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Bax, N.J. E.O. Salo, B.P Snyder, C.A. Simenstad, and W.J. Kinney. 1978. Salmon out-migration studies in Hood Canal: a summary - 1977. Proceedings of a Symposium on Salmonid Ecosystems of the North Pacific Ocean. McNeil, W.J. and D.C. Himsworth (eds.) Oregon State University, Corvalis. Sea Grant College Program 1980. pp. 171-201.
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Durkin, J.T. 1982. Migration characteristics of coho salmon smolts in the Columbia River and its estuary. Estuarine Comparison, pp. 365-376.
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Fisher, J.P. and W.G. Pearcy. 1989. Distribution and residence times of juvenile fall and spring chinook salmon in Coos Bay, Oregon. Fishery Bulletin, U.S. 88:51-58.

Pearcy, W.G., C. D. Wilson, A.W. Chung, and J.W. Chapman. 1989. Residence times, distribution, and production of juvenile chum salmon in Netarts Bay, Oregon. Fishery Bulletin U.S. 87(3):553-568.
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Quinn, T.P. and C. Groot. 1984. The effect of water flow rate on bimodal orientation of juvenile chum salmon, Oncorhynchus keta. Animal Behavior 32:628-629.
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Shreffler, D.K. Fisheries surveys for the proposed commercial boat marina in Neah Bay, Washington. January-June 1993. Battelle/Marine Sciences Laboratory, Sequim, WA. Report for Makah Tribe, Neah Bay, Washington under Contract Number 19823.
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Simenstad, C.A., W.J. Kinney S.S. Parker, E.O. Salo, J.R. Cordell, and H. Buechner. 1980. Prey community structure and trophic ecology of outmigrating juvenile chum and pink salmon in Hood Canal, Washington. A synthesis of three years' studies 1977-1979. University of Washington. Fisheries Research Institute, FRI-UW-8026.
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Simenstad, C.A. and W.J. Kinney. 1978. Trophic relationships of outmigrating chum salmon in Hood Canal, Washington. 1977. Report to Washington Department of Fisheries. University of Washington. Fisheries Research Institute. FRI-UW-7810.
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Simenstad, C.A., K.L. Fresh, and E.O. Salo. 1982. The role of Puget Sound and Washington Coastal Estuaries in the life history of Pacific Salmon: an unappreciated function.
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Wissmar, R.C. and C.A. Simenstad. 1988. Energetic constraints of juvenile chum salmon migrating in estuaries. Can J. fish. Aquat. Sci. 45:1555-1560.
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Anderson, E.P., 1985. Use by juvenile chinook salmon of artificial habitat constructed from dredged material in the Columbia River estuary. Can. Contract Report Hydrogr. Ocean Sci. 20:4-15.
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Bailey, J.R. B.L. Wing, and C.R. Mattson. Zooplankton abundance and feeding habits of fry of Pink Salmon, Oncorhynchus gorbuscha, and chum salmon, Oncorhynchus keta, Traitors Cove, Alaska, with speculations on the carrying capacity of the area. Fishery Bulletin, vol 73, no. 4, pp. 846-861.
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Cordell, J.R. and C.A. Simenstad. 1981. Community structure and standing stock, of epibenthic zooplankton at five sites in Grays Harbor, Washington. Report to U.S. Army Corps of Engineers.University of Washington. Fisheries Research Institute.FRI-UW-120.
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Cordell, J.R. 1986. Structure and dynamics of an epibenthic harpacticoid assemblage and the role of predation by juvenile salmon. University of Washington. Masters Thesis. 1986.
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D'Amours, D. 1987. Trophic phasing of juvenile chum salmon and harpacticoid copepods in the Fraser River Estuary. Doctoral Dissertation. University of British Columbia.
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Hiss, J.M., J.L. Schroeder, and S. Lind. 1988. The effect of beach nourishment on salmonid prey resources of Lincoln Park Beach, Seattle, Washington: pre-project conditions. U.S. Fish and Wildlife Service. Report to U.S. Army Corps of Engineers.
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Hiss, J.M., S.R. Hager, J.L. Schroeder, and E.E. Knudsen. 1990. Impact of beach gravel enhancement on epibenthic zooplankton at Lincoln Park, Seattle, Washington. U.S. Fish and Wildlife Service.
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Kantz, G. 1986. Temporal distribution and reproductive patterns of harpacticoid copepods from Los-Angeles-Long Beach Harbors. Journal of Crustacean Biology 6(1):79-88 (1986).
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Kask, B.A., T.J. Brown, and C.D. McAllister. 1986. Nearshore epibenthos of the Campbell River estuary and Discovery Passage, 1982, in relation to juvenile chinook diets. Canadian Technical report Fisheries and Aquatic Science, No. 1449.
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Leon, H. 1980. Terminal 107 environmental studies benthic community impact study for Terminal 107 (Kellogg Island) and vicinity. Report to Port of Seattle. March 1908.
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Levings, C.D. and A.I. Moody. 1976. Studies of intertidal vascular plants, especially sedge, on the disrupted Squamish River Delta, British Columbia. Canada Fisheries and Marine Service Technical Report #606.
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Levings, C.D. 1982. Short term use of a low tide refuge in a sandflat by juvenile chinook (Onchorhynchus tshawytscha), Fraser River Estuary. Can Tech. Rep. Fish. Aquat. Sci 1982. no. 1111.
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Levings, C.D. 1974. River diversion and intertidal benthos at the Squamish River Delta, British Columbia. Fresh water on the sea. Proceedings from a symposium on the influence of fresh water outflow on biological processes in fjords and coastal waters, 22-25 April, 1974.Geilo, Norway.Skreslet, S., R. Leinbo, J. Matthews,and E. Sakshaug (eds).
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Levings, C.D.. Feeding behavior of juvenile salmon and significance of habitat during estuary and early sea phase. Workshop on the Postsmolt Biology of Salmonids in Ranching Systems, Umeaa (Sweden) 1992. Nord. J., Freshwater. Res. 1994, vol. 69, pp. 7-16.
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Levings, C.D. 1992. Estuarine science and management needed to maintain Pacific salmon production. Changes in Fluxes in Estuaries: Implications From Science to Management. Dyner, K.R., R.J. Orth, (eds.) Fredensborg, Denmark Olsen and Olsen 1994. pp. 417-421.
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Levings, C.D. and R. M. Thom. 1994. Habitat changes in Georgia Basin: implications for resource management and restoration. Review of the marine environment and biota of Strait of Georgia, Puget Sound and Juan de Fuca Strait. 1994. Canadian Technical Report of Fisheries and Aquatic Sciences No. 1948. Proceedings of the BC Washington Symposium on the Marine Environment.
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Levings, C.D., C.D. McAllister, J.S. MacDonald, T.J. Brown, M.S. Kotyk, and B.A. Kask. 1989. Chinook salmon (Oncorhynchus tshawytscha) and estuarine habitat: a transfer experiment can help evaluate estuary dependency. pp. 116-122 in C.D. Levings, L.B. Holtby, and M.A. Henderson (eds), Proceedings, National Workshop: effects of habitat alteration on salmonid stocks. Can. Spec. Publ. Fish. Aquat. Sci. 105.
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Levings, C.D., C.D. McAllister, and B.D. Change. 1986. Differential use of the Campbell River Estuary, BC by wild and hatchery-reared juvenile chinook salmon. Can. J. fish. Aquat. Sci. Vol. 43:7:1386-1397.
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Levings, C.D., K. Conlin, and B. Raymond. 1991. Intertidal habitats used by juvenile chinook salmon (onchorynchus tshawytscha) rearing in the north arm of the Fraser River Estuary. Marine Pollution Bulletin. 1991.Vol. 23:(1)20-26.
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Levy, D.A. and C.D. Levings. 1978. A description of the fish community of the Squamish River Estuary, British Columbia: relative abundance, seasonal changes, and feeding habits of salmonids. Department of Fisheries and the Environment, Fisheries and Marine Service Resource Services Branch. Fisheries and Marine Service Manuscript Report No. 1475.
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Lister, D.B., R.J. Beniston, R. Kellerhals , and M.Miles. 1993. Influence of bank material size on juvenile salmonid use of rearing habitat. Report for the International Riprap Workshop, Fort Collins, Colorado. 1993.
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Meyer, J.H., T.A. Pearce, and S.G. Patlan. 1981. Distribution and food habits of juvenile salmonids in the Duwamish Estuary. Report to U.S. Army Corps of Engineers. March 1981
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Naiman, R.J. 1979. Detritus and juvenile salmon production in the Nanaimo Estuary: 3. Importance of detrital carbon to the estuarine ecosystem. J. Fish. Res. Board Canada. 1979. 36(5) pp. 504-520.
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Parametrix, Inc. 1994. Metro North Beach epibenthic monitoring program. Report to King County Department of Metropolitan Services. 1994.
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Pearce, T.A., J.H. Meyer, and R.S. Boomer. 1982. Distribution and food habits of juvenile salmon in the Nisqually Estuary, Washington, 1979-1980. U.S. Depart. of the Interior. U.S. Fish and Wildlife.
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Pentec Environmental. 1991. Epifauna sampling at the Port of Everett and Lower Snohomish Estuary 1987-1991. Project No. 21-023. Report to Port of Everett. December 991.
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Ryall, P. Levings, C.E. 1987. Juvenile salmon utilization of rejuvenated tidal channels in the Squamish Estuary, British Columbia. Canadian Manuscript Report Fisheries and Aquatic Sciences, No. 1904.
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Shreffler, D.K. C.A. Simenstad, and R. Thom. 1992. Foraging by juvenile salmon in a restored estuarine wetland. Wetland Ecosystem Team. Fisheries Research Institute. University of Washington. Estuaries. June 1992. 15(2):204-213.
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Sibert, J.R. 1979. Detritus and juvenile salmon production in the Nanaimo Estuary: II. Meiofauna available as food to juvenile chum salmon (Oncorhynchus keta). Journal of Fisheries Research Board, Canada 36(5):497-503.
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Simenstad, C.A., H.B. Anderson, and J.R. Cordell. 1993. Analysis of changes in benthic and epibenthic invertebrate communities in Commencement Bay, Washington. In Commencement Bay Cumulative Impact Study. Report to U.S. Army Corps of Engineers.
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Simenstad, C.A., K.L. Fresh, J. Flemma, and D. Clarke. 1992. Effects of estuarine habitat modifications on anadromous salmonids: a literature survey. University of Washington. Fisheries Research Institute, Wetland Ecosystem Team. FRI-UW-9123.

Simenstad, C.A., J.R. Cordell, D.M. Milword, and E.O. Salo. Unpublished report. Diet composition of juvenile salmon (Oncorhynchus spp.) in an urbanized estuary: results of three years' studies in Commencement Bay, Puget Sound, Washington., 1983-1985. Draft Final Report to the Port of Tacoma. University of Washington. Fisheries Research Institute. 71 pp. as cited in Ratte, L.D. 1985. Under-Pier ecology of juvenile Pacific Salmon (Oncorhynchus spp.) in Commencement Bay, Washington. Masters Thesis. University of Washington. School of Fisheries.
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Simenstad, C.A. and E.O. Salo. Foraging success as a determinant of estuarine and nearshore carrying capacity of juvenile chum salmon (Onchorhynchus keta) in Hood Canal, Washington. University of Washington. Fisheries Research Institute. Proceedings of the North Pacific Aquaculture Symposium, Melteff, B.R., and R.A. Neve (eds). University of Alaska. Alaska Sea Grant Program 1982, pp. 21-37.
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Tanner, C.D. and G.T. Williams. 1990. Kellogg Island (Terminal 107) intertidal habitat restoration pre-project assessment report. Report to Port of Seattle. Parametrix. Seattle, WA.
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Thom, R.M. 1987. The biological importance of Pacific Northwest estuaries. Northwest Environmental Journal 3:21-42.
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Thom, R.M., C.A. Simenstad, J.r. Cordell and E.O. Salo. 1988 Fisheries mitigation plan for expansion of moorage at Blaine Marina, Blaine, Washington. Report to Port of Bellingham. University of Washington. Fisheries Research Institute. Wetland Ecosystem Team. FR-UW-8817. addresses: pp/sp and sm Annotation

Walker, D.I., R.J. Lukatelich, G. Bastyan, and A.J. McComb. 1989. Effect of boat moorings on seagrass beds near Perth, Western Australia. Aquatic Botany 36:69-77.
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Webb, D.G. Predation by juvenile salmonids on harpacticoid copepods in a shallow subtidal seagrass bed: effects on copepod community structure and dynamics. Doctoral Thesis. University of British Columbia, August 1989.
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Ehringer, J.N. 1993. Results of analysis of prop scar damage at the Fort Desoto Aquatic Habitat Management Area 1992/1993. Hillsborough Community College/Brandon, Tampa, Florida.
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David Evans and Associates, Inc. 1991. Commencement Bay cumulative impact study. Historic review of special aquatic sites. Report to Army Corps of Engineers. May 1991
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Fonesca, M.S. and W.J. Kenworthy. 1987. Effects of current on photosynthesis and distribution of seagrasses. Aquatic Botany 27:59-78
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Giesen, W.B.J.T., M.M. van Katjik, and C. den Haartog. 1990. Eelgrass condition and turbidity in the Dutch Wadden Sea. Aquatic Botany 37:71-85.
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Levings, C.D. 1985. Juvenile salmonid use of habitats altered by a coal port in the Fraser River Estuary, British Columbia. Marine Pollution Bulletin, 16:5:248-254.
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Levings, C.D. and N.G. McDaniel. 1976. Industrial disruption of invertebrate communities on beaches in Howe Sound, B.C. Canadian Fisheries and Marine Service Technical Report #663.
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Levy, D.A., T.G. Northcote, K.J. Hall, and I. Yesaki. 1989. Juvenile salmonid responses to log storage in littoral habitats of the Fraser River Estuary and Babine Lake. Proceedings of the National Workshop on Effects of Habitat Alteration on Salmonid Stocks. Canadian Special Publication of Fisheries and Aquatic Science 105, C.D. Levings, L.B. Holtby and M.A. Henderson (eds).
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Shreffler, D.K. 1993. Subtidal eelgrass/macroalgae surveys for the proposed breakwaters at the U.S. Coast Guard station at Ediz Hook, Washington, March 1993. Battelle/Marine Sciences Laboratory, Sequim, WA. Prepared for U.S. Army Corps of Engineers. Contract DE-AC06-76RLO 1830. PNL-8656 UC-XXX.

Thom, R.M., A.B. Borde, L.D. Atrim, W.W. Gardiner, J.G. Norris, S.Wyllie- Echeverria. July 1997.Eelgrass and biological resource surveys at Shaw Island Ferry Terminal.Report to Washington State Department of Transportation. Task Order Number 4(Project No. 27449).

Thom, R.M. and D.K. Shreffler. 1996. Eelgrass meadows near ferry terminals in Puget Sound. Characterization of assemblages and mitigation impacts. August 23, 1996.
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Anderson, E.P., I.K. Birtwell, S.C. Beyers, A.V. Hincks, and G.W. O'Connell. 1981. Environmental effects of harbor construction activities at Steveston, British Columbia. Part 1, Main Report.Canadian Technical Report Fisheries and Aquatic Sciences, #1070.
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Cheney, D., R. Oestman, G. Volkhardt, and J. Getz. Creation of rocky intertidal and shallow subtidal habitats to mitigate for the construction of a large marina in Puget Sound,Washington. 994. Fifth Annual Conference on Aquatic Habitat Enhancement.Bulletin on Marine Science vol. 55,#2-3
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Feist, B.E. 1991. Potential impacts of pile driving on juvenile pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon behavior and distribution. University of Washington. School of fisheries. Masters Thesis.
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Iannuzzi, T.J. M.P. Weinstein, K.G. Sellner, and J.C. Barrett. 1996. Habitat disturbance and marina development: An assessment of ecological effects. 1. Changes in primary production due to dredging and marina construction. Estuaries vol. 19 no. 2A. pp. 257-271.
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Kennedy, M. 1990. Eelgrass mitigation plan for dredging and dock construction at La Conner Marina, La Conner, Washington. Report for Port of Skagit County, October 1990. University of Washington. Fisheries Research Institute, Wetlands Ecosystem Team.
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Mortesen, D.G., B.P. Snyder and E.O Salo. 1976. An analysis of the literature on the effects of dredging on juvenile salmonids.University of Washington. Fisheries Research Institute,FRI-UW-7605.

Olson, A.M. , S. Visconty, B. Witherspoon III, K. Sweeney, R.M. Thom and D.K. Shreffler. 1997. Light environment and eelgrass shading around three WSDOT ferry terminals pp 71-101. In Simenstad C.A., R.M. Thom and A.M. Olson (eds). 1997. Mitigation between regional transportation needs and preservation of eelgrass beds. Research report vol., 2 Washington State Transportation Commission/USDOT.
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Salo, E.O., N.J. Bax, T.E. Prinslow, C.J. Whitmus, B.P. Snyder, and C.A. Simenstad. 1979. The effects of construction of naval facilities on the outmigration of juvenile salmonids from Hood Canal, Washington.Report to U.S. Navy.University of Washington.Fisheries Research Institute.FRI-UW-8006.
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Simenstad, C.A., J. R. Cordell, J. Norris, A.M. Olson, and R.M. Thom. 1995. Mitigation between regional transportation needs and preservation of eelgrass beds. Interim report of Phase 1 results to Washington State Department of Transportation. December 1995.
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Slotta, L.S. D.R. Hancock, J.E. McCauley, C,.K. Sullitt, J.M. Sander and K.J. Williamson. 1974. An examination of some physical and biological impacts of dredging in estuaries. Interim Progress Report to the Division of Environmental Systems and Resources. Interdisciplinary Studies of the School of Engineering and Oceanography, Oregon State university.
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Sweeny, C.M. 1996. Eelgrass mitigation policy for overwater structures in Washington State. University of Washington. School of Marine Affairs. Masters Thesis.
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Thom, R.M., A.B. Borde, L.D. Atrim and W.W. Gardiner. Eelgrass and biological resource surveys at Bremerton, Kingston, Southworth, and Vashon Island Ferry Terminals. April 1997. Battelle, Pacific Northwest Division, Richland, WA. Report for Washington Department of Transportation, Olympia, WA. PNWD-2386.
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Thom, R.M., D,K, Shreffler, and J. Schafer. 1995. Mitigation plans for impacts to subtidal vegetation associated with reconstruction and expansion of the ferry terminal at Clinton, Whidbey Island, Washington. (PNL10844). WSDOT.
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Thom, R.M. D.K. Shreffler, C.A. Simenstad, A.M. Olson, S. Wyllie-Echeverria, J.R. Cordell, and J. Schafer. Mitigating impacts from ferry terminals on eelgrass (Zostera marina L.). Battelle Marine Sciences Laboratory. University of Washington.Wetland Ecosystem Team. School of Marine Affairs. Environmental Affairs Office, Washington State Department of Transportation. Olympia, Washington.
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Thom, R.M., C.A. Simenstad, J.R. Cordell. 1986. Early successional development of a benthic-epibenthic community at a newly constructed beach in Slip 1, Commencement Bay, Washington. Report to Port of Tacoma. University of Washington. Fisheries Research Institute, FRI-UW-8603.
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Thom, R.M. C.A. Simenstad, J.R. Cordell and E.O, Salo. 1989. Fish and their epibenthic prey in a marina (Blaine Marina) and adjacent mudflats and eelgrass meadow in a small estuarine bay. Report to Port of Bellingham. University of Washington. Fisheries Research Institute. Wetland Ecosystem Team. FRI-UW-8901.
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Thom, R.M., C.A. Simenstad, J.r. Cordell and E.O. Salo. 1988 Fisheries mitigation plan for expansion of moorage at Blaine Marina, Blaine, Washington. Report to Port of Bellingham. University of Washington. Fisheries Research Institute. Wetland Ecosystem Team. FR-UW-8817. addresses: pp/sp and sm Annotation

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Stein, J.E., T. Hom, T.K. Collier, D.W. Brown, and U. Varanasi. 1995. Contaminant exposure and biochemical affects in outmigrant juvenile chinook salmon from urban and nonurban estuaries of Puget Sound, Washington. Environmental Toxicology Chemistry, 1995. vol. 14, no. 6., pp

Thom, R.M. 1984. Primary production in Grays Harbor estuary, Washington. Bull. Southern California Academy Sciences. 83:99-105.

Thom, R.A. 1990. A review of eelgrass (Zostera marina L.) transplanting projects in the Pacific Northwest. The Northwest Environmental Journal 6:127-137.

Thom, R.M. 1987. Benthic primary production in the eelgrass meadow at the Padilla Bay National Estuarine Research Reserve, Washington. University of Washington. Fisheries Research Institute. Report to NOAA/OCRM/MEMD.

Thom, R.M. 1993. Eelgrass (Zostera marina) transplant monitoring in Grays Harbor, after 29 months. Report #PNL-8519. Battelle Marine Sciences Laboratory, Richland. Department of Energy. Washington D.C. January 1993.

Thom, R.M. and R.G. Albright. 1990. Dynamics of benthic vegetation standing-stock, irradiance, and water properties in central Puget Sound. Fisheries Research Institute. University of Washington. Marine Biology 104, 129-141 (1990).

Thom, R.M., L.D. Antrim, A.B. Borde, W.W. Gardiner, D.K. Shreffler, P.G. Farley, J.G. Norris, S.Wyllie-Echeverria, and T.P. McKenzie. 1997. Puget Sound's eelgrass meadows: factors contributing to depth distribution and spatial patchiness.

Thom, R.M. and L. Hallum. 1991. Long-term changes in the areal extent of tidal marshes, eelgrass meadows and kelp forests of Puget Sound. University of Washington. Fisheries Research Institute. FRI-UW-9008. June 1990. Annotation

Thom, R.M., B. Miller, and M. Kennedy. 1991. Temporal patterns of grazers and vegetation in a temperate seagrass system. NOAA Technical Report Series OCRM/MEMD. University of Washington. Fisheries Research Institute. 1991. FRI-UW-9122 Annotation
 

Thom, R.M., T. L. Parkwell, D.K. Niyogi, and D.K. Shreffler. 1993. Effects of graveling on the primary productivity, repsiration and nutrient flux of two estuarine tidal flats. Battelle Marine Sciences Laboratory, Sequim Wa. Marine Biology 118, 329-341 (1994).

Walters, C.J., R. Hilborn, R.M. Peterman, and M.J. Staley. 1978. Model for examining early ocean limitation of Pacific salmon production. Journal of the Fisheries Research Board of Canada. 35:1303-1315.

addresses: sm, pp/sp

Wyllie-Echeverria, S., J.R. Cordell, J. Haddad, and M.J. Hershman. 1994. Biological monitoring of vegetation characteristics and epibenthic organisms from transplanted and reference eelgrass patches at LaConner, Skagit County, Washington, 1990-1994. Report for Port of Skagit County. University of Washington. School of Marine Affairs. Fisheries Research Institute. SMA 94-2.

Wyllie-Echeverria, S., J.R. Cordell, J. Haddad, L. Tear, and M.J. Hershman. Biolgoical monitoring of vegetation characteristics and epibenthic organisms from transplanted and reference eelgrass patches at LaConner, Skagit County, Washington: final report. Report for Port of Skagit County. SMA95-3.