Anne Shaffer

Instructor · she/her


I’m a senior marine scientist/marine ecologist with a career spanning passion for northeast Pacific nearshore ecosystem conservation and restoration. I lead a small and extremely talented team of staff and collaborators to identify and implement large, complex science and restoration initiatives addressing ecosystem services, conservation, and restoration of the nearshore Salish Sea. This science has led to groundbreaking advances in understanding of how nearshore ecosystems function, how to identify priority nearshore ecosystem functions for conservation and restoration, how the disruption of nearshore ecosystem functions can act as a barrier for watershed ecosystem restoration, how to design and implement landscape scale nearshore ecosystem restoration, and the synergistic nearshore ecosystem  responses to landscape restoration actions, including large scale dam removals. 


PhD Biology, 2017, University of Victoria; M.A. Marine Biology, 1986, Moss Landing Marine Laboratory; B.S. Zoology, 1983, San Francisco State University

Research Interests

My primary areas of interest are coastal ecosystem forming and functional processes, identifying anthropogenic stresses to coastal systems ,and identifying place based strategies on how conserve and restore vanishing wild coastal ecosystems. Much of this interest in focused on the intersections of kelp forest ecosystem function, forage fish ecology,  and large scale dam removals

Another mission of my work is to educate the next generation of scientists and managers on wise long term ecosystem conservation and management.


Shaffer JA, KA Simonsen, D Parks, J Michel, J  Bauman, and B Oxborrow. In revision.A Case Study Linking Marine Ecosystem Response to Shoreline Armor Removal and Large Dam Removals in the Elwha River and Nearshore, Washington, USA.

Shaffer, J.A. D Parks, K. Campbell, A Morgane, B. Hueske, P. Adams, J. Bauman. In press. Coastal beaver, Chinook, coho, chum salmon and trout response to nearshore changes resulting from diking and large-scale dam removals: synergistic ecosystem engineering and restoration in the coastal zone  Nature Conservation. 

Shaffer, A., Gross, J., Black, M., Kalagher, A. and Juanes, F., 2023. Dynamics of juvenile salmon and forage fishes in nearshore kelp forests. Aquatic Conservation: Marine and Freshwater Ecosystems

Shaffer, A and C. Stipek 2022. The herring highway. An ARC GIS story map.

Shaffer, A., Parks, D., Michel, J., Simonsen, K., Campbell, K., Oxborrow, B., Hall, J. and Weslowski, J., 2021. Restoration of Coastal Beach Forming Ecosystem Processes through Shoreline Armoring Removal of a Former Mine Site Increases Our Understanding of Coastal Resiliency and Large Scale Landslides Along the Northeast Pacific Coastline. International Journal of Mining, Reclamation and Environment, pp.1-19.

Shaffer, J.A. 2021. Piscine Orthoreovirus (PRV) and ectoparasites of young of the year juvenile herring, Clupea pallasii, of the Salish Sea. The Osprey. International Journal of Salmon and Steelhead Conservation.pp.17-21.

Shaffer, J.A., S.H. Munsch,   and J.R. Cordell 2020. Kelp Forest Zooplankton, Forage Fishes, and Juvenile Salmonids of the Northeast Pacific Nearshore. Marine and Coastal Fisheries, 12(1), pp.4-20.

Shaffer, A., Parks, D., Schoen, E.R. and Beauchamp, D., 2019. Salmon, forage fish, and kelp. Frontiers in Ecology and the Environment, 17(5), pp.258-258.

Shaffer, J.A., F. Juanes, D. Parks, J. Michel, and C. Walls. 2019. Dam removal as a management strategy for fisheries recovery: lessons from the Elwha River nearshore and implications for Formosa landlocked salmon. In: Proceedings of the International symposium on the 100th Anniversary of the Discovery of Formosa Landlocked Salmon, JC Gwo, YT Shieh and DP Burridge (eds), National Taiwan Ocean University Press. pp 59-64

Shaffer, J.A., S. Munsch, and F. Juanes  2018. Functional diversity responses of a nearshore fish community to restoration driven by large-scale dam removal. Estuarine, Coastal and Shelf Science, 213, pp.245-252.

Lincoln, A.E., JA Shaffer. and TP Quinn  2018. Opportunistic use of estuarine habitat by juvenile bull trout, Salvelinus confluentus, from the Elwha River before, during, and after dam removal. Environmental Biology of Fishes, pp.1-11.

Shaffer, J.A., F. Juanes, F., TP Quinn, D. Parks, D., T McBride, J Michel, J., C Naumann, M  Hocking,   and C Byrnes   2017. Nearshore fish community responses to large scale dam removal: implications for watershed restoration and fish management. Aquatic Sciences, pp.1-18.

Shaffer, J.A., E. Higgs., C.  Walls. and F. Juanes, F., 2017. Large-scale Dam Removals and Nearshore Ecological Restoration: Lessons Learned from the Elwha Dam Removals. Ecological Restoration, 35(2), pp.87-101.

Shaffer, A.   M. Carrasquilla-Henao & F. Juanes, 2016. Book Review: Marine Community Ecology and Conservation  M.D. Bertness, J.F. Bruno, B.R. Silliman, J.J. Stachowicz. (Eds) Sunderland, MA: Sinauer Associates. Marine Ecology

Rich, Samantha L., J.A. Shaffer, M.J. Fix, J. Dawson,  2014. Restoration considerations of large woody debris in the nearshore Elwha River, Olympic Peninsula. Ecological Restoration: 32(3).

Flores, L., J Harrison-Cox, J., S Wilson, D Batker, A Shaffer,  and D Parks,   2013. Nature’s Value in Clallam County: The Economic Benefits of Feeder Bluffs and 12 Other Ecosystems. Earth Economics: Tacoma, Washington

Parks, D., A. Shaffer and D. Barry.  2013.. Drift cell sediment processes and ecological function for forage fish: Implications for ecological restoration in impaired Pacific Northwest marine ecosystems. Journal of Coastal Research. 29:4, 984-997.

QuinnT. P, N. Harris J. A. Shaffer, C. Byrnes, and P. Crain . 2013. Juvenile coho salmon, Oncorhynchus kisutch, in the Elwha River estuary prior to dam removal: Seasonal occupancy, size distribution, and comparison to nearby Salt Creek. Transactions of the American Fisheries Society. 142:4, 1058-1066

Quinn, T., A. Shaffer, J. Brown, N. Harris, C. Byrnes, and P. Crain. 2013. Juvenile Chinook salmon, Oncorhynchus tshawytscha, use of the Elwha River estuary prior to dam removal. Environmental Biology of Fishes.

Shaffer J.A., P. Crain, T. Kassler, D. Penttila, and D Barry. 2012.  Geomorphic Habitat Type, Drift Cell, Forage Fish, and Juvenile Salmon: Are They Linked? Journal of Environmental Science and Engineering A(1):688-703.

Shaffer, J. A. M. Beirne, T. Ritchie, R. Paradis, D. Barry, and P. Crain. 2009. Fish use of the Elwha estuary and the role anthropogenic impacts to physical processes play in nearshore habitat function for fish. Hydrobiologia 636:179–190.

Shaffer, J.A, P. Crain, B. Winter, M. McHenry, C. Lear and T. Randle. 2008. Nearshore Restoration of the Elwha River Through Removal of the Elwha and Glines Canyon Dams: An Overview. Northwest Science. 82:48-58.

Shaffer, J.A., T. Ritchie, P. Crain, M. Beirne, and C. Lear. 2008. Nearshore function of the central Strait of Juan de Fuca for juvenile fish, including Puget Sound Chinook salmon.

Ward, L., P. Crain, B. Freymond, M. McHenry, D. Morrill, G. R. Pess, R. Peters, J. A. Shaffer, B. Winter, B. Wunderlich. 2008. Elwha River Fish Restoration Plan, developed pursuant to the Elwha River Ecosystem and Fisheries Restoration Act, Public Law 102-495. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-90, 168 p

Norris, J, I. Ward, A. Shaffer and C. Lear 2007. Eelgrass mapping of the Elwha Nearshore.  in Proceedings, Puget Sound Georgia Basin Conference , Puget Sound Water Quality Authority, Olympia Washington.

Shaffer,J.A., D. Penttila, M. McHenry and D. Vilella.2007. Observations of Eulachon, Thaleichthys pacificus, in the Elwha River, Olympic Peninsula, Washington. Northwest Science.81(1):76-81

Shaffer ,J.A., L. Ward, P. Crain, B. Winter, K. Fresh, and C. Lear. 2005. Elwha and Glines Canyon dam removals: nearshore restoration and salmon recovery of the central Strait of Juan de Fuca,  in Proceedings, Puget Sound Research Conference 2005, Puget Sound Water Quality Action Team, Olympia Washington.

Shaffer, J.A.2004. Salmon in the Nearshore: What do we know and where do we go?A synthesis discussion concluding the all day special session entitled ‘Salmon in the Nearshore’ of the 2004 Pacific Estuarine Research Society (PERS). Available on line from the PERS webpage,

Shaffer,  J.A.2004. Preferential use of nearshore kelp habitats by juvenile salmon and forage fish.  In T.W. Droscher and D.A. Fraser (eds). Proceedings of the 2003 Georgia Basin/Puget Sound Research Conference. .htm

Shaffer, J.A.2004. Water quality as a contemporary limiting factor to Olympia oyster (Ostreloa conchaphila) restoration in Washington state.  In T.W. Droscher and D.A. Fraser (eds). Proceedings of the 2003 Georgia Basin/Puget Sound Research Conference. 

Shaffer,J.A.  2002. Macroalgae blooms and nearshore habitat and resources of the Strait of Juan de Fuca. In: Proceeding, Puget Sound Research 2001. Puget Sound Water Quality Action Team, Olympia, Washington. 

Shaffer, J.A. 2000. Seasonal variation in understory kelp bed habitats of the Strait of Juan de Fuca. Journal of Coastal Research. 16 (3) 768-775.

Shaffer,  J.A. and C.  Burge. 1999Ulvoid mats and shellfish of the Strait of Juan de Fuca: a pilot study. Estuarine and Coastal Sciences Association Bulletin. (32) 56-59.

Shaffer, J.A.1998. Kelp habitats of Inland Waters of Western Washington. Puget Sound Research 98. Puget Sound Watershed Action Team, Olympia, Washington.

Shaffer, J. A., D. Doty, R. Buckley and J. West 1995. Crustacean Community  Composition and  Trophic Use of Drift Vegetation Habitat by Juvenile  Splitnose  Rockfish, Sebastes diploproa. Marine Ecology Progress Series. 123 (1-3).

Shaffer, J. A. and D. S. Parks 1994. Seasonal Variations in  and Observations of Landslide  Impacts on the Algal Composition of a Puget Sound  Nearshore Kelp Forest. Botanica Marina. 37: 315-323.

Teaching Schedule