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Draft Report


Literature Review Bibliography


1999 Clear Creek Phase I Monitoring Report.pdf. (n.d.).

2001 Clear Creek Phase I Monitoring Report.pdf. (n.d.).

2002 Clear Creek Juvenile Salmonid Study Report.pdf. (n.d.).

2003 Clear Creek Phase I Montoring Report.pdf. (n.d.).


Aaron, D. T., Ellings, C. E., Woo, I., Simenstad, C. A., Takekawa, J. Y., Turner, K L., Smith, A. L., & Takekawa, J. E., (2014). Foraging and Growth Potential of Juvenile Chinook Salmon after Tidal Restoration of a Large River DeltaTransactions of the American Fisheries Society , 143(6), 1515-1529


Bass, A. L. (2010). Juvenile Coho Salmon Movement and Migration Through Tide Gates (master’s thesis). Retrieved from National Sea Grant Library.



Beamish, R.J., & Mahnken, Conrad. (2001). A critical size and period hypothesis to explain natural regulation of salmon abundance and the linkage to climate and climate changeProgress in Oceanography (Vol. 49, pp. 423-437) 



Beauchamp, D. A. (2009). Bioenergetic ontogeny: linking climate and mass-specific feeding to life-cycle growth and survival of salmon. In American Fisheries Society Symposium (Vol. 70, pp. 1–19).



Beechie, T. J., Liermann, M., Beamer, E. M., & Henderson, R. (2005). A Classification of Habitat Types in a Large River and Their Use by Juvenile Salmonids. Transactions of the American Fisheries Society, 134(3), 717–729.


Beechie, T. J., Sear, D. A., Olden, J. D., Pess, G. R., Buffington, J. M., Moir, H., Roni, P., & Pollock, M. M. (2010). Process-based principles for restoring river ecosystems. BioScience60(3), 209-222.


Bellmore, J. R., Baxter, C. V., Martens, K., & Connolly, P. J. (2013). The floodplain food web mosaic: a study of its importance to salmon and steelhead with implications for their recovery. Ecological Applications, 23(1), 189–207.


Bottom, D. L., Jones, K. K., Cornwell, T. J., Gray, A., & Simenstad, C. A. (2005). Patterns of Chinook salmon migration and residency in the Salmon River estuary (Oregon). Estuarine, Coastal and Shelf Science, 64(1), 79–93.


Bottom, D.L., C.A. Simenstad, J. Burke, A.M. Baptista, D.A. Jay, K.K. Jones, E. Casillas, & M.H. Schiewe. (2005). Salmon at river’s end: the role of the estuary in the decline and recovery of Columbia River salmon. U.S. Dept. Commerece, NOAA Tech. Memo. NMFSNWFSC-68, 246


Borja, Á., Dauer, D. M., Elliott, M., & Simenstad, C. A. (2010). Medium-and long-term recovery of estuarine and coastal ecosystems: patterns, rates and restoration effectivenessEstuaries and Coasts33(6), 1249-1260.


Bourret, S. L., Caudill, C. C., & Keefer, M. L. (2016). Diversity of juvenile Chinook salmon life history pathways. Reviews in Fish Biology and Fisheries, 26(3), 375–403.



Brewitt, K. S., Danner, E. M., & Moore, J. W. (2017). Hot eats and cool creeks: juvenile Pacific salmonids use mainstem prey while in thermal refuges. Canadian Journal of Fisheries and Aquatic Sciences, 74(10), 1588–1602. https://doi.org/10.1139/cjfas-2016-0395


Campbell, L. A., Bottom, D. L., Volk, E. C., & Fleming, I. A. (2015). Correspondence between scale morphometrics and scale and otolith chemistry for interpreting juvenile salmon life histories. Transactions of the American Fisheries Society, 144(1), 55–67.



Clements, S., Stahl, T., & Schreck, C. B. (2012). A comparison of the behavior and survival of juvenile coho salmon (Oncorhynchus kisutch) and steelhead trout (O. mykiss) in a small estuary system. Aquaculture, 362, 148–157.



Colvin, R., Giannico, G. R., Li, J., Boyer, K. L., & Gerth, W. J. (2009). Fish use of intermittent watercourses draining agricultural lands in the Upper Willamette River Valley, Oregon. Transactions of the American Fisheries Society, 138(6), 1302–1313.



Cordell, J. R., Tanner, C. D., & Aitkin, J. K. (1999). Fish assemblages and juvenile salmon diets at a breached-dike wetland site, Spencer Island, Washington, 1997-98.



Craig, B. E., Simenstad, C. A., & Bottom, D. L. (2014). Rearing in natural and recovering tidal wetlands enhances growth and life‐history diversity of Columbia Estuary tributary coho salmon Oncorhynchus kisutch populationJournal of fish biology85(1), 31-51. (2014)



Davis, J. C., & Davis, G. A. (2011). The influence of stream-crossing structures on the distribution of rearing juvenile Pacific salmon. Journal of the North American Benthological Society, 30(4), 1117–1128.


Davis, M. J., Ellings, C. S., Woo, I., Hodgson, S., Larsen, K. and Nakai, G. (2017), Gauging resource exploitation by juvenile Chinook salmon (Oncorhynchus tshawytscha) in restoring estuarine habitat. Restoration Ecolology.



Ebbert, J. C., Bortleson, G. C., Fuste, L. A., and Prych, E. A.. (1987)  Water Quality in the Lower Puyallyup River Valley and Adjacent Uplands, Pierce County, Washington.   U.S. Geologic Survey Watershed Report 86-4154, Prepared in Cooperation with the Puyallup Tribe of Indians.


Environmental Science Associates (2016) Farming in the Floodplain Project Existing Conditions Report.  Prepared for PCC Farmland Trust Farming in the Floodplain Project.



Environmental Science Associates (2017) Farming in the Floodplain Project Finding and Recommendations Report. Prepared for PCC Farmland Trust Farming in the Floodplain Project.



Ellings, C. S., Davis, M. J., Grossman, E. E., Woo, I., Hodgson, S., Turner, K. L., Nakai, G., Takekawa, G.E., Takekawa, J. Y. (2016). Changes in habitat availability for outmigrating juvenile salmon (Oncorhynchus spp.) following estuary restoration. Restoration Ecology, 24(3), 415–427.



Elliott, M., Mander, L., Mazik, K., Simenstad, C., Valesini, F., Whitfield, A., & Wolanski, E. (2016). Eco-engineering with ecohydrology: successes and failures in estuarine restoration. Estuarine, Coastal and Shelf Science176, 12-35.


Euliss Jr, N. H., LaBaugh, J. W., Fredrickson, L. H., Mushet, D. M., Laubhan, M. K., Swanson, G. A., Winter, T. C., Rosenberry, D. O., & Nelson, R. D. (2004). The wetland continuum: a conceptual framework for interpreting biological studies. Wetlands, 24(2), 448–458.



Fresh, K. L. (2006). Juvenile Pacific Salmon in Puget Sound. National Oceanic and Atmospheric Administration Seattle, WA Pacific Marine Environmental Labs.


Goertler, P. A., Simenstad, C. A., Bottom, D. L., Hinton, S., & Stamatiou, L. (2016). Estuarine habitat and demographic factors affect juvenile Chinook (Oncorhynchus tshawytscha) growth variability in a large freshwater tidal estuary. Estuaries and Coasts, 39(2), 542–559.



Gray, A., Simenstad, C. A., Bottom, D. L., & Cornwell, T. J. (2002). Contrasting functional performance of juvenile salmon habitat in recovering wetlands of the Salmon River estuary, Oregon, USA. Restoration Ecology, 10(3), 514–526.


Greene, C., Hall, J., Beamer, E., Henderson, R., & Brown, B. (2012). Biological and physical effects of “fish-friendly” tide gates. Final Report for the Washington State Recreation and Conservation Office, January 2012. NOAA Natl. Mar. Fish. Serv., NW Fish. Sci. Center, Seattle, WA, and Skagit River System Coop., LaConner, WA.



Greene, C. M., Jensen, D. W., Pess, G. R., Steel, E. A., & Beamer, E. (2005). Effects of environmental conditions during stream, estuary, and ocean residency on Chinook salmon return rates in the Skagit River, Washington. Transactions of the American Fisheries Society, 134(6), 1562–1581.



Gregory, R. S., & Levings, C. D. (1998). Turbidity reduces predation on migrating juvenile Pacific salmon. Transactions of the American Fisheries Society, 127(2), 275–285.



Groot, C., & Margolis, L. (1991). Pacific salmon life histories. UBC press.



Hamman. J., Hamlet, A., Lee, S., Fuller, R., & Grossman, E. (2016) Combined Effects of Projected Sea Level Rise, Storm Surge, and Peak River Flows on Water Levels in the Skagit FloodplainNorthwest Science, Vol. 90, No. 1, 2016




Hanson, K., Ostrand, K., & Glenn, R. (2012). Physiological characterization of juvenile Chinook salmon utilizing different habitats during migration through the Columbia River Estuary. Comparative biochemistry and physiology. Part A, Molecular & integrative physiology 163(3-4):343-9 




Hering, D. K., Bottom, D. L., Prentice, E. F., Jones, K. K., & Fleming, I. A. (2010). Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel. Canadian Journal of Fisheries and Aquatic Sciences, 67(3), 524–533.


Hines, E. E., & Landis, W. G. (2014). Regional risk assessment of the Puyallup River Watershed and the evaluation of low impact development in meeting management goals. Integrated Environmental Assessment & Management, 10(2), 269–278.



Hood, W. G., Grossman, E. E., & Veldhuisen, C. (2016). Assessing tidal marsh vulnerability to sea-level rise in the Skagit Delta. Northwest Science, 90(1), 79–93.



Jeffres, C. A., Opperman, J. J., & Moyle, P. B. (2008). Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river. Environmental Biology of Fishes, 83(4), 449–458.



Johnson, G. E., Storch, A., Skalski, J. R., Bryson, A. J., Mallette, C., Borde, A. B., Van Dyke, E. S., Sobocinski, K. L., Sather, N. K., Teel, D. J., Dawley, E. M., Ploskey, G. R., Jones, T. A., Zimmerman, S. A., Kuligowski, D. R. (2011). Ecology of juvenile salmon in shallow tidal freshwater habitats of the lower Columbia River. 2007–2010. Pacific Northwest National Laboratory (PNNL), Richland, WA (US).



Jones, K. K., Cornwell, T. J., Bottom, D. L., Campbell, L. A., & Stein, S. (2014). The contribution of estuary-resident life histories to the return of adult Oncorhynchus kisutch. Journal of Fish Biology, 85(1), 52–80.



Kahler, T. H., & Quinn, T. P. (1998). Juvenile and resident salmonid movement and passage through culverts. Washington State Department of Transportation.



Kemp, P. S., Gessel, M. H., & Williams, J. G. (2005). Fine-scale behavioral responses of Pacific salmonid smolts as they encounter divergence and acceleration of flow. Transactions of the American Fisheries Society, 134(2), 390–398.



Lind-Null, A., Larsen, K., & Reisenbichler, R. R. (2008a). Characterization of estuary use by Nisqually Hatchery Chinook based on otolith analysis. US Geological Survey.



Lind-Null, A., Larsen, K., & Reisenbichler, R. R. (2008b). Pre-Restoration habitat use by Chinook Salmon in the Nisqually Estuary using otolith analysis. US Geological Survey.



Lott, M. A. (2004). Habitat-specific feeding ecology of ocean-type juvenile Chinook salmon in the lower Columbia River Estuary [thesis]. Seattle (WA): University of Washington. m321p227.pdf.



Maier, G., & Simenstad, C. (2009). The Role of Marsh-Derived Macrodetritus to the Food Webs of Juvenile Chinook Salmon in a Large Altered Estuary. Estuaries and Coasts 32:984–998






Marcarelli, A. M., Baxter, C. V., Mineau, M. M., & Hall, R. O. (2011a). Quantity and quality: unifying food web and ecosystem perspectives on the role of resource subsidies in freshwaters. Ecology, 92(6), 1215–1225.


McIvor, C. C., & Odum, W. E. (1988). Food, predation risk, and microhabitat selection in a marsh fish assemblage. Ecology, 69(5), 1341–1351.



McMahon, T. E., & Hartman, G. F. (1989). Influence of cover complexity and current velocity on winter habitat use by juvenile coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Sciences, 46(9), 1551–1557.



McNatt, R. A., Bottom, D. L., & Hinton, S. A. (2016). Residency and movement of juvenile Chinook salmon at multiple spatial scales in a tidal marsh of the Columbia River estuary. Transactions of the American Fisheries Society, 145(4), 774–785.



Müller-Solger, A. B., Jassby, A. D., & Müller-Navarra, D. C. (2002). Nutritional quality of food resources for zooplankton (Daphnia) in a tidal freshwater system (Sacramento-San Joaquin River Delta). Limnology and Oceanography, 47(5), 1468–1476.


Neilson, J. D., Geen, G. H., & Bottom, D. (1985). Estuarine growth of juvenile chinook salmon (Oncorhynchus tshawytscha) as inferred from otolith microstructure. Canadian Journal of Fisheries and Aquatic Sciences, 42(5), 899–908.



Palmer, M. A., Bernhardt, E. S., Allan, J. D., Lake, P. S., Alexander, G., Brooks, S., Carr, J., Clayton, S., Dahm, C. N., Follstad Shah, J., Galat, D. L., Loss, S. G., Goodwin, P., Hart, D. D., Hasset, B., Jenkinson, R., Kondolf, G. M., Lave, R., Meyer, J. L., O’Donnel, T. K., Pagano, L., and Sugguth, E. (2005). Standards for ecologically successful river restoration. Journal of applied ecology42(2), 208-217.


Poirier, J., Lohr, S., Whitesel, T. A., Johnson, J., & Team, C. A. (2009). Assessment of Fishes, Habitats, and Fish Passage at Tide gates on Deer Island Slough and lower Tide Creek. Project Report. Prepared by U.S. Fish and Wildlife Service Columbia River Fisheries Program Office Conservation Assessment Team



Quinn, T. P. (2011). The behavior and ecology of Pacific salmon and trout. UBC press. report.



Roegner, G. C., Dawley, E. W., Russell, M., Whiting, A. and Teel, D. J. (2010). Juvenile Salmonid Use of Reconnected Tidal Freshwater Wetlands in Grays River, Lower Columbia River Basin. Transactions of the American Fisheries Society, 139: 1211–1232.


Roni, P., Pess, G., Beechie, T., & Morley, S. (2010). Estimating Changes in Coho Salmon and Steelhead Abundance from Watershed Restoration: How Much Restoration is Needed to Measurably Increase Smolt Production.  North American Journal of Fisheries Management, 30(6), 1469–1484



Sather, N. K. (2008). Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary(Masters Thesis) Oregon State Unviversity



Semmens, B. X. (2008). Acoustically derived fine-scale behaviors of juvenile Chinook salmon (Oncorhynchus tshawytscha) associated with intertidal benthic habitats in an estuary. Canadian Journal of Fisheries and Aquatic Sciences, 65(9), 2053–2062.


Simenstad, C. A., & Cordell, J. R. (2000). Ecological assessment criteria for restoring anadromous salmonid habitat in Pacific Northwest estuariesEcological Engineering15(3), 283-302



Simenstad, C. A., Fresh, K. L., & Salo, E. O. (1982). The Role of Puget Sound and Washington Coastal Estuaries in The Life History of Pacific Salmon: An Unappreciated Function. Estuarine Comparisons. Academic Press, New York, 14, 343–364.



Simenstad, C. A., Hood, W. G., Thom, R. M., Levy, D. A., & Bottom, D. L. (2002). Landscape structure and scale constraints on restoring estuarine wetlands for Pacific Coast juvenile fishes. Concepts and controversies in tidal marsh ecology, 597-630.



Simenstad, C.A., M. Ramirez, J. Burke, M. Logsdon, H. Shipman, C. Tanner, J. Toft, B. Craig, C. Davis, J. Fung, P. Bloch, K. Fresh, S. Campbell, D. Myers, E. Iverson, A. Bailey, P. Schlenger, C. Kiblinger, P. Myre, W. Gerstel, and A. MacLennan. 2011. Historical Change of Puget Sound Shorelines: Puget Sound Nearshore Ecosystem Project Change Analysis. Puget Sound Nearshore Report No. 2011-01. Published by Washington Department of Fish and Wildlife, Olympia, Washington, and U.S. Army Corps of Engineers, Seattle, Washington.



Sommer, T. R., Harrell, W. C., & Nobriga, M. L. (2005). Habitat Use and Stranding Risk of Juvenile Chinook Salmon on a Seasonal Floodplain. North American Journal of Fisheries Management, 25(4), 1493–1504.



Sommer, T. R., Nobriga, M. L., Harrell, W. C., Batham, W., & Kimmerer, W. J. (2001). Floodplain rearing of juvenile Chinook salmon: evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences, 58(2), 325–333.


Swales, S., & Levings, C. D. (1989). Role of off-channel ponds in the life cycle of coho salmon (Oncorhynchus kisutch) and other juvenile salmonids in the Coldwater River, British Columbia. Canadian Journal of Fisheries and Aquatic Sciences, 46(2), 232–242.



Thom, R. M., Borde, A. B., Blanton, S. L., Woodruff, D. L., & Williams, G. D. (2001). The influence of climate variation and change on structure and processes in nearshore vegetated communities of Puget Sound and other Northwest estuaries. In Proceedings of the 2001 Puget Sound Research Conference. Puget Sound Action Team. Olympia, WA.



Truelove, N. K. (2005). Effects of estuarine circulation patterns and stress on the migratory behavior of juvenile salmonids (Oncorhynchus sp.). Master’s Thesis Oregon State University.



Waples, R. S., Teel, D. J., Myers, J. M., & Marshall, A. R. (2004). Life-history divergence in Chinook salmon: historic contingency and parallel evolution. Evolution, 58(2), 386–403.



Warner, M. D., Mass, C. F., & Salathe E. P. (2015)  Changes in Winter Atmospheric Rivers along the North American West Coast in CMIP5 Climate Models. Journal of Hydrometerology , 16, 118-128.



Warner, M. D.C. F. Mass, and E. P. Salathé, 2012Wintertime extreme precipitation events along the Pacific Northwest coast: Climatology and synoptic evolution. Mon. Wea. Rev.14020212043. 


Webster, S. J., Dill, L. M., & Korstrom, J. S. (2007). The effects of depth and salinity on juvenile Chinook salmon Oncorhynchus tshawytscha (Walbaum) habitat choice in an artificial estuary. Journal of Fish Biology, 71(3), 842–851.



Weitkamp, L. A., Bentley, P. J., & Litz, M. N. (2012). Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuaryFish. Bull. 110:426–450



Welch, W. B., Johnson, K. H., Savoca, M. E., Lane, R. C., Fasser, E. T., Gendaszek, A. S., Marshall, C., Clothier, B. C., & Knoedler, E. N. (2015). Hydrogeologic framework, groundwater movement, and water budget in the Puyallup River Watershed and vicinity, Pierce and King Counties, Washington (No. 2015-5068). US Geological Survey.


Zajanc, D., Kramer, S. H., Nur, N., & Nelson, P. A. (2013). Holding behavior of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) smolts, as influenced by habitat features of levee banks, in the highly modified lower Sacramento River, California. Environmental Biology of Fishes, 96(2–3), 245–256.



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