References by Topic

References by Topic | References by Project

Click here to view references organized by tidal marsh restoration and monitoring projects.

Why Monitor?

Johnson, G.E. and H.L. Diefenderfer (editors). 2010. Evaluating cumulative ecosystem response to restoration projects in the Columbia River estuary, Final Annual Report 2009. PNNL-16561. Report to the U.S. Army Corps of Engineers, Portland District, by Pacific Northwest National Laboratory, Richland, Washington.

Keddy, P. A. 2000. Wetland ecology: Principles and conservation. Cambridge University Press, 614pp.

Lee, K. 1993. Compass and Gyroscope: integrating science and politics for the environment. Washington, D.C: Island Press, 255pp.

Woo, I., R.Fuller, M. Iglecia, K. Turner, J. Takekawa. 2011. The Nature Conservancy: Port Susan Bay Estuary Restoration Monitoring Plan. Unpublished report to The Nature Conservancy. US Geological Survey, Western Ecological Research Center, 505 Azuar Drive Vallejo CA 94592. 115pp.

Zedler, J.B. 2005. Ecological restoration: guidance from theory. San Francisco Estuary and Watershed Science 3(2):1-31.

Design

Brophy, L.S. (Green Point Consulting). 2009. Effectiveness Monitoring for Tidal Wetland Restoration and Reference Sites in the Siuslaw River Estuary. Prepared for Ecotrust, Portland, OR. 125pp.

Brophy, L.S., and S. van de Wetering. 2012. Ni-les'tun Tidal Wetland Restoration Effectiveness Monitoring: Baseline: 2010-2011. Corvallis, Oregon: Green Point Consulting, the Institute for Applied Ecology, and the Confederated Tribes of Siletz Indians. 114 pp.

Calloway, J. C., Sullivan, G., Desmond, J. S., Williams, G. D., and Zedler, J. B. Assessment and monitoring. 2001. Pages 271-335 in Zedler, J. B. (Editor), Handbook for Restoring Tidal Wetlands. CRC Press, Boca Raton.

Ellings, C. S. 2011. Draft Nisqually National Wildlife Refuge Estuary restoration project monitoring framework. Nisqually National Wildlife Refuge and Ducks Unlimited, Olympia, WA.

Ellings, C., K. Turner, E. Grossman, K. Larsen, J. Cutler, S. Rubin, I. Woo, J.Y. Takekawa, A. Lind-Null, C. Curran, F. Leischner, S. Hodgson, A. David, J. Dorner, J. Barham and J. Takekawa. 2011. Expanding research to keep pace with extensive restoration in the Nisqually Delta. 2011 Salish Sea Ecosystem Conference. Poster Presentation. Vancouver, B. C.

Hood, W. G. 2009. Habitat Monitoring Strategy for the Tidal Skagit Delta. Skagit River System Cooperative, LaConner, WA. 43pp.

Johnston, K.K., Del Giudice-Tuttle, E., Medel, I.D., Piechowski, C.J., Cooper, D.S., Dorsey, J., and Anderson, S. 2012. The Ballona Wetlands Ecological Reserve Baseline Assessment Program: Second Year Report. Santa Monica Bay Restoration Commission. Prepared for the California State Coastal Conservancy, Los Angeles, California. 215 pp.

Murtaugh2001_OnRejectionRatesPairedIntervention

NAVFAC 2004. Guidance for habitat restoration monitoring: framework for monitoring plan development and implementation. Unpublished report to the Naval Facilities Engineering Command Risk Assessment Working Group. Environmental Assessment Division Argonne National Laboratory, 9700 S. Cass Avenue Argonne, IL 60439 130pp.

Neckles, H. A., M. Dionne, D. M. Burdick, C. T. Roman, R. Buchsbaum, and E. Hutchins. 2002. A monitoring protocol to assess tidal restoration of salt marshes on local and regional scales. Restoration Ecology 10:556-563.

Rice, C., P. Roni, J. Hall, J. Chamberlin, G. Hood, G. Guntenspergen, L. Johnson, H. Imaki, M. Calvi, A. Portinga, C. Crandell, and L. Tear. 2011. Draft monitoring plan for the Qwuloolt restoration project. Unpublished report. 70pp.

Roegner, G.C., H.L. Diefenderfer, A.B. Borde, R.M. Thom, E.M. Dawley, A.H. Whiting, S.A. Zimmerman, and G.E. Johnson. 2008. Protocols for Monitoring Habitat Restoration Projects in the Lower Columbia River and Estuary. PNNL-15793. Report by Pacific Northwest National Laboratory, National Marine Fisheries Service, and Columbia River Estuary Study Taskforce submitted to the U.S. Army Corps of Engineers, Portland District, Portland, Oregon.

Simenstad, C., M. Logsdon, K. Fresh, H. Shipman, M. Dethier, J. Newton, 2006. Conceptual model for assessing restoration of Puget Sound nearshore ecosystems. Puget Sound Nearshore Partnership Report No. 2006-03. Published by Washington Sea Grant Program, University of Washington, Seattle, Washington.

Taylor2003_SaltMarshRestorationWhatScientistAreDiscovering

Thayer, G. W., T. A. McTigue, R. J. Bellmer, F. M. Burrows, D. H. Merkey, A. D. Nickens, S. J. Lozano, P. F. Gayaldo, P. J. Polmateer, and P. Thomas Pinit. 2003. Science-Based Restoration Monitoring of Coastal Habitats, Volume One: A Framework for Monitoring Plans Under the Estuaries and Clean Waters Act of 2000 (Public Law 160-457). NOAA Coastal Ocean Program Decision Analysis Series No. 23, Volume 1. NOAA National Centers for Coastal Ocean Science, Silver Spring, MD. 35pp. plus appendices.

Thayer, G. W., T. A. McTigue, R. J. Salz, D. H. Merkey, F. M. Burrows, and P. F. Gayaldo, (eds.). 2005. Science-Based Restoration Monitoring of Coastal Habitats, Volume Two: Tools for Monitoring Coastal Habitats. NOAA Coastal Ocean Program Decision Analysis Series No. 23. NOAA National Centers for Coastal Ocean Science, Silver Spring, MD. 628pp. plus appendices.

Thom, R. M., and K. F. Wellman. 1996. Planning Aquatic Ecosystem Restoration Monitoring Programs. IWR Report 96-R-23, Institute of Water Resources, and Waterways Experimental Station, U.S. Army Corps of Engineers, Alexandria, VA, and Vicksburg, MS.

Woo, I. and J. Y. Takekawa. 2008. Restoration of the Nisqually Estuary: monitoring initial progress of the Nisqually National Wildlife Refuge tidal restoration. Unpublished monitoring plan. U. S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA. 11pp.

Woodward, A. and Hollar, K., 2011, Monitoring habitat restoration projects: U.S. Fish and Wildlife Service Pacific Region Partners for Fish and Wildlife Program and Coastal Program Protocol: U.S. Geological Survey Techniques and Methods 2-A11, 36pp.

Design: Adaptive Management

Zedler, J. B., and J.C. Callaway. 2003. Adaptive restoration: A strategic approach for integrating research into restoration projects. Pp.167-174 in D. J. Rapport, W. L. Lasley, D. E. Rolston, N. O. Nielsen, C. O. Qualset, and A. B. Damania, eds. Managing for Healthy Ecosystems. Lewis Publishers, Boca Raton, Florida.

Design: Before-After Control-Impact

Roman, C.T., Raposa, K.B., Adamowicz, S.C., James-Pirri, M., and J.G. Catena. 2002. Quantifying vegetation and nekton response to tidal restoration of a New England salt marsh. Restoration Ecology 10(3): 450-460.

Smith, P.E., D.R. Orvos, and J. Cairns. 1993. Impact assessment using the before-after control-impact (BACI) model: concerns and comments. Canadian Journal of Fisheries and Aquatic Sciences 50:627-637.

Stewart-Oaten, A., W. W. Murdoch, and K. R. Parker. 1986. Environmental Impact Assessment: “pseudoreplication” in time? Ecology 67:929-940.

Stewart-Oaten, A., J. R. Bence, and C. W. Osenberg. 1992. Assessing effects of unreplicated perturbations: no simple solutions. Ecology 73:1396-1404.

Stewart-Oaten, A. 2003. On rejection rates of paired intervention analysis: comment. Ecology 84:2795- 2799.

Underwood, A. J. 1992. Beyond BACI: the detection of environmental impacts on populations in the real, but variable, world. J. Exp. Mar. Biol. Ecol. 161:145-178.

Zedler, J.B. 2005. Ecological restoration: guidance from theory. San Francisco Estuary and Watershed Science 3(2):1-31.

Design: Data Analysis and Management

Bennett, E.M. 2005. A systems model approach to determining resilience surrogates for case studies. Ecosystems 8:945-957.

Conquest, L. L. 2000. Analysis and Interpretation of Ecological Field Data Using BACI Designs: Discussion. Journal of Agricultural, Biological, and Environmental Statistics 5(3):293-296.

Parker, V.T. and S.T.A Pickett. 1997. Restoration as an ecosystem process: implications of the modern ecological paradigm. Pp.17-23 In: Urbanska, K.M., Webb, N.R., Edwards, P.J., editors. Restoration ecology and sustainable development. Cambridge (UK): Cambridge University Press.

Pickett, S.T.A. and Parker, V.T. 1994. Avoiding the old pitfalls: opportunities in a new discipline. Restoration Ecology 2:75-79.

Smith, P.E., D.R. Orvos, and J. Cairns. 1993. Impact assessment using the before-after-control-impact (BACI) model: concerns and comments. Canadian Journal of Fisheries and Aquatic Sciences 50:627-637.

Stewart-Oaten, A., W. W. Murdoch, and K. R. Parker. 1986. Environmental Impact Assessment: “pseudoreplication” in time? Ecology 67:929-940.

Stewart-Oaten, A., J. R. Bence, and C. W. Osenberg. 1992. Assessing effects of unreplicated perturbations: no simple solutions. Ecology 73:1396-1404.

Stewart-Oaten, A. 2003. On rejection rates of paired intervention analysis: comment. Ecology 84:2795-2799.

Thom, R.M., A.B. Borde, N.R. Evans, C.W. May, G.E. Johnson, and J.A. Ward. 2004. A Conceptual Model for the Lower Columbia River Estuary Prepared by Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers, Portland District. Available online at: http://lcrep.org/conceptual_model/html/about.htm (accessed 14 June 2012)

Underwood, A. J. 1992. Beyond BACI: the detection of environmental impacts on populations in the real, but variable, world. J. Exp. Mar. Biol. Ecol. 161:145-178.

Wissmar, R.C. and P.A. Bisson, editors. 2003. Strategies for restoring river ecosystems: sources of variability and uncertainty in natural and managed systems. Bethesda, MD: American Fisheries Society.

Zar, J.H. 1999. Biostatistical Analysis. Fourth edition. Upper. Saddle River, NJ: Prentice Hall, 663pp.

Zedler, J.B. 2005. Ecological restoration: guidance from theory. San Francisco Estuary and Watershed Science 3(2):1-31.

Design: Spatial Scale

Restoration

Borde A.B., A.J. Bryson, A. Cameron, C. Corbett, E.M. Dawley, B.D. Ebberts, R. Kauffman, G.C. Roegner, M.T. Russell, A. Silva, J.R. Skalski, R.M. Thom, J. Vavrinec, III, D.L. Woodruff, S.A. Zimmerman, G.E. Johnson, and H.L. Diefenderfer. 2010. Evaluating Cumulative Ecosystem Response to Restoration Projects in the Lower Columbia River and Estuary, 2009. PNNL-19440, Pacific Northwest National Laboratory, Richland, WA.

Diefenderfer H.L., R.M. Thom, G.E. Johnson, J.R. Skalski, K.A. Vogt, B.D. Ebberts, G.C. Roegner, and E. Dawley. 2011. A Levels-of-Evidence Approach for Assessing Cumulative Ecosystem Response to Estuary and River Restoration Programs. Ecological Restoration 29(1-2):111-132.

Johnson G.E., R.M. Thom, A.H. Whiting, G.B. Sutherland, T.J. Berquam, B. Ebberts, N.M. Ricci, J.A. Southard, and J.D. Wilcox. 2003. An Ecosystem-Based Restoration Plan with Emphasis on Salmonid Habitats in the Lower Columbia River and Estuary. PNNL-14412, Pacific Northwest National Laboratory, Richland, WA.

Miller, J. A., and C. A. Simenstad. 1997. A comparative assessment of a natural and created estuarine slough as rearing habitat for juvenile chinook and coho salmon. Estuaries 20:792-806.

Philip Williams & Associates, Ltd., and P. M. Faber. 2004. Design Guidelines for Tidal Wetland Restoration in San Francisco Bay. The Bay Institute and California State Coastal Conservancy, Oakland, CA. 83pp.

Puget Sound Nearshore Partnership Technical Reports

Simenstad, C.A. and R.M. Thom. 1996. Functional equivalency trajectories of the restored Gog Le-Hi-Te estuarine wetland. Ecological Applications 6:38-56.

Simenstad, C. A., and J. R. Cordell. 2000. Ecological assessment criteria for restoring anadromous salmonid habitat in Pacific Northwest estuaries. Ecol. Engineering 15:283-302.

Simenstad, C., D. Reed, and M. Ford. 2006. When is restoration not? Incorporating landscape-scale processes to restore self-sustaining ecosystems in coastal wetland restoration. Ecological Modeling 26: 27–39.

Thom RM. 2000. Adaptive management of coastal ecosystem restoration projects. Ecological Engineering 15(3-4):365-372.

Thom R.M., G.D. Williams, A.B. Borde, J.A. Southard, S.L. Sargeant, D.L. Woodruff, J.C. Laufle, and S. Glasoe. 2005. Adaptively Addressing Uncertainty in Estuarine and Near Coastal Restoration Projects. Journal of Coastal Research. JCR 40(sp. iss.):94-108.

Thom R.M., H.L. Diefenderfer, J.E. Adkins, C. Judd, M.G. Anderson, K.E. Buenau, A.B. Borde, and G.E. Johnson. 2011. Guidelines, processes and tools for coastal ecosystem restoration, with examples from the United States. Plankton & Benthos Research. 5(Suppl.), 185-201. doi:10.3800/pbr.5.185

Thom R.M., E. Haas, N.R. Evans, and G.D. Williams. 2011. Lower Columbia River and Estuary Habitat Restoration Prioritization Framework. Ecological Restoration 29(1-2):94-110.

Williams, P. B. and P. M. Faber (2001). Salt marsh restoration experience in the San Francisco Bay Estuary. Journal of Coastal Research (Special Issue 27): 203-211.

Yang Z., K.L. Sobocinski, D.W. Heatwole, T. Khangaonkar, R.M. Thom, and R. Fuller. 2010. Hydrodynamic and Ecological Assessment of Nearshore Restoration: A Modeling Study. Ecological Modeling 221(7):1043-1053.

Physical: Hydrology

Bos, J. 2010. Standard operating procedure for seawater sampling, version 2. Washington State Department of Ecology Environmental Assessment Program. EAP025.

Brand, L. A., L. M. Smith, A. Smith, I. Woo, W. Chan, T. Graham, K. Taylor, and J. Y. Takekawa. 2012. Assessing early tidal marsh restoration at the Green Island Unit of the Napa Plant Site Restoration Project within the Napa-Sonoma Marshes Wildlife Area. Data Summary Report, U.S. Geological Survey, Western Ecological Research Center, Vallejo, CA. 133pp.

EPA Office of Water and Office of Science and Technology. 2001. Nutrient criteria technical guidance manual: estuarine and coastal marine waters. Epa-822-B-01-003.

Fagherazzi, Sergio 2008. Geomorphic structure of tidal hydrodynamics in salt marsh creeks. Water Resources Research 44(2).

Hood, W. G. 2002a. Landscape allometry: From tidal channel hydraulic geometry to benthic ecology. Canadian Journal of Fisheries and Aquatic Sciences 59:1418–1427.

Kennish, M.J. (editor). 2003. Estuarine Research, Monitoring, and Resource Protection. Boca Raton, Florida: CRC Press, 297p.

Kennish, M.J., and A.R. Townsend. 2007. Nutrient enrichment and estuarine eutrophication. Ecological Applications 17(5): S1–S2.

National Estuarine Research Reserve System (NERRS). 2012. Nutrient and chlorophyll monitoring program and database design version 1.6.Technical Report, NOAA/NERRS Nutrient Monitoring Committee, National Oceanic and Atmospheric Administration, Silver Spring, Maryland.

Temmerman, S., T. J. Bouma, G. Govers, and D. Lauwaet 2005. Flow paths of water and sediment in a tidal marsh: relations with marsh developmental stage and tidal inundation height. Estuaries 28(3): 338 – 352.

Thorne K. M., K. J. Buffington, K.M. Swanson and J.Y. Takekawa. In review. Frequency of storm events and climate change implications for salt marshes in San Francisco Bay, California. Quaternary International.

Torres, Raymond 2007. Effects of topographic structure on salt marsh currents. Journal of Geophysical Research 112(f2).

U. S. EPA 1997. Volunteer stream monitoring: a methods manual. EPA 841-B-97-003. November U. S. Environmental Protection Agency, Office of Wetlands, Oceans & Watersheds, 4503F, Washington, DC 20460.

Physical: Sediment

CERP. 2009. Quality assurance system requirements (QASR) manual for the comprehensive everglades restoration plan (CERP). Available online at: http://www.evergladesplan.org/pm/program_docs/qasr.aspx (accessed 4 Jan 2012)

CERP. 2009. Quality assurance system requirements (QASR) manual for the comprehensive everglades restoration plan (CERP), soil and sediment sampling procedures chapter 7. Available online at: http://www.evergladesplan.org/pm/pm_docs/qasr/qasr_2009/qasr_2009_chap_07.pdf (accessed 4 Jan 2012)

CERP. 2009. Quality assurance system requirements (QASR) manual for the comprehensive everglades restoration plan (CERP), methods for in-situ surveys and physical measurements appendix 7b. Available online at:
http://www.evergladesplan.org/pm/pm_docs/qasr/qasr_2009/qasr_2009_app_07-b.pdf (accessed 4 Jan 2012)

Christiansen, T., P.L. Wiberg, and T.G. Milligan. 2000. Flow and Sediment Transport on a Tidal Salt Marsh Surface. Estuarine, Coastal and Shelf Science. 50: 315-331.

Neubauer, S.C., I.C. Anderson, J.A. Constantine and S.A. Kuehl. 2002. Sediment Deposition and Accretion in a Mid-Atlantic (USA) Tidal Freshwater Marsh. Estuarine, Coastal and Shelf Science. 54: 713-727.

Pasternack, G.B. and G.S. Brush. 1998. Sedimentation Cycles in a River-Mouth Tidal Freshwater Marsh. Estuaries. 21: 407-415.

Thomas, S. and P. V. Ridd. 2004. Review of methods to measure short time scale sediment accumulation. Marine Geology 207: 95 – 114.

Woo, I., J. Y. Takekawa, A. Rowan, R. Gardiner, O. Bernstein, and G. T. Block. 2007. The Tubbs Setback Restoration Project: Final Report. U. S. Geological Survey, Unpubl. Progress Rep. Vallejo, CA

Physical: Elevation

Athearn, N., Takekawa, J.Y., Jaffe, B., Hattenbach, B.J., and A.C. Foxgrover. 2010. Mapping elevations of tidal wetland restoration sites in San Francisco Bay: comparing accuracy of aerial LiDAR with a singlebeam echosounder. Journal of Coastal Research 26(2): 312-319.

Callaway, J. C., G. Sullivan, J. S. Desmond, G. D. Williams, and J.B. Zedler. 2001. Assessment and monitoring. Pp.271-335 In J. B. Zedler, editor. Handbook for Restoring Tidal Wetlands. CRC Press. Boca Raton, Florida.

Foxgrover, A.C. and Jaffe, B.E., 2005. South San Francisco Bay 2004 Topographic LiDAR Survey: Data Overview and Preliminary Quality Assessment. U.S. Geological Survey Open-File Report OFR-2005-1284. 57p.

Foxgrover, A.C., Finlayson, D.P., and Jaffe, B.E., 2011, 2010 Bathymetry and digital elevation model of Coyote Creek and Alviso Slough, south San Francisco Bay, California: U.S. Geological Survey Open-File Report 2011–1315, 20 p. and datasets, available at: http://pubs.usgs.gov/of/2011/1315/.

Hetherington, D.; German, S.; Utteridge, M.; Cannon, D.; Chisholm, N., and Tegzes, T., 2007. Accurately representing a complex estuarine environment using terrestrial lidar. RSPSoc Conference (Newcastle Upon Tyne, U.K., September 2007) 5p.

Hood, W. G. 2006. A conceptual model of depositional, rather erosional, tidal channel development in the rapidly prograding Skagit River Delta (Washington, USA). Earth Surface Processes and Landforms. DOI:10.1002/esp.1381.

Hood, W. G. 2007. Scaling tidal channel geometry with marsh island area: a tool for habitat restoration, linked to channel formation process. Water Resources Research 43: W03409.

Lowe, T., 2003. Assessing the potential of LiDAR/bathymetry integration within the Thames estuary. FIG Working Week 2003 (Paris, France). Paper number PP20.2, 15p.

Populus, J.; Barreau, G.; Fazilleau, J.; Kerdreux, M., and L’Yavanc, J., 2001. Assessment of the LIDAR topographic technique over a coastal area. In: Proceedings of CoastGIS 2001 (Halifax, Canada). 12p.

Takekawa, J.Y., I. Woo, N. D. Athern, S. Demers, R. J. Gardiner, W. M. Perry, N. K. Ganju, G. G. Shellenbarger, and D. H. Schoellammer. 2010. Measuring sediment accretion in early tidal marsh restoration. Wetlands Ecology and Management 18(3): 297-305 doi: 10.1007/s 11273-009-9170-6.

Wang, C. and Philpot, W.D., 2007. Using airborne bathymetric lidar to detect bottom type variation in shallow waters. Remote Sensing of Environment 106: 123–135.

Woo, I., R. Storesund, J.Y. Takekawa, R.J. Gardiner, and S. Ehret. 2009. Integrating Terrestrial LiDAR and Stereo Photogrammetry to Map the Tolay Lakebed in Northern San Francisco Bay. Pp.279-284 In Webb, R.M.T., and Semmens, D.J., editors. Planning for an uncertain future—Monitoring, integration, and adaptation. Proceedings of the Third Interagency Conference on Research in the Watersheds: U.S. Geological Survey Scientific Investigations Report 2009-5049.

Yang, X., 2005. Use of LIDAR elevation data to construct a high resolution digital terrain model for an estuarine marsh area. International Journal of Remote Sensing 26(23), 5163–5166.

Zedler, J. B. 2001. Handbook for Restoring Tidal Wetlands. CRC Press. Boca Raton, FL. 439pp.

Biological: Invertebrates

Ellings, C.S. and Hodgson, S., 2007. Nisqually Estuary Baseline Fish Ecology Study: 2003-2006. Nisqually National Wildlife Refuge and Nisqually Indian Tribe, Olympia, Washington.

Gray, A., C.A. Simenstad, D.L. Bottom, and T.J. Cornwell, 2002. Contrasting functional performance of juvenile salmon habitat in recovering wetlands of the Salmon River Estuary, Oregon, U.S.A. Restoration Ecology 10:514-526.

Hayes, D. B., Ferreri, C. P. and Taylor, W.W., 1996. Active fish capture methods. Pages 193-220 in B. R. Murphy and D. W. Willis, editors. Fisheries techniques, 2nd edition. American Fisheries Society, Bethesda, Maryland.

Kaminski, R.M. and H.H. Prince. 1981b. Dabbling duck and aquatic macroinvertebrate responses to manipulated wetland habitat. Journal of Wildlife Management 45:1-15.

Kaminski, R.M. and H.H. Prince. 1981a. Dabbling duck activity and foraging responses to aquatic macroinvertebrates. The Auk 98:115-126.

Kaminski, R.M., and H.H. Prince. 1984. Dabbling duck--habitat associations during spring in Delta Marsh, Manitoba. Journal of Wildlife Management 48:37-50.

Simenstad, C.A., A.J. Wick, J.R. Cordell, R.M. Thom, and G.D. Williams, 2001. Decadal development of a created slough in the Chehalis River estuary: year 2000 results. Report to U.S. Army Corps of Engineers, Seattle District.

Takekawa, J. Y., A. K. Miles, D. C. Tsao-Melcer, D. H. Schoellhamer, S. Fregien and N. D. Athearn. 2009. Dietary flexibility in three representative waterbirds across salinity and depth gradients in salt ponds of San Francisco Bay. Hydrobiologia 626: 155-168.

U.S. EPA. 2002. Methods for Evaluating Wetland Condition: Developing an Invertebrate Index of Biological Integrity for Wetlands. Office of Water, U.S. Environmental Protection Agency, Washington, DC. EPA-822-R-02-019.

US Geological Survey. 2010. Invertebrate lab manual. Unpublished benthic invertebrate sieving and sorting protocols. USGS, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA.

Weller, M. W. and L. H. Fredrickson. 1974. Avian ecology of a managed glacial marsh. Living Bird 12:269-291.

Biological: Birds

Brand, L. A., L. M. Smith, A. Smith, I. Woo, W. Chan, T. Graham, K. Taylor, and J. Y. Takekawa. 2012. Assessing early tidal marsh restoration at the Napa Plant Site Restoration Project within the Green Island Unit of the Napa-Sonoma Marshes Wildlife Area. Data Summary Report, U. S. Geological Survey, Western Ecological Research Center, Vallejo, CA. 135 pp.

Conway, C. J. 2008. Standardized North American Marsh Bird Monitoring Protocols. Wildlife Research Report #2008-01. U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, Tucson, AZ.

Croonquist, M. J. and R. P. Brooks. 1991. Use of avian and mammalian guilds as indicators of cumulative impacts in riparian wetland areas. Environmental Monitoring 15:701–714.

FAO. 2007. Wild Birds and Avian Influenza: an introduction to applied field research and disease sampling techniques. Edited by D. Whitworth, S.H. Newman, T. Mundkur and P. Harris. FAO Animal Production and Health Manual, No. 5. Rome. (also available at www.fao.org/avianflu)

Greene, T., A. Jones, G. Dennis, and T. Sachtleben. 2010. Distance sampling to determine kaka (Nestor meridionalis septentrionalis) density within Waipapa Ecological Area, Pureora. New Zealand Journal of Ecology 34 (3): 297 – 305.

Gregory, R. D., D. W. Gibbons, and P. F. Donald. 2004. Bird census and survey techniques. Pp.17-55 In Sutherland, W. J., I. Newton, and R. Green, editors. Bird ecology and conservation: a handbook of techniques. Oxford University Press. New York, NY. 386pp.

Kaminski, R.M., and H.H. Prince. 1981a. Dabbling duck activity and foraging responses to aquatic macroinvertebrates. The Auk 98:115126.

Kaminski, R.M., and H.H. Prince. 1984. Dabbling duck--habitat associations during spring in Delta Marsh, Manitoba. Journal of Wildlife Management 48:37-50.

Taft, O. W., P. M. Sanzenbacher, and S. M. Haig. 2008. Movements of wintering Dunlin Calidris alpina and changing habitat availability in an agricultural wetland landscape. Ibis 150: 541-549.

Thomas, L., S.T. Buckland, E.A. Rexstad, J. L. Laake, S. Strindberg, S. L. Hedley, J. R.B. Bishop, T. A. Marques, and K. P. Burnham. 2010. Distance software: design and analysis of distance sampling surveys for estimating population size. Journal of Applied Ecology 47: 5-14. DOI: 10.1111/j.1365-2664.2009.01737.x

Thompson, W. L. 2002. Towards reliable bird surveys: accounting for individuals present but not detected. The Auk 119:18–25.

Weller, M. W. and L. H. Fredrickson. 1974. Avian ecology of a managed glacial marsh. Living Bird 12:269-291.

Woo, I., K. Turner, A. Smith, P. Markos, and J. Y. Takekawa. 2011. Assessing habitat development in response to large scale restoration at the Nisqually River Delta. Unpublished data summary report to the National Fish and Wildlife Foundation, Puget Sound Marine Conservation Fund #2006-0180-017. USGS Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA. 21pp.

Biological: Fish

Ellings, C.S. and S. Hodgson. 2007. Nisqually Estuary Baseline Fish Ecology Study: 2003-2006. Nisqually National Wildlife Refuge and Nisqually Indian Tribe, Olympia, Washington.

Gelfenbaum, G., T. Mumford, J. Brennan, H. Case, M. Dethier, K. Fresh, F. Goetz, M. van Heeswijk, T.M., Leschine, M. Logsdon, D. Myers, J. Newton, H. Shipman, C.A. Simenstad, C. Tanner, and D. Woodson, 2006. Coastal Habitats in Puget Sound: A research plan in support of the Puget Sound Nearshore Partnership. Puget Sound Nearshore Partnership Report No. 2006-1. Published by the U.S. Geological Survey, Seattle, Washington.

Hayes, D. B., Ferreri, C. P. and Taylor, W.W., 1996. Active fish capture methods. Pages 193-220 in B. R. Murphy and D. W. Willis, editors. Fisheries techniques, 2nd edition. American Fisheries Society, Bethesda, Maryland.

Johnson, D. H., B. M. Shrier, J. S. O’Neal, J. A. Knutzen, X. Augerot, T. A. O’Neil, and T. Pearsons, editors. 2007. Salmonid field protocols handbook: techniques for assessing status and trends in salmon and trout populations. American Fisheries Society in association with State of the Salmon, Bethesda, Maryland. 478pp. Available online at: http://www.stateofthesalmon.org/fieldprotocols/ (last accessed 25 May 2012)

Levy, D. A. and C. Northcote. 1982. Juvenile salmon residency in a marsh area of the Fraser River Estuary. Can. J. Fish. Aquat. Sci. 39: 270-276.

Lind-Null, A., Larsen, K., Reisenbichler, R. 2008a. Pre-Restoration habitat use by Chinook Salmon in the Nisqually Estuary using otolith analysis: U.S. Geological Survey Open File Report 2008-1021, 13p.

Lind-Null, A., Larsen, K., Reisenbichler, R. 2008b. Characterization of estuary use by Nisqually Hatchery Chinook based on otolith analysis: U.S. Geological Survey Open File Report 2008-1102, 12p.

Lind-Null, A., Larsen, K. 2009. Pre-Restoration habitat use by Chinook Salmon in the Nisqually Estuary using otolith analysis: An additional year: U.S. Geological Survey Open File Report 2009-1106, 18p.

Miller, J. A., and C. A. Simenstad. 1997. A comparative assessment of a natural and created estuarine slough as rearing habitat for juvenile chinook and coho salmon. Estuaries 20:792-806.

Biological: Small Mammals

Manley, P.N.; Van Horne, B.; Roth, J.K.; Zielinski, W.J.; McKenzie, M.M.; Weller, T.J.; Weckerly, F.W.; Vojta, C. 2006. Multiple species inventory and monitoring technical guide. Gen. Tech. Rep. WO 73. Washington, DC: U.S. Department of Agriculture, Forest Service, Washington Office. 204 p.

Nelson, L. and F.W. Clark. 1973. Correction for sprung traps in catch/effort calculations of trapping results. Journal of Mammalogy 54(1):295-298.

Padgett-Flohr, G. E. and H. Shellhammer. 2002. Data collection protocols: surveying for the Salt Marsh Harvest Mouse (Reithrodontomys raviventris), California Vole (Microtus californicus) and other small mammals, Wetland Regional Monitoring Program, San Francisco Estuary Institute, Oakland CA.

Ecological: Habitat: Aerial Photography and Remote Sensing

Janisch, J. 2006. Standard operating procedures for estimating large woody debris loads intersecting headwater channels. V. 1.0. Unpublished report of the Washington State Department of Ecology, Environmental Assessment Program. Lacy, WA.

Woo, I, K. L. Turner, J. Y. Takekawa. 2011b. Monitoring and Evaluation of the Nisqually Delta Restoration Project. Project progress report to Nisqually National Widlife Refuge, Olympia, WA. U. S. Geological Survey, San Francisco Bay Estuary Field Station, Vallejo, CA. Unpubl. report. 25pp.

Ecological: Habitat: Vegetation Methods

Bonham, C.D. 1989. Measurements for Terrestrial Vegetation, John Wiley & Sons, Inc., NewYork, N.Y.

Carlisle, B., M. Carullo, J. Smith, C. Wigand, R. McKinney, M. Charpentier, D. Fillis, , and M. Stolt 2006. Rapid method for assessing estuarine (salt) marshes in New England version 1.4 – October 2006. Modified by: Hilary Neckles and Glenn Guntenspergen USGS, Patuxent Wildlife Research Center, Laurel, MD.

Collins, J. N., D. Goodman-Collins, and J. Stalker. 2010. Data collection protocol: plant community structure of intertidal—upland ecotone, Wetland Regional Monitoring Program, San Francisco Estuary Institute, Oakland CA.

Elzinga, C., D. Salzer, and J. Willoughby, 1998. Measuring & Monitoring Plant Populations, BLM Technical Reference 1730-1, BLM/RS/ST-98/005+1730, Bureau of Land Management, Natural Science and Technology Center, Lakewood, Colo.

Erwin, K.L. 1990. Wetland evaluation for restoration and creation. Pages 429-458, In J.A. Kusler and M.E. Kentula (eds.) Wetland Creation and Restoration: The Status of the Science, Island Press, Washington, D.C.

Hays, R.L., C. Summers, and W. Seitz, 1981. Estimating Wildlife Habitat Variables. FWS/OBS-81/47, Biological Report. U.S. Fish and Wildlife Service, Washington, D.C.

Krebs, C. J. 1999. Ecological Methodology, 2nd edition. Benjamin/Cummings, New York, NY.

Stehman, S. and D. Salzer. 2000. Estimating density from surveys employing unequal-area belt transects. Wetlands. 20(3): 512-519.

Vasey, M, J Callaway, VT Parker. 2002. Data collection protocol: tidal wetland vegetation. Wetland Regional Monitoring Program, San Francisco Estuary Institute, Oakland CA.

Washington State Department of Transportation (WSDOT). 2008. WSDOT Wetland Mitigation Site Monitoring Methods. Available online at: http://www.wsdot.wa.gov/NR/rdonlyres/C211AB59-D5A2-4AA2-8A76-3D9A77E01203/0/MethodsWhitePaper052004.pdf
(accessed 24 April 2012).

Zedler, J.B. 2001. Handbook for restoring tidal wetlands. CRC Press, New York.

Ecological: Habitat: Vegetation Project Applications

Adamus, P.R. 2005. Science review and data analysis for tidal wetlands of the Oregon Coast. Part 2 of a Hydrogeomorphic Guidebook. Report to Coos Watershed Association, US Environmental Protection Agency, and Oregon Dept. of State Lands, Salem.

Belleveau, L. J. In review. Determining how soil salinity and tidal inundation influence the distribution, species diversity and growth of salt marsh vegetation: implications for the restoration of the Nisqually Delta, Washington. M.S. Thesis, The Evergreen State College, Olympia, Washington.

Simenstad, C.A. and R.M. Thom. 1996. Functional equivalency trajectories of the restored Gog Le-Hi-Te estuarine wetland. Ecological Applications 6:38-56.

Takekawa, J. Y., M. A. Bias, I. Woo, K. L. Turner, A. R. Westhoff, G. T. Downard, and F.A. Reid. 2005. Restoration Research and Monitoring in Bayland Wetlands of the San Francisco Bay Estuary: The Tolay Creek Restoration Project. U. S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA. Unpubl. report. 72pp.

Takekawa, J.Y., A.K. Miles, N.D. Athearn, S.E. Spring, M.K. Saiki, F. Mejia, I. Woo, and K.S. Goodenough. 2005. Habitat Restoration Monitoring for the Napa-Sonoma Marsh Restoration Project, 2005. U. S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA. Unpubl. report. 78pp.

Tanner, C.D., J.R. Cordell, J. Rubey, L.M. Tear. 2002. Restoration of freshwater intertidal habitat functions at Spencer Is., Everett, Washington. Res. Ecol. 10: 564-576.

Thom R.M., R. Zeigler, and A.B. Borde. 2002. Floristic Development Patterns in a Restored Elk River Estuarine Marsh, Grays Harbor, Washington. Restoration Ecology 10(3):487-496.

Williams, P.B. and M.K. Orr. 2002. Physical evolution of restored breached levee salt marshes in the San Francisco Bay estuary. Res. Ecol. 10: 527-537.

Woo, I., R. Fuller, M. Iglecia, K. Turner, J. Takekawa. 2011. The Nature Conservancy: Port Susan Bay Estuary Restoration Monitoring Plan. Unpublished report to The Nature Conservancy. U. S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA. 115pp.

Woo, I., J. Y. Takekawa, and R. Gardiner. 2006. Guadalcanal Tidal Marsh Restoration: 2006 Progress Report. Unpublished report to California Department of Transportation, District 4, Oakland, CA. U. S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA. 64pp.

Woo, I., J. Y. Takekawa, A. Rowan, R. Gardiner, O. Bernstein, and G. T. Block. 2007. The Tubbs Setback Restoration Project: Final Report. U. S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA. Unpubl. report. 75pp.

Woo, I., J. Y. Takekawa, A. Rowan, L. Dembosz, and R. Gardiner. 2008. The Benicia-Martinez (BenMar) Restoration Project: 2007 Annual Report. U. S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA. Unpubl. report. 44pp.

Ecological: Habitat: Channels

Hood W. G. 2010. Tidal channel meander formation by depositional rather than erosional processes: examples from the prograding Skagit River Delta. Earth Surface Processes and Landforms 35: 319 – 330.