
Assessment Framework as a Tool for Integrating and Communicating Watershed Health Indicators for the San Francisco Estuary. SFEI Contribution No. 634. San Francisco Estuary Institute: Oakland, CA.
2011. 
Basic Regional Spatial Analysis of Non - Indigenous Invasive Species (NIS) Spartina Invasions in the San Francisco Estuary. SFEI Contribution No. 372. San Francisco Estuary Institute: Richmond, Ca.
2001. 
Bay Area Wetlands Ecosystem Goals Project: Draft Functional Correspondence between Past and Present Key Habitats. SFEI Contribution No. 123. San Francisco Estuary Institute.
1998. 
Bay Area Wetlands Ecosystem Goals Project: Key Baylands Habitats. SFEI Contribution No. 122. San Francisco Estuary Institute.
1998. 
Bay Area Wetlands Ecosystem Goals Project: Key Baylands Species. SFEI Contribution No. 121. San Francisco Estuary Institute.
1998. 
Bay Area Wetlands Regional Monitoring Program (Abstract, SOE 2001). San Francisco Estuary Institute: Richmond, CA.
2001. 
Baylands Ecosystem Habitat Goals. SFEI Contribution No. 330. U. S. Environmental Protection Agency, San Francisco, Calif./S.F. Bay Regional Water Quality Control Board, Oakland, Calif. p 328.
1999. 
BAYLANDS ECOSYSTEM HABITAT GOALS: REPORT ON THE PROCESS TO SET REGIONAL GOALS FOR WETLANDS RESTORATION IN THE SAN FRANCISCO BAY AREA. SFEI Contribution No. 227. San Francisco Estuary Institute: Richmond, CA.
1998. 
Baylands Vegetation Mapping Protocol (Version 1.0). SFEI Contribution No. 304. San Francisco Estuary Institute: Oakland, CA.
2004. 
California Rapid Assessment Method (CRAM) - Part 2. SFEI Contribution No. 285. San Francisco Estuary Institute.
2003. 
California Rapid Assessment Method for Wetlands v. 1.0. SFEI Contribution No. 246. San Francisco Estuary Institute. p 18.
2002. Carbon-isotope, diatom, and pollen evidence of late Holocene salinity changes in a brackish marsh in the San Francisco Estuary. Quaternary Research 55, 66-76 . SFEI Contribution No. 467.
2003. Cartographic analysis of historical and modern baylands boundaries for Marin County, California. SFEI Contribution No. 229. Marin County Community Develpment Agency. p 88 pp.
1998. Comparison of Methods to Map California Riparian Areas. . SFEI Contribution No. 522.
2006. 
Conceptual models of freshwater influences on tidal marsh form and function, with an historical perspective. SFEI Contribution No. 327. Department of Environmental Services: City of San Jose, CA. p 237 pp.
1999. Contamination of Tidal Wetlands. SFEI Contribution No. 228. Richmond CA.
1998. Coyote Creek Watershed Historical Ecology Study: Historical Conditions and Landscape Change in the Eastern Santa Clara Valley, California. SFEI Contribution No. 426. San Francisco Estuary Institute.
2006. 


CRAM Evaluation of Wetland Conditions. SFEI Contribution No. 544. Elk Grove, California. p 15.
2007. 
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. 
Data Collection Protocol Distribution, Abundance, and Treatment of Non-indigenous Speicies of Cordgrass in the San Francisco Estuary. SFEI Contribution No. 247. San Francisco Estuary Institute: Oakland, CA. p 44.
2002. 
Demonstration of a Watershed Approach to Wetland Restoration Planning for Load Reductions: A Pilot Demonstration Project Using GreenPlan-IT in the Santa Rosa Plain, Sonoma County, California. SFEI Contribution No. 996. San Francisco Estuary Institute: Richmond. CA.
. 2017. 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.





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. 
2008.
DRAFT California Rapid Assessment (CRAM) Verification Approach. SFEI Contribution No. 283. San Francisco Estuary Institute: Oakland, CA. p p. 9.
2003. 2003.
Draft Guidelines for Developing the CRAM Metrics. SFEI Contribution No. 284. San Francisco Estuary Institute: Oakland, CA. p 2.
2003. 
Ecological Connections between Baylands and Uplands: Examples from Marin County. SFEI Contribution No. 521.
2007. 
Establishing Critical Datum Elevations for Wetland Restoration. Coastal Zone . SFEI Contribution No. 484.
2001. Executive Summary 2002 (Wetlands Science Program). SFEI Contribution No. 250. San Francisco Estuary Institute. p 4.
2002. 
Executive Summary: SFEI Component of the Integrated Regional Wetlands Monitoring Pilot Project. SFEI Contribution No. 251. San Francisco Estuary Institute. p 2.
2002. 
Final Draft Master List of NIS Plant Species. SFEI Contribution No. 366. San Francisco Estuary Institute.
2001. 
First Annual Report of the Montezuma Wetlands Restoration Project Technical Review Team. SFEI Contribution No. 102. San Francisco Estuary Institute: Oakland, CA.
2004. 
Flood Control Channel Classification Scheme for the San Francisco Bay Region. . San Francisco Bay Region Flood Control Channel Classification . SFEI Contribution No. 1046. San Francisco Estuary Institute: Richmond, CA.
2021. 
Framework to coordinate water quality improvement and wildlife habitat conservation to protect California streams, wetlands, and riparian areas.
2016. Project funded by an USEPA Wetland Program Development Grant (Region 9) #99T05901: Framework for Coordinated Assessment of CA Wildlife Habitat and Aquatic Resource Areas
. SFEI Contribution No. 776. San Francisco Estuary Institute: Richmond, CA. p 89.The emergence of comparable landscape approaches to wildlife conservation and water quality improvement through federal and California state regulatory and management programs provides an opportunity for their coordination to better protect California’s aquatic resources, especially streams, wetlands, and riparian areas. Such coordination is patently desirable. A framework has been developed to help coordinate restoration and compensatory mitigation across policies governing wildlife conservation and water quality in the landscape context. The framework is based on the Wetland and Riparian Area Monitoring Plan (WRAMP) of the California Wetland Monitoring Workgroup (CWMW) of the Water Quality Monitoring Council. The framework presented in this memorandum is a version of the standard WRAMP framework. It only differs from the standard framework to better accommodate wildlife conservation planning, assessment and reporting. To distinguish this version from the standard version, it is termed the 'WRAMP for wildlife'.

The Historical Ecology of Napa Valley: An Introduction. SFEI Contribution No. 557.
2008. 

The Historical Geography and Biogeography of Tidal Salt Marshes (Abstract). San Francisco Estuary Institute.
2002. 
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. 
Introduced Tidal Marsh Plants in the San Francisco Estuary: Regional Distribution and Priorities for Control. SFEI Contribution No. 321. San Francisco Estuary Institute: Richmond CA. p 42.
1998. 
Lower Peninsula Watershed Condition Assessment 2016: Southwest San Francisco Bay, Santa Clara County, San Francisquito to Stevens Creeks. Technical memorandum prepared for the Santa Clara Valley Water District. . SFEI Contribution No. 809. San Francisco Estuary Institute: Richmond. p 53.
2017. 
LTMS Symposium on Methylmercury in Dredging Operations and Dredged Sediment Reuse in the San Francisco Estuary. San Francisco Estuary Institute: Oakland, Ca.
2010. 2010.
Mercury and Methylmercury Processes in North San Francisco Bay Tidal Wetland Ecosystems. CalFed with San Francisco Estuary Institute as primary contractor.
2005. Mercury and Methylmercury Processes in North San Francisco Bay Tidal Wetland Ecosystems. SFEI Contribution No. 449. San Francisco Estuary Institute: Oakland, CA.
2008. 
Mercury and tidal wetland restoration. In Chapter 6 in Brown, L. (ed.). DRAFT CALFED Whitepaper on: Ecological Processes in Tidal Wetlands of the Sacramento-San Joaquin Estuary and Their Implications for Proposed Restoration Efforts of the Ecosystem Restoration Program.. Chapter 6 in Brown, L. (ed.). DRAFT CALFED Whitepaper on: Ecological Processes in Tidal Wetlands of the Sacramento-San Joaquin Estuary and Their Implications for Proposed Restoration Efforts of the Ecosystem Restoration Program.
2000. Mercury and tidal wetland restoration. CalFED Journal . SFEI Contribution No. 339.
2002. Monitoring the US West Coast: An Assessment of California’s Estuaries and the Pacific Ocean:Spatial Hierarchy and its Rationale. SFEI Contribution No. 120. San Francisco Estuary Institute: Oakland, CA.
2002. 