Josh Collins; Grosso, C.; Rodriguez, M.; Kimball, J. 2021. Aquatic, Wetland, and Riparian Habitat Mapping Committee -- Draft Charter.

Dusterhoff, S.; Shaw, S.; McKnight, K. 2021. Flood Control Channel Classification Scheme for the San Francisco Bay Region.  Josh Collins, Ed.. San Francisco Bay Region Flood Control Channel Classification .  SFEI Contribution No. 1046. San Francisco Estuary Institute: Richmond, CA.

Rodriguez, M.; Kimball, J.; Grosso, C.; Josh Collins; Askevold, R. 2021. OPC Coastal Wetlands, Beaches and Watersheds Inventory Factsheet, March 2021th ed.

Lowe, S. 2019. West Valley Watershed Assessment 2018: Baseline Ecological Condition Assessment of Southwest San Francisco Bay Creeks in Santa Clara County; Calabazas, San Tomas Aquino, Saratoga,  Sunnyvale East and West.  Salomon, M., Pearce, S., Josh Collins, Titus, D., Eds..  SFEI Contribution No. 944. San Francisco Estuary Institute: Richmond.
This report describes baseline information about the amount and distribution of aquatic resources, and evaluates the overall ecological conditions of streams using the California Rapid Assessment Method (CRAM), for the West Valley watershed in Santa Clara County; consisting of Sunnyvale East and West Channels, Calabazas Creek, San Tomas Aquino and Saratoga creeks, and many smaller tributaries.

Robinson, A.; Richey, A.; Slotton, D.; Josh Collins; Davis, J. 2018. North Bay Mercury Biosentinel Project: 2016 - 2017.  SFEI Contribution No. 868.

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.

Lowe, S. 2017. 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.  Salomon, M., Pearce, S., Josh Collins, Titus, D., Eds..  SFEI Contribution No. 809. San Francisco Estuary Institute: Richmond. p 53.

Greenbaum, E.; Beagle, J.; Collins, J. N.; Gould, C.; Grenier, J. Letitia; Grossinger, R. M.; Hagerty, S.; Lockhart, B.; Lowe, J.; McKnight, K.; et al. 2017. Resilient By Design Briefing Book.

Pearce, S.; Lowe, S.; Collins, J. N. 2016. CRAM Fieldwork 2015 to Support Caltrans Project Tasks 2 & 3.

Pearce, S.; Lowe, S.; Collins, J. N. 2016. Depressional wetland habitat development curve.

Pearce, S.; Lowe, S.; Collins, J. N. 2016. The effects of aquatic area abundance, buffer, and hydrology on depressional wetland condition based on CRAM.

Lowe, S.; Sim, L.; Shusterman, G.; Grosso, C.; Collins, J. N. 2016. Enhancements to EcoAtlas? CRAM analysis tools: Habitat Development Curves and Ecoregional Cumulative Distribution Function plots (CDFs).

Josh Collins; Lowe, S. 2016. Framework to coordinate water quality improvement and wildlife habitat conservation to protect California streams, wetlands, and riparian areas. 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'.

Pearce, S.; Lowe, S.; Collins, J. N. 2016. Relationship between wetland condition, stress, and buffer.

Pearce, S.; Lowe, S.; Collins, J. N. 2016. Relationship between wetland size and CRAM condition scores for depressional wetlands.

Lowe, S.; Salomon, M.; Pearce, S.; Josh Collins; Titus, D. 2016. Upper Pajaro River Watershed Condition Assessment 2015. Technical memorandum prepared for the Santa Clara Valley Water District - Priority D5 Project.  SFEI Contribution No. 810. San Francisco Estuary Institute: Richmond, CA. p 60.
In 2015 The Santa Clara Valley Water District and it's consultants conducted a watershed wide survey to characterize the distribution and abundance of the aquatic resources within the upper Pajaro River watershed wtihin Santa Clara County, CA based on available GIS datasets, and to assess the overall ecological condition of streams within the watershed based on a statistically based random sample design and the California Rapid Assessment Method for streams (CRAM).

Lowe, S.; Grosso, C.; Pearce, S.; Robinson, A.; Salomon, M.; Kauhanen, P.; Shusterman, G.; Bezalel, S. N.; Collins, J. N.; Titus, D.; et al. 2015. Stream Health of the Coyote Creek and Guadalupe River Watersheds using WRAMP.

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.

Lowe, S.; Collins, J. N.; Pearce, S. 2014. Developmental Trajectory for California Tidal Marsh Restoration and Mitigation Projects.

Dusterhoff, S. D.; Beagle, J.; Collins, J. N.; Doehring, C. 2014. 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.

Dusterhoff, S.; Collins, J. N.; Hale, T.; Lowe, S.; Kunze, M.; Cayce, K. 2014. RipZET: A GIS-Based Decision Support Tool for Estimating Riparian Zones at the Watershed and/or Project Scale.

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.

Lowe, S.; Collins, J. N.; Romsos, S. 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.

Lowe, S.; Josh Collins; Pearce, S. 2013. Statistical Design, Analysis, and Graphics for the Guadalupe River Watershed Assessment 2012.  SFEI Contribution No. 687. San Francisco Estuary Institute: Richmond, CA.

Robinson, A.; Slotten, D.; Collins, J. N.; Davis, J. A. 2013. Using Biosentinels to assess Methylmercury Risk in Wetland Restoration Projects.

Williams, M.; Collins, J. N.; Pearce, S.; Grossinger, R.; Lent, M.; Oram, J.; Koehler, J.; Hoenicke, R. 2012. Napa River Watershed Profile: Past and Present Characteristics with Implications for Future Management of the Changing Napa River Valley. San Francisco Estuary Institute: Richmond, CA. p 172.

Lowe, S.; Williams, M.; Robinson, A.; Collins, J. N.; Grenier, J. Letitia; Klatt, M.; Bezalel, S. N. 2012. Riparian Mercury Biosentinels for the San Francisco Bay Area.

Collins, J. N.; Davis, J. A.; Hoenicke, R.; Jabusch, T. W.; Swanson, C.; Gunther, A.; Nur, N.; Trigueros, P. 2011. 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.

Cayce, K.; Klatt, M.; Kass, J.; Williams, M.; Collins, J. N. 2011. Bay Area Aquatic Resource Inventory.

Collins, J. N.; Goodman-Collins, D. Darcie; Stalker, J. 2010. Data Collection Protocol Plant Community Structure of Intertidal--Upland Ecotone.

Grosso, C.; Oram, J. J.; Bezalel, S. N.; Featherston, T.; Ross, J.; May, M.; Frontiera, P.; Collins, J. N.; Williams, M.; Cayce, K.; et al. 2010. Environmental Data Upload and Visualization Tools.

Grossinger, R. M.; Whipple, A.; Rankin, D.; Collins, J. N. 2010. Historical Delta Landscapes: Conceptual models for building a diverse and resilient future.

Whipple, A.; Grossinger, R. M.; Rankin, D.; Collins, J. N. 2010. The Historical Yolo Basin Landscape: What parts make the whole?.

Hunt, J. A.; Yee, D.; Collins, J. N. 2010. LTMS Symposium on Methylmercury in Dredging Operations and Dredged Sediment Reuse in the San Francisco Estuary. San Francisco Estuary Institute: Oakland, Ca.

Collins, J. N. 2010. Managers' wrap-up.

Collins, J. N. 2010. Roundtable discussion.

Collins, J. N.; Williams, M.; Lowe, S. 2010. Third Summary Report Montezuma Wetlands Restoration Project Technical Review Team. San Francisco Estuary Institute: Oakland, CA.

Klatt, M.; Cayce, K.; Williams, M.; Collins, J. N. 2009. Bay Area Base Map of Aquatic Habitats.

Collins, J. N.; Solek, C.; Connor, K. O. '; Fetscher, E.; Clark, C.; Rey, K.; Morrissette, S.; Eicher, A.; Pasquinelli, R.; Ritter, K.; et al. 2009. California?s Statewide Survey Of Tidal Wetland Condition.

Collins, J. N.; Cayce, K.; Williams, M. 2009. Riparian Area Mapping Model Overview.

McKee, L. J.  .; Collins, J. N.; Pearce, S.; Gilbreath, A. N.; Bigelow, P.; Ridolfi, K. 2008. Alameda Creek Sediment Forum.

Collins, J. N.; Grenier, J. Letitia; Sutula, M. 2008. Developing Tools to Help Protect and Manage California  Wetlands, Streams, and Riparian Resources.

Salomon, M.; Collins, J. N.; Striplen, C. J.; Brewster, E.; Grossinger, R. M. 2008. The Historical Ecology of Miller Creek http://www.nbwatershed.org/millercreek/.

Grossinger, R. M.; Collins, J. N.; Beller, E. E.; Gardner, S. 2008. The Historical Ecology of Napa Valley: An Introduction.  SFEI Contribution No. 557.

Yee, D.; Collins, J. N.; Grenier, J. Letitia; Krabbenhoft, D.; Takekawa, J. Y.; Tsao-Melcer, D.; Olund, S.; Woo, I.; DeWild, J.; Schwarzbach, S.; et al. 2008. Mercury and Methylmercury Processes in North San Francisco Bay Tidal Wetland Ecosystems.  SFEI Contribution No. 449. San Francisco Estuary Institute: Oakland, CA.

Collins, J. N.; Hoenicke, R. 2008. Setting Goals and Defining Watershed and Stream "Health" to Better Integrate Policies, Programs, and Projects.

Collins, J. N.; Hoenicke, R. 2007. Aligning Socio-Economic and Ecological Condition Valuation.

Collins, J. N. 2007. CRAM Evaluation of Wetland Conditions.  SFEI Contribution No. 544. Elk Grove, California. p 15.

Collins, J. N.; Grenier, J. Letitia; Didonato, J.; Geupel, G.; Kucera, T.; Lidicker, B.; Rainey, B.; Rottenborn, S. 2007. Ecological Connections between Baylands and Uplands: Examples from Marin County.  SFEI Contribution No. 521.

Collins, J. N. 2007. Monitoring the Water Quality Impacts of Wetland Restoration.

Beller, E. E.; Grossinger, R. M.; Askevold, R. A.; Pearce, S.; Collins, J. N.; McKee, L. J.  .; Hoenicke, R.; Gardner, S. 2007. Streams, Wetlands, and Woodlands in the Napa Valley: New Perspectives from Old Maps.

Collins, J. N.; Odaya, M.; Sutula, M.; Stein, E.; Cayce, K.; Zhang, E. 2006. Comparison of Methods to Map California Riparian Areas. . SFEI Contribution No. 522.

Grossinger, R. M.; Askevold, R. A.; Striplen, C. J.; Brewster, E.; Pearce, S.; Cayce, K.; McKee, L. J.  .; Collins, J. N. 2006. 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.

Collins, J. N.; Grosso, C. 2006. Second Annual Report Montezuma Wetlands Restoration Project Technical Review Team.  SFEI Contribution No. 516.

Grossinger, R. M.; Collins, J. N.; Cayce, K.; Askevold, R. A.; Featherston, T.; Zhang, E. 2006. U.S. Coast Survey Maps of SFBay http://maps.sfei.org/tSheets/viewer.htm.

Grossinger, R. M.; Collins, J. N.; Enright, C.; Culberson, S.; Mueller-Solger, A. 2005. Changing Delta Geometry and Ecology: The Effects of Historical Landscape Modification on Water Quality and Ecosystem Structure in Suisun Marsh and Delta.

Collins, J. N.; Wheetly, M.; Potter, C.; Breaux, A.; Clark, R.; Featherston, T.; May, M.; Cayce, K.; Stein, E.; Sutula, M.; et al. 2005. An Integrated Wetlands Assessment Program for the San Francisco Bay Area and California.

Yee, D.; Collins, J. N.; Grenier, J. Letitia; Takekawa, J. Y.; Schwarzbach, S.; Tsao-Melcer, D.; Woo, I.; Marvin-DiPasquale, M.; Agee, J. L.; Kieu, L. H.; et al. 2005. Mercury and Methylmercury Processes in North San Francisco Bay Tidal Wetland Ecosystems. CalFed with San Francisco Estuary Institute as primary contractor.

Collins, J. N.; Clark, R.; Sutula, M. A.; Stein, E. D.; Fetscher, A. E. 2005. A practical guide for the development of a wetland rapid assessment method: the California experience. J. of the American Water Resources Association . SFEI Contribution No. 448.

Collins, J. N.; Grosso, C.; Wittner, E. 2005. San Francisco Bay Mercury Research Coordination Meeting February 23, 2005 Presentation- Cross-scale  Exploration of Stressor-State Correlations EMAP Estuaries SF Bay Intensification Project.

Grossinger, R. M.; Collins, J. N.; Askevold, R. A. 2005. T-Sheet User Guide: Application of the Historical U.S. Coast Survey Maps to Environmental Management in the San Francisco Bay Area.  SFEI Contribution No. 427. San Francisco Estuary Institute: SF. p 45.

Collins, J. N.; Zhang, E.; May, M.; Breaux, A.; Martindale, M.; Tuxen, K.; Delaney, M.; Featherston, T. 2005. The Wetland Project Tracker.

Collins, J. N.; Pearce, S. 2004. Analysis of Reference Tidal Channel Plan Form for the Montezuma Wetlands Restoration Project.  SFEI Contribution No. 80. San Francisco Estuary Institute: Oakland, CA.

Collins, J. N.; Stralberg, D. 2004. Baylands Vegetation Mapping Protocol (Version 1.0).  SFEI Contribution No. 304. San Francisco Estuary Institute: Oakland, CA.

Collins, J. N. 2004. Elkhorn Slough Tidal Marsh Plan: Possible Lessons from the Bay Area Wetland Ecosystem Goals Project (PowerPoint presentation).

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.

Collins, J. N.; Culberson, S. D.; Foin, T. C. 2004. The Role of Sedimentation in Estuarine Marsh Development within the San Francisco Estuary, California, USA. Journal of Coastal Research 20, 970-979 . SFEI Contribution No. 404.

Collins, J. N. 2004. Summary of the MeHg Panels of the 2004 CalFed Science Conference. Prepared with the advice and review of the Panelists. CalFed Science Conference, 2004, 2.

Collins, J. N.; Grossinger, R. M. 2004. Synthesis of Scientific Knowledge: for maintaining and improving functioning of the South Bay Ecosystem and Restoring Tidal Salt Marsh and Associated Habitats over the next 50 years at Pond and Pond-Complex Scales.  SFEI Contribution No. 308.

Grossinger, R. M.; Collins, J. N.; Striplen, C. J. 2004. Wetland Habitat Changes in the Rodeo Lagoon Watershed, Golden Gate National Recreation Area, Marin County, CA.  SFEI Contribution No. 116. San Francisco Estuary Institute: Oakland, CA.

Collins, J. N.; Grosso, C.; Sutula, M.; Wittner, E.; Stralberg, D. 2003. Ambient Survey of Intertidal Ecological Health and Stressors.

Collins, J. N.; Stralberg, D.; Siegel, S. 2003. Bay Area Wetlands Ecosystem Goals Project: Bay Area Wetland Project Map.

Collins, J. N. 2003. California Rapid Assessment Method (CRAM) - Part 1.

Collins, J. N. 2003. California Rapid Assessment Method (CRAM) - Part 2.  SFEI Contribution No. 285. San Francisco Estuary Institute.

Collins, J. N. 2003. 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.

Collins, J. N. 2003. Coyote Hills Area Habitat Conceptual Planning for 2002-03.

Collins, J. N.; Didonato, J.; Baker, R.; Ackerman, H.; Wolin, F.; Kent, J. 2003. Coyote Hills Wetland Enhancement and Drainage Improvement (Project Summary Outline).

Collins, J. N. 2003. CRAM: Synopsis of first CRAM Core Team meeting, 4.

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.; Sutula, M.; Stein, E. 2003. DRAFT California Rapid Assessment Method for Wetlands v. 2.0 : User's Manual and Scoring Forms, 102.

Collins, J. N. 2003. Draft Guidelines for Developing the CRAM Metrics.  SFEI Contribution No. 284. San Francisco Estuary Institute: Oakland, CA. p 2.

Collins, J. N.; Striplen, C. J.; Brewster, E.; Richard, C.; Burns, T.; Strode, E.; Grossinger, R. M. 2003. Physical and Ecological Characteristics of the Historical Baylands of South San Francisco Bay.

Grossinger, R. M.; Collins, J. N.; Striplen, C. J.; Brewster, E.; Richard, C.; Burns, T.; Strode, E. 2003. Physical and Ecological Characteristics of the Historic Baylands of South San Francisco Bay (Poster for the 2003 State of the Estuary Conference).

Collins, J. N.; Schwarzbach, S. E.; Luoma, S. N.; Yee, D.; Davis, J. A. 2003. Potential for increased mercury accumulation in the Estuary food web: Issues in San Francisco Estuary Tidal Wetlands Restoration. San Francisco Estuary and Watershed Science 1 . SFEI Contribution No. 288.

Collins, J. N.; May, M.; Grosso, C. 2003. Practical Guidebook to the Control of Invasive Aquatic and Wetland Plants of the San Francisco Bay - Delta Region.  SFEI Contribution No. 127. San Francisco Estuary Institute.

Collins, J. N. 2003. Regional Wetlands Monitoring in San Francisco Bay (Abstract).

Collins, J. N. 2003. Regional Wetlands Monitoring in San Francisco Bay (Transcript).

Collins, J. N. 2003. South and Central Bay Wetlands Projects.

Collins, J. N.; Wittner, E.; Grosso, C. 2003. South Bay Updates Modern Baylands Habitat Coverage Bay Area EcoAtlas Information System.  SFEI Contribution No. 282. San Francisco Estuary Institute: Oakland, CA.

Collins, J. N. 2003. Sustaining Regional Partnerships for Conservation: Sharing the Future.

Collins, J. N. 2003. Universal Wetland Ecological Features (Graphic).

Collins, J. N. 2002. California and the World Ocean 2002 (Abstract for Session on California Coastal Wetlands Issues).

Collins, J. N.; Sutula, M.; Stein, E.; Jones, P. 2002. California Rapid Assessment Method for Wetlands v. 1.0.  SFEI Contribution No. 246. San Francisco Estuary Institute. p 18.

Collins, J. N. 2002. Crissy Field Monitoring Technical Review Team (Project Description).

Collins, J. N.; May, M.; Smith, D.; Klohr, S.; Zaremba, K. 2002. 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.

Collins, J. N. 2002. Executive Summary 2002 (Wetlands Science Program).  SFEI Contribution No. 250. San Francisco Estuary Institute. p 4.

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.

Collins, J. N. 2002. Geographic Scope of the Wetlands Science Program, 1.

Collins, J. N.; Ingram, B. L.; Malamud-Roam, K.; Malamud-Roam, F.; Watson, E. 2002. The Historical Geography and Biogeography of Tidal Salt Marshes (Abstract). San Francisco Estuary Institute.

Collins, J. N. 2002. Invasion of San Francisco Bay by Smooth Cordgrass, Spartina alterniflora: A Forecast of Geomorphic Effects on the Intertidal Zone.

Collins, J. N. 2002. Major Technical Components of the Wetlands Science Program, 6.

Collins, J. N. 2002. Management Questions for the Wetlands Science Program, 1.

Collins, J. N. 2002. Management Structure of the Wetlands Science Program, 10.

Collins, J. N.; Yee, D.; Davis, J. A. 2002. Mercury and tidal wetland restoration. CalFED Journal . SFEI Contribution No. 339.

Collins, J. N. 2002. Mission Statement for the Wetlands Science Program.

Collins, J. N. 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.

Collins, J. N.; Grosso, C. 2002. Montezuma Wetlands Monitoring Project Technical Review Team (TRT) First Information Package.

Collins, J. N. 2002. Pacific Estuarine Ecosystem Indicators Research Consortium (PEEIR): Generalized Conceptual Models Wetlands Regional Monitoring Program.

Collins, J. N. 2002. Program Development for the Wetlands Science Program, 1.

Collins, J. N. 2002. Program Origins of the Wetlands Science Program, 1.

Collins, J. N. 2002. San Francisco Estuary Wetalnds Regional Monitoring Program Plan: Version 1, Framework and Protocols.  SFEI Contribution No. 248. San Francisco Estuary Institute: Oakland, CA. p 94.

Collins, J. N. 2002. San Francisco Estuary Wetlands Regional Monitoring Program Plan: Protocols for Tier 3 (Intensive Monitoring).  SFEI Contribution No. 249.

Davis, J. A.; Collins, J. N.; May, M. 2002. Sediment Contaminants.

Collins, J. N. 2002. Statement of Need (Wetlands Science Program), 1.

Collins, J. N. 2002. Summary of Crissy Field Monitoring Elements. San Francisco Estuary Institute.

Greenfield, B. K.; Davis, J. A.; Collins, J. N.; Grenier, J. Letitia. 2002. The tidal marsh food web.  SFEI Contribution No. 472. University of California: Berkeley, CA. p 12 pp.

Collins, J. N.; May, M. 2001. 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.

Collins, J. N.; Jones, P. 2001. Bay Area Wetlands Regional Monitoring Program (Abstract, SOE 2001). San Francisco Estuary Institute: Richmond, CA.

Collins, J. N. 2001. Coyote Hills Historic Baylands.

Collins, J. N. 2001. Establishing Critical Datum Elevations for Wetland Restoration. Coastal Zone . SFEI Contribution No. 484.

Collins, J. N. 2001. Estuarine Wetlands Restoration in the San Francisco Bay Area: the Roles of Not-for-Profits (Transcript), 8.

Collins, J. N. 2001. Final Draft Master List of NIS Plant Species.  SFEI Contribution No. 366. San Francisco Estuary Institute.

Collins, J. N. 2001. Historic Drainage Patterns of the Alameda Watershed (Transcript).

Collins, J. N.; Jones, P.; Lipton, D.; Bonnefil, R.; Levine, J.; Hicks, J. 2001. Montezuma Wetlands Monitoring Project Technical Review Team (TRT) Charter.

Collins, J. N. 2001. Mosquito Landscapes - Part 2 (Transcript).

Collins, J. N. 2001. An Overview of the Expected Physical Relationships between the Intertidal and Shallow Bay Zones of the San Francisco Estuary (Transcript).

Collins, J. N. 2001. Pacific Estuarine Ecosystem Indicators Research Consortium (PEEIR): PEEIR Project Description.

Collins, J. N. 2001. Possible Geomorphic Effects of Invasive Spartina alterniflora in the San Francisco Estuary.

Collins, J. N. 2001. Program Strategy for the Wetlands Science Program.

Collins, J. N.; May, M. 2001. Protocols to Monitor and Assess the Distribution, Abundance, and Treatment of Invasive Spartina in the San Francisco Estuary.  SFEI Contribution No. 364.

Collins, J. N.; Sutula, M.; Wittner, E.; Vasey, M.; Parker, T.; Callaway, J. 2001. QAPP for environmental monitoring and assessment program West Coast Pilot 2002 Intertidal Assessment: California Intensification.  SFEI Contribution No. 234. San Francisco Estuary Institute: Oakland, CA.

Collins, J. N. 2001. Restoration of the San Francisco Region: the Role of NGOs (Abstract). San Francisco, CA: Richmond, CA.

Collins, J. N. 2001. SFEI Wetlands Program Strategy, 6.

Collins, J. N. 2001. Wetlands Regional Monitoring Program. Comparison of Indicators and Methods for Past Wetlands Restoration Projects.  SFEI Contribution No. 362.

Collins, J. N. 2001. Wetlands Regional Monitoring Program. Draft Data Collection Protocols.  SFEI Contribution No. 365.

Collins, J. N. 2001. Wetlands Regional Monitoring Program Prospectus, 9.

Collins, J. N. 2001. Wetlands Regional Monitoring Program. Wetlands Management Questions for the San Francisco Estuary.

Collins, J. N. 2001. Wetlands Regional Monitoring Program. WRMP Program Plan 2001.

Collins, L. M.; Grossinger, R. M.; McKee, L. J.  .; Riley, A.; Collins, J. N. 2001. Wildcat Creek Watershed: A Scientific Study of Physical Processes and Land Use Effects.  SFEI Contribution No. 363. San Francisco Estuary Institute: Richmond, CA.

Collins, J. N. 2001. Will Knowing Tidal Elevation Help Explain Variations in Sediment Chemistry and Microbial Processes Among Sample Plots in Tidal Marshes?.  SFEI Contribution No. 290. San Francisco Estuary Institute. p 6.

Collins, J. N.; Schwarzbach, S. E.; Luoma, S. N.; Yee, D.; Davis, J. A. 2000. 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.

Monroe, M.; Olofson, P. R.; Collins, J. N.; Grossinger, R. M.; Haltiner, J.; Wilcox, C. 1999. 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.

Collins, J. N.; Brewster, E.; Grossinger, R. M. 1999. 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.

Collins, J. N. 1999. Effects of the Goals Project (Transcript).

Collins, J. N. 1999. The Environment of the East Bay Shoreline When Europeans First Arrived (Transcript).

Collins, J. N. 1999. Evolution and Natural Maintenance of Tidal Marshes in San Pablo Bay (Transcript).

Collins, J. N. 1999. Mosquito Landscapes - Part 1 (Transcript).

Grossinger, R. M.; Collins, J. N.; Brewster, E.; Der, Z. 1999. What did this place used to look like, anyway? An Example of Historical Ecology Research from the San Francisco Bay Area, CA (Abstract for Society for Ecological Restoration Conference 1999).

Grossinger, R. M.; Collins, J. N.; Hoenicke, R.; Collins, L. M. 1998. A Bay Area Watersheds Science Approach (Abstract).

Collins, J. N. 1998. Bay Area Wetlands Ecosystem Goals Project: Draft Functional Correspondence between Past and Present Key Habitats.  SFEI Contribution No. 123. San Francisco Estuary Institute.

Collins, J. N. 1998. Bay Area Wetlands Ecosystem Goals Project: Key Baylands Habitats.  SFEI Contribution No. 122. San Francisco Estuary Institute.

Collins, J. N. 1998. Bay Area Wetlands Ecosystem Goals Project: Key Baylands Species.  SFEI Contribution No. 121. San Francisco Estuary Institute.

Collins, J. N. 1998. 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.

Collins, J. N. 1998. The Baylands: Past, Present, and Change (Abstract).

Collins, J. N.; Der, Z.; Wong, C.; Grossinger, R. M. 1998. Cartographic analysis of historical and modern baylands boundaries for Marin County, California.  SFEI Contribution No. 229. Marin County Community Develpment Agency. p 88 pp.

Collins, J. N. 1998. Comments on the Intersection of Land, Water, and People (Transcript).

Collins, J. N.; May, M. 1998. Contamination of Tidal Wetlands.  SFEI Contribution No. 228. Richmond CA.

Grossinger, R. M.; Alexander, J.; Cohen, A. N.; Collins, J. N. 1998. 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.

Collins, J. N. 1998. Mosquito Landscapes (Abstract).

Collins, J. N. 1998. RMP Annual Meeting 1998 (Transcript).

Collins, J. N.; Grossinger, R. M. 1998. Spatial analysis of historical, modern, and future wetlands landscapes of the Bay Area. Bay Area Wetlands Ecosystem Goals Project.  SFEI Contribution No. 319.

Collins, J. N.; Der, Z.; Grossinger, R. M. 1998. Spatial Analysis of the Baylands Ecosystem.  SFEI Contribution No. 320. p 120.

Collins, J. N. 1998. Uncertainty in Biodiversity Planning: Lessons from the Bay Area (Transcript).

Collins, J. N. 1998. The Watershed and the Baylands (Transcript).

Collins, J. N. 1997. Brief Overview of Historical Suisun Tidal Marsh Form and Ecological Function with Notes on Restoration Science (Transcript).

Collins, J. N.; Culberson, S. D.; Foin, T. C.; Garcia, E. J.; Gill, R. E. 1997. Recovery strategies for the California clapper rail (Rallus longirostris obsoletus) in the heavily urbanized San Francisco estuarine ecosystem. Landscape and Urban Planning 38, 229-243 . SFEI Contribution No. 207.

Collins, J. N. 1997. Watershed Conference (Transcript).

Collins, J. N. 1997. Watershed Management in the Bay Area (Transcript).

Grossinger, R. M.; Collins, J. N.; Brewster, E.; Der, Z. 1996. Geography of Wetlands in the San Francisco Estuary (Transcript).

Collins, J. N. 1996. What are Data? (Transcript), 17.

Collins, J. N. 1996. What is a Tidal Marsh?, 1.

Collins, J. N.; Monroe, M.; Wilcox, C.; Olofson, P. 1995. Bay Area Wetlands Ecosystem Goals Project: Focus Team Orientation Package.

Collins, J. N. 1995. Bay Area Wetlands Ecosystem Goals Project: Focus Team Orientation Talking Points.

Collins, J. N. 1995. Bay Area Wetlands Ecosystem Goals Project: Starting Considerations.

Collins, J. N. 1995. A Very Brief Overview on The Histories of Some Marin County Creeks (Transcript).