columbia river crossing biological assessment · columbia river crossing biological assessment 10-2...

COLUMBIA RIVER CROSSING BIOLOGICAL ASSESSMENT

June 2010 10-1

10. REFERENCES 1

2

Adams, P.B., C.B. Grimes, J.E. Hightower, S.T. Lindley, and M.L. Moser. 2002. Status Review 3 for North American Green Sturgeon, Acipenser medirostris. NMFS, Southwest Fisheries 4 Science Center. Santa Cruz, CA. Available at: http://www.nmfs.noaa.gov/pr/pdfs5 /statusreviews/greensturgeon.pdf. Accessed May 12, 2009. 6

Ager, L.M. 1976. A biotelemetry study of the movements of the walleye in Central Hills 7 Reservoir, Tennessee. Proceedings, Annual Conference Southeastern Association of 8 Game and Fish Commissioners 30:311-323. 9

Akkanen, J. and J.V.K. Kukkonen. 2001. Effects of water hardness and dissolved organic 10 material on bioavailability of selected organic chemicals. Environmental Toxicology and 11 Chemistry 20(10):2303-2308. 12

Ali, M.A. 1958. The ocular structure, retinomotor and photobehavioral responses of juvenile 13 Pacific salmon. Ph.D. dissertation, Univ. British Columbia, Vancouver BC, Canada. 14

Ali, M.A. 1960. The effect of temperature on the juvenile sockeye salmon retina. Can. J. Zool. 15 38:169-171. 16

Ali, M.A. 1962. Influence of light intensity on retinal adaptation in Atlantic salmon (Salmo 17 salar) yearlings. Can. J. Zool. 40:561-570. 18

Alpers, C.N., H. E. Taylor, and J.L. Domagalski (editors). 2000a. Metals Transport in the 19 Sacramento River, California, 1996–1997 - Volume 1: Methods and Data. U.S. 20 Geological Survey, Water-Resources Investigations Report 99-4286. Sacramento, 21 California. 22

Alpers, C.N., R.C. Antweiler, H. E. Taylor, P. D. Dileanis, and J.L. Domagalski. 2000b. Metals 23 Transport in the Sacramento River, California, 1996–1997 – Volume 2: Interpretation of 24 Metal Loads. U.S. Geological Survey, Water-Resources Investigations Report 00-4002. 25 Sacramento, California. 26

Anderson, C.W., F.A. Rinella and S.A. Rounds. 1996. Occurrence of Selected Trace Elements 27 and Organic Compounds and Their Relation to Land Use in the Willamette River Basin, 28 Oregon, 1992–94. U.S. Geological Survey, Water-Resources Investigations Report 29 96– 4234, Portland, Oregon. 30

Angliss, R.P. and B.M. Allen. 2007. Stock Assessment Report for Steller Sea Lion (Eumetopias 31 jubatus): Eastern U.S. Stock. NOAA Fisheries Tech Memo. NOAA-TM-AFSC-193. 32 Available at: http://www.nmfs.noaa.gov/pr/pdfs/sars/ak2008slst-e.pdf. Accessed 33 May 12, 2009. 34

Arkoosh, M.R., E. Casillas, E. Clemons, B. McCain, and U. Varanasi. 1991. Suppression of 35 immunological memory in juvenile Chinook salmon (Oncorhynchus tshawytscha) from 36 an urban estuary. Fish and Shellfish Immunology 1:261-277. 37


10-2 June 2010

Arkoosh, M.R., E. Casillas, E. Clemons, J. Evered, J.E. Stein, and U. Varanasi. 1998. Increased 1 susceptibility of juvenile Chinook salmon (Oncorhynchus tshawytscha) from a 2 contaminated estuary to the pathogen Vibrio anguillarum. Transactions of the American 3 Fisheries Society 127:360-374. 4

Bain, D.E., J.C. Smith, R. Williams, and D. Lusseau. 2006. Effects of vessels on behavior of 5 Southern Resident killer whales (Orcinus spp.). Contract Report for the National Marine 6 Fisheries Service, Seattle, Washington. 7

Balcomb, K. 2009. Personal communication. E-mail from K. Balcomb, Center for Whale 8 Research, to Jennifer Lord, Parametrix biologist, on November 12, 2009. 9

Baldwin, D.H., J.F. Sandahl, J.S. Labenia, and N.L. Scholz. 2003. Sublethal effects of copper on 10 coho salmon: impacts on non-overlapping receptor pathways in the peripheral olfactory 11 nervous system. Environmental Toxicology and Chemistry 22(10):2266-2274. 12

Bash, J., C. Berman, and S. Bolton. 2001. Effects of Turbidity and Suspended Solids on 13 Salmonids. Washington State Transportation Center. Seattle, Washington. Prepared for 14 the Washington State Transportation Commission. November 2001. 15

Bax, N., E.O. Salo, and B.P. Snyder. 1980. Salmonid outmigration studies in Hood Canal. 16 University of Washington, Fisheries Research Institute Final Report FRIUW-8010, 17 55 pp. 18

Beamesderfer, Raymond C. and Bruce E. Rieman. 1991. Abundance and Distribution of 19 Northern Squawfish, Walleyes, and Smallmouth Bass in John Day Reservoir, Columbia 20 River. Oregon Department of Fish and Wildlife. Clackamas, Oregon. Transactions of the 21 American Fisheries Society 120:439-447, 1991. 22

Beamesderfer, R.C.P. and M.A.H. Webb. 2002. Green sturgeon status review information. S.P. 23 Cramer and Associates, Gresham, Oregon. 44p. 24

Berg, L. 1982. The effect of exposure to short-term pulses of suspended sediment on the 25 behavior of juvenile salmonids. P. 177-196 in G.F. Hartman et al. [eds.] Proceedings of 26 the Carnation Creek workshop: a 10-year review. Department of Fisheries and Oceans, 27 Pacific Biological Station, Nanaimo, Canada. 28

Berg, L. and T.G. Northcote. 1985. Changes in territorial, gill-flaring, and feeding behaviour in 29 juvenile coho salmon (Oncohynchus kisutch) following short-term pulses of suspended 30 sediment. Canadian Journal of Fisheries and Aquatic Sciences 42: 1410-1417. 31

BES (City of Portland, Bureau of Environmental Services). 2005. Columbia Slough: Current 32 Characterization Documents, "Chapter 5, Streamflow and Hydrology Characterization.” 33 Portland, Oregon: City of Portland. Available at: http://www.portlandonline.com/34 bes/index.cfm? c=36081&a=63585. Accessed May 27, 2009. 35

BES. 2006. Columbia Slough Sediment Program Watershed Action Plan. Available at: 36 http://www.portlandonline.com/bes/index.cfm?c=49910&a=175908. Accessed 37 September 2009. 38

BES. 2007. Columbia Slough Watershed Long-Term Monitoring Plan. Available at: 39 http://www.portlandonline.com/bes/index.cfm?c=33221&a=175915. Accessed 40 September 2009. 41


June 2010 10-3

Bigg, M.A. 1982. An assessment of killer whale (Orcinus orca) stocks off Vancouver Island. 1

Bigg, M.A., P.F. Olesiuk, G.M. Ellis, J.K.B. Ford, and K.C. Balcomb. 1990. Social organization 2 and genealogy of resident killer whales (Orcinus orca) in the coastal waters of British 3 Columbia and Washington State. Report of the International Whaling Commission, 4 Special Issue 12:383-398. 5

Birtwell, I.K. and G.M. Kruzynski. 1989. In situ and laboratory studies on the behaviour and 6 survival of Pacific salmon (genus Oncorhynchus). Hydrobiologia 188/189:543–560. 7

Bjornn, T.C. and Reiser, D.W. 1991. Habitat requirements of salmonids in streams. In: Meehan, 8 W.R. Influences of forest and rangeland management of salmonid fishes and their 9 habitats. Bethesda, MD: American Fisheries Society: 83-138. 10

Blackwell, S.B., Lawson, J.W., and Williams, M.T. 2004. Tolerance by ringed seals (Phoca 11 hispida) to impact pile-driving and construction sounds at an oil production island. 12 Journal of the Acoustical Society of America, 115, 2346-2357. 13

BLM (Bureau of Land Management). 1998. Survey protocols for Survey and Manage Strategy 2 14 vascular plants: species information. Available at: http://www.blm.gov/or/plans/15 surveyandmanage/SP/VascularPlants/cover.htm. Accessed August 8, 2007. 16

Boehlert, G.W. and J.B. Morgan. 1985. Turbidity enhances feeding abilities of larval Pacific 17 herring, Clupea harengus pallasi. Hydrobiologia 123: 161-170. 18

Boggs, C.T., M.L. Keefer, C.A. Peery, J.T. Dalen, P.L. Madson, R.H. Wertheimer, K. Collis, 19 A.F. Evans. 2008. A multi-year summary of steelhead kelt studies in the Columbia and 20 Snake rivers. Technical Report 2008-13, Idaho Cooperative Fish and Wildlife Research 21 Unit, University of Idaho, Moscow, Idaho. 22

Bottom D.L., C.A. Simenstad, J. Burke, A.M. Baptista, D.A. Jay, K.K. Jones, E. Casillas, and 23 M.H. Schiewe. 2005. Salmon at river’s end: The role of the estuary in decline and 24 recovery of Columbia River salmon. NOAA Technical Memorandum NMFS-NWFSC-25 68, Northwest Fisheries Science Center, NMFS, Seattle, Washington. 26

Brett, J.R. 1995. Energetics. Pages 3–68 in Groot C., Margolis L., Clarke W.C., eds. 27 Physiological Ecology of Pacific Salmon. Vancouver, British Columbia, Canada: 28 UBC Press. 29

Brick, J. 2008. Personal communication. Email from Jim Brick, ODFW Biologist/and ODOT 30 Liaison, Oregon Department of Fish and Wildlife to Jenny Lord, Biologist, Parametrix, 31 on February 20, 2008. 32

Brown, Richard, David Geist. 2002. Determination of Swimming Speeds and Energetic 33 Demands of Upriver Migrating Fall Chinook Salmon (Oncorhynchus tshawytscha) in the 34 Klickitat River, WA. Project No. 2001-02400, BPA Report DOE/BP-00000652-9). 76 35 electronic pages. August 2002. 36

Buchanen, D.V., R.M. Hooten, and J.R. Mooring. 1981. Northern squawfish (Ptychocheilus 37 oregonensis) predation on juvenile salmonids in sections of the Willamette River basin, 38 Oregon. Canadian Journal of Fisheries and Aquatic Sciences 38:360-364. 39


10-4 June 2010

Burgner, R.L. 1991. Life history of sockeye salmon (Oncorhynchus nerka). In Pacific Salmon 1 Life Histories, C. Groot and L. Margolis (eds), pp. 1–118. University of British Columbia 2 Press, Vancouver, Canada. 3

Busby, P.J., T.C. Wainright, G.J. Bryant, L.J. Lierheimer, R.S. Waples, F.W. Waknitz, and I.V. 4 Lagomarsino. 1996. Status review of west coast steelhead from Washington, Idaho, 5 Oregon, and California. NOAA Technical Memorandum NMFS-NWFSC-27. NMFS 6 Northwest Fisheries Science Center, Seattle, Washington. 7

Caltrans (Californian Department of Transportation). 2009. Technical Guidance for Assessment 8 and Mitigation of the Hydroacoustic Effects of Pile Driving on Fish. Sacramento, 9 California. 10

Carlson, T.J., G. Ploskey, R.L. Johnson, R.P. Mueller, and M.A. Weiland. 2001. Observations of 11 the Behavior and Distribution of Fish in Relation to the Columbia River Navigation 12 Channel and Channel Maintenance Activities. PNNL-13595, Pacific Northwest National 13 Laboratory, Richland, Washington. 14

Carpenter, K. 2010. Personal communication. Email communication from Kurt Carpenter, 15 Hydrologist, USGS, to William Hall, Biologist, Parametrix, on February 1, 2010. 16

Carr, S.A., M.H. Laurinolli, C.D.S. Tollefson, and S.P. Turner. 2006. Cacouna Energy LNG 17 Terminal: Assessment of underwater noise impacts. Jasco Research Ltd. Halifax, Nova 18 Scotia. 19

Carrasquero, J. 2001. Over-Water Structures: Freshwater Issues. White paper submitted to 20 Washington Department of Fish and Wildlife, Washington Department of Ecology, and 21 Washington Department of Transportation. 22

Carter, J.A., G.A. McMichael, I.D. Welch, R.A. Harnish, and B.J. Bellgraph. 2009. Seasonal 23 Juvenile Salmonid Presence and Migratory Behavior in the Lower Columbia River. 24 PNNL-18246, Pacific Northwest National Laboratory. Richland, Washington. 25

Cary, G.A., J.A. McMahon, and W.J. Kuc. 1987. The effect of suspended solids and naturally 26 occurring dissolved organics in reducing the acute toxicities of cationic polyelectrolytes 27 to aquatic organisms. Environmental Toxicology and Chemistry 6:469-474. 28

Casillas E., M.R. Arkoosh, E. Clemons, T. Hom, D. Misitano, T.K. Collier, J.E. Stein, and U. 29 Varanasi. 1995a. Chemical contaminant exposure and physiological effects in outmigrant 30 juvenile Chinook salmon from urban estuaries of Puget Sound, Washington. Proceedings 31 of Puget Sound Research ‘95. Puget Sound Water Quality Authority, Olympia, 32 Washington. 33

Casillas E., M.R. Arkoosh, E. Clemons, T. Hom, D. Misitano, T.K. Collier, J.E. Stein, and U. 34 Varanasi. 1995b. Estuaries chemical contaminant exposure and physiological effects in 35 out-migrant juvenile Chinook salmon from selected urban estuaries of Puget Sound, 36 Washington. Proceedings of the 1994 Northeast Pacific Chinook and Coho Salmon 37 Workshop: Salmon Ecosystem Restoration: Myth and Reality edited by M. Keefe. 38 American Fisheries Society, Oregon Chapter, Corvallis, Oregon. 39


June 2010 10-5

Casillas, E., B.T.L. Eberhard, T.K. Collier, M.M. Krahn, and J.E. Stein. 1998a. Hylebos fish 1 injury study: round 2, part 3: exposure of juvenile Chinook salmon to chemical 2 contaminants specific to the Hylebos Waterway: Tissue concentrations and biochemical 3 responses. National Marine Fisheries Service, Northwest Fisheries Science Center, 4 Seattle, Washington. 5

CBR (Columbia Basin Research). 2009. Columbia River Data Access in Real Time (DART) 6 Reports. Interactive queries. University of Washington, School of Aquatic and Fisheries 7 Sciences. Available at http://www.cbr.washington.edu/dart/dart.html. Accessed 8 September 10, 2009. 9

Cederholm, C.J. and E.O. Salo. 1979. The effects of logging road landslide siltation on the 10 salmon and trout spawning gravels of Stequaleho Creek and the Clearwater River basin, 11 Jefferson County, Washington, 1972-1978. FRI-UW-7915. Fisheries Research Institute, 12 University of Washington, Seattle, Washington. 99 p. 13

CEG (Cosmopolitan Engineering Group). 2008. Technical Report: Columbia River Discharge 14 Schematic Design. Tacoma, Washington. 15

Celedonia, M.T., R.A. Tabor, S. Sanders, S. Damm, D.W. Lantz, T.M. Lee, Z. Li, J. Pratt, B.E. 16 Price, and L. Seyda. 2008. Movement and Habitat Use of Chinook Salmon Smolts, 17 Northern Pikeminnow, and Smallmouth Bass Near the SR 520 Bridge. 2007 Acoustic 18 Tracking Study. Final Report to WSDOT. USFWS, Western Washington Fish and 19 Wildlife Office, Fisheries Division, Lacey, Washington. October 2008. 20

CH2M HILL. 2005. I-5: Delta Park (Victory Boulevard to Lombard Section) Multnomah 21 County, Oregon, Biological Resources Technical Report. Final Technical Report. 22 December 2005. 23

Chapman, D.W. 1986. Salmon and Steelhead Abundance in the Columbia River in the 24 Nineteenth Century. Trans. Am. Fish. Soc. 115:662-670. 25

Chilcote, M. 1999. Conservation Status of Lower Columbia River Coho Salmon. Oregon 26 Department of Fish and Wildlife, 99-3, Portland, Oregon. 27

Clarke D., C. Dickerson, and K. Reine. 2002. Characterization of Underwater Sounds Produced 28 by Dredges. Dredging 2002. ASCE, Orlando, Florida, p 64-64. 29

Coccoli, H. 2004. Hood River subbasin plan: including lower Oregon Columbia Gorge 30 tributaries. Hood River Soil and Water Conservation District. Prepared for the Northwest 31 Power and Conservation Council, Portland, OR. Available at: http://www.nwcouncil.org32 /fw/subbasinplanning/Hood/plan. 33

Collis, K., R.E. Beaty, and B.R. Crain. 1995. Changes in catch rate and diet of northern 34 squawfish associated with the release of hatchery-reared juvenile salmonids in a 35 Columbia River reservoir. North American Journal of Fisheries Management 15:346-357. 36

Collis, K., D.D. Roby, D.P. Craig, S. Adamany, J. Adkins, and D.E. Lyons. 2002. Colony size 37 and diet composition of piscivorous waterbirds on the lower Columbia River: 38 Implications for losses of juvenile salmonids to avian predation. Transactions of the 39 American Fisheries Society 131:537-550. 40


10-6 June 2010

Columbia Basin Bulletin. 2010. Researches in January observe increased predation by Steller sea 1 lions on white sturgeon. Available at: http://www.cbbulletin.com/375791.aspx. Accessed 2 February 5, 2010. 3

COP (City of Portland). 2005. Draft 2005 Portland Watershed Management Plan. Bureau of 4 Environmental Services, City of Portland. October 2005. 5

COP. 2008. 2008 Portland Stormwater Management Manual. Bureau of Environmental Services. 6 Available at: http://www.portlandonline.com/BES/index.cfm?c=47952. Accessed 7 October 8, 2009. 8

COP. 2009a. Current Characterization Documents for the Columbia Slough. Available at: 9 http://www.portlandonline.com/bes/index.cfm?c=36081&. Accessed October 8, 2009. 10

COP. 2009b. Hayden Island Plan. Adopted by Portland City Council August 19, 2009, 11 Ordinance No. 183124. Effective Date: September 18, 2009. Available at: 12 http://www.portlandonline.com/bps/index.cfm?c=34248&a=280799. Accessed 13 October 1, 2009. 14

COV (City of Vancouver). 2007. Vancouver City Center Vision & Subarea Plan. Available at: 15 http://www.cityofvancouver.us/upload/images/EconDev/VCCVFINALREPORT061807.16 pdf. Accessed October 8, 2009. 17

CRC (Columbia River Crossing). 2008a. Traffic Technical Report. Available at: 18 http://www.columbiarivercrossing.org/FileLibrary/TechnicalReports19 /Transit_TechnicalReport.pdf. January 2008. 20

CRC. 2008b. Hydraulic and Scour Parameters Report. Unpublished Technical Report. November 21 2008. 22

CRC. 2008c. Land Use Technical Report. Available at: http://www.columbiarivercrossing.com23 /FileLibrary/TechnicalReports/Land_Use_TechnicalReport.pdf. 24

CRC. 2009. Memorandum from CRC for FPAC: Hydroacoustic Analysis Discussion Fish 25 Passage Advisory Committee Presentation. October 20, 2009. 26

CRC (Columbia River Crossing) Fish-Run Working Group. 2009. Run timing for listed aquatic 27 and marine species occurring in the Columbia River Crossing Action Area (Columbia 28 River and North Portland Harbor). Unpublished data. Information compiled from ODFW, 29 WDFW, and NMFS species experts. 30

CREDDP (Columbia River Estuary Data Development Program). 1984. The Columbia River 31 Estuary Atlas of Physical and Biological Characteristics. 32

CRETM-LMER (Columbia River Estuarine Turbidity Maxima-Land-Margin Ecosystem 33 Research). 2000. Land-Margin Ecosystem Research Project, Columbia River Estuary 34 Turbidity Maxima. Available at: http://depts.washington.edu/cretmweb/. Accessed 35 October 8, 2009. 36

Cooper, A.C. 1965. The effect of transported stream sediments on the survival of sockeye and 37 pink salmon eggs and alevins. Int. Pac. Salmon Fish. Comm. Bull. 18. 71 p. 38


June 2010 10-7

Cudaback, C.N. and D.A. Jay. 1996. Formation of the Columbia River plume – Hydraulic 1 control in action? Pages 139-154 in D.G. Aubrey and C.T. Friedrichs, editors. Coastal 2 and estuarine studies 53: buoyance effects on coastal and estuarine dynamics. American 3 Geophysical Union, Washington, D.C. 4

Davies-Colley, R.J. and D.G. Smith. 2001. Turbidity, Suspended Sediment, and Water Clarity: A 5 Review. Journal of the American Water Resources Association. Vol. 37, No. 5. 6 October 2001. 7

Dawley, E.M., R.D. Ledgerwood, T.H. Blahm, C.W. Sims, J.T. Durkin, R.A. Kim, A.E. Rankin, 8 G.E. Monan, and F.J. Ossiander. 1986. Migrational Characteristics, Biological 9 Observations, and Relative Survival of Juvenile Salmonids Entering the Columbia River 10 Estuary, 1966–1983. Northwest Fisheries Science Center, National Marine Fisheries 11 Service, National Oceanic and Atmospheric Administration, Seattle, Washington. 12

Daykin, P.N. 1965. Application of mass transfer theory to the problem of respiration of fish eggs. 13 J. Fish. Res. Board Can. 22(1):159-171. 14

DEA (David Evans and Associates). 2006. Columbia River Crossing Hydrographic and 15 Geophysical Investigation: High Resolution Bathymetric Mapping, River Bed Imaging, 16 and Subbottom Investigation. Prepared for the Oregon Department of Transportation and 17 the Washington State Department of Transportation. 18

DEQ (Oregon Department of Environmental Quality). 1991. Total Maximum Daily Load for 19 2,3,7,8-TCDD in the Columbia River Basin. February 1991. 20

DEQ. 1998. Columbia Slough Total Maximum Daily Loads (TMDLs) for: Chlorophyll a, 21 Dissolved Oxygen, pH, Phosphorus, Bacteria, DDE/DDT, PCBs, Pb, Dieldrin and 22 2,3,7,8-TCDD. 23

DEQ. 2002. Total Maximum Daily Load (TMDL) for Lower Columbia River Total Dissolved 24 Gas. September 2002. 25

DEQ. 2007a. Oregon’s 2004/2006 Integrated Report Online Database. Available at: 26 http://www.deq.state.or.us/wq/assessment/rpt0406/search.asp. Accessed October 8, 2009. 27

DEQ. 2007b. Guidance for assessing bioaccumulative chemicals of concern in sediment. 28 Portland, Oregon. 29

DEQ. 2009. Water Quality Assessment Database: 2004/2006 Integrated Report Database. 30 Available at: http://www.deq.state.or.us/wq/assessment/rpt0406/search.asp#db. Accessed 31 November 6, 2009. 32

Dickerson, C. K.J. Reine, and D.G. Clarke. 2001. Characterization of underwater sounds 33 produced by bucket dredging operations. DOER Technical Notes Collection (ERCC 34 TN-DOER-E14), US Army Engineer Research and Development Center, Vicksburg, MS. 35 Available at: www.wes.army.mil/el/dots/doer. 36

Doppelt, B., R. Hamilton, C.D. Williams, M. Koopman, and S. Vynne. 2009. Preparing for 37 Climate Change in the Upper Willamette River Basin of Western Oregon, Co-Beneficial 38 Planning for Communities and Ecosystems. Institute for Sustainable Environment 39 National Center for Conservation Science and Policy. March 2009. 40


10-8 June 2010

DSL (Oregon Department of State Lands). 2009. Essential Salmonid Habitat Maps. Available at: 1 http://www.oregon.gov/DSL/PERMITS/counties_ess.shtml. Accessed May 2009. 2

DWR (Oregon Department of Water Resources). 2008. Sand Hollow – Umatilla Basin Regional 3 Aquifer Recovery Hand Out. 4

Ecology (Washington Department of Ecology). 2006. Water Quality Standards for Surface 5 Waters of the State of Washington Chapter 173-201A WAC. Washington State 6 Department of Ecology. Publication Number 06-10-091. Amended November 20, 2006. 7

Ecology. 2006. General Use Level Designation for Basic (TSS), Enhanced, and Oil Treatment 8 and Conditional Use Level Designation for Phosphorus Treatment for Americast’s 9 Filterra. November 2006, revised December 2009. 10

Ecology. 2008. Department of Ecology Environmental Assessment Program, Quarterly Report 11 Progress Report #2 and #3, Burnt Bridge Creek Total Maximum Daily Load (TMDL). 12 November 2008. Available at: http://www.ecy.wa.gov/programs/wq/tmdl13 /burntbridge/qtlyrpts/BBCqtr2-3-112608.pdf. Accessed March 3, 2009. 14

Ecology. 2009a. Burnt Bridge Creek Water Quality Improvement Project. Available at: 15 http://www.ecy.wa.gov/programs/wq/tmdl/burntbridge/BurntBrtmdl.html. Accessed 16 February 18, 2009. 17

Ecology. 2009b. Washington State’s Water Quality Assessment [303(d)]. Available at: 18 http://www.ecy.wa.gov/programs/wq/303d/. Accessed July 8, 2009. 19

Ecology. 2009c. Washington Department of Ecology River & Stream Water Quality Monitoring. 20 Available at: http://www.ecy.wa.gov/apps/watersheds/riv/station.asp?sta=28c070. 21 Accessed March 3, 2009. 22

Ecology. 2009d. State of Washington Shoreline Management Information page. Available at: 23 http://www.ecy.wa.gov/programs/sea/SMA/index.html. Accessed June 4, 2009. 24

Ecology. 2009e. Publication Summary: Chapter 197-11 WAC, SEPA Rules. Available at: 25 http://www.ecy.wa.gov/biblio/wac19711.html. Accessed November 6, 2009. 26

Edwards, E., G. Gebhart, and O.E. Maughan. 1983. Habitat suitability information: smallmouth 27 bass. U.S. Fish and Wildlife Service. FWS/OBS-82/10.36. 28

Everhart, W.H., A.W. Eipper, and W.D. Youngs. 1953. Principles of Fishery Science. Cornell 29 University Press, London. 30

FHWG (Fish Hydroacoustics Working Group). 2008. Agreement in principal for interim criteria 31 for injury to fish from pile driving activities. Memorandum between FHWA, NOAA 32 Fisheries NW and SW Region, USFWS Regions 1 and 8, Caltrans, and ODOT. June 12, 33 2008. 34

Fields, P.E. 1966. Final report on migrant salmon light guiding studies at Columbia River dams. 35 Contract No. DA-45-108. CIVEN 6-23-29. Portland, Oregon. 36

Finneran, J.J., R. Dear, D.A. Carder, and S.H. Ridgway. 2003. Auditory and behavioral 37 responses of California sea lions (Zalophus californianus) to single underwater impulses 38 from an arc-gap transducer. Journal of the Acoustical Society of America, 114, 39 1667-1677. 40


June 2010 10-9

Fish Commission of Oregon. 1953. Processed Report: Columbia River. Smelt or eulachon. 8 1 electronic pages. 2

Fisher, T., and R. Hinrichsen. 2006. Abundance-based trend results for Columbia basin salmon 3 and steelhead ESUs. Appendix F. Prepared for Bonneville Power Administration, 4 Portland, Oregon. 5

Foote, A.D., R.W. Osborne, and A.R. Hoelzel. 2004. Whale-call response to masking boat noise. 6 Nature 428:910. 7

Ford, J.K.B., G.M. Ellis, and K.C. Balcomb. 2000. Killer whales: the natural history and 8 genealogy of Orcinus orca in British Columbia and Washington State, 2nd edition. UBC 9 Press, Vancouver, British Columbia. 10

Ford, J.K.B., G.M. Ellis, and P.F. Olesiuk. 2005. Linking prey and population dynamics: did 11 food limitation cause recent declines of 'resident' killer whales (Orcinus orca) in British 12 Columbia? Fisheries and Oceans Canada, Nanaimo, British Columbia. 13

FPC (Fish Passage Center). 2008. Spawning, strandings, and entrapments information page. 14 Available at: http://www.fpc.org/spawning/spawning_strandings.html. Accessed 15 February 27, 2009. 16

FPC (Fish Passage Center). 2010. Ives Island Water Elevation and Water Temperature Data. 17 Available at: http://www.fpc.org/ivesisland/ivesisland.html. Accessed February 2, 2010. 18

Fraley, J.J. and B.B. Shepard. 1989. Life history, ecology and population status of migratory bull 19 trout (Salvelinus confluentus) in the Flathead Lake and River system, Montana. 20 Northwest Science NOSCAX 63(4):133-142. 21

Fresh, K.L., E. Casillas, L.L. Johnson, and D.L. Bottom. 2005. Role of the estuary in the 22 recovery of Columbia River Basin salmon and steelhead: An evaluation of the effects of 23 selected factors on salmonid population viability. U.S. Department of Commerce, NOAA 24 Technical Memorandum NMFS-NWFSC-69, 105 p. 25

Friesen. T.A. 2005. Biology, behavior, and resources of resident and anadromous fish in the 26 lower Willamette River. Final report of research, 2000–2004. Information Report No. 27 2007-03. Oregon Department of Fish and Wildlife, Salem, Oregon. 28

Frost, K.J., and L.F. Lowry, 1988: Effects of industrial activities on ringed seals in Alaska, as 29 indicated by aerial surveys. In Port and ocean engineering under Arctic conditions. Vol. 30 II. Symposium on noise and marine mammals. Edited by W.M. Sackinger, M.O. Jeffries, 31 J.L. Imm, and S.D. Treacy. Geophysical Institute, University of Alaska Fairbanks, 32 Fairbanks. pp. 15–25. 33

Frost, K.J., L.F. Lowry, J.R. Gilbert, and J.J. Burns. 1988. Ringed seal monitoring: relationships 34 of distribution and abundance to habitat attributes and industrial activities. Final Rep. 35 Contract No. 84-ABC-00210 submitted to U.S. Dep. Interior, Minerals Management 36 Service, Anchorage, AK. 101 pp. 37


10-10 June 2010

Fuhrer, G.J., D.Q. Tanner, J.L. Morace, S.W. McKenzie, and K.A. Skach. 1996. Water Quality 1 of the Lower Columbia River Basin: Analysis of Current and Historical Water Quality 2 Data through 1994. USGS Water-Resources Investigations Report 95-4294, U.S. 3 Geological Survey. Available at: http://or.water.usgs.gov/pubs_dir/Abstracts/95-4 4294.html. Accessed October 8, 2009. 5

Gardner, M.B. 1981. Effects of turbidity on feeding rates and selectivity of bluegills. 6 Transactions of the American Fisheries Society 110: 446-450. 7

Garrett, A. 2006. Personal communication. E-mail from Ann Garrett, Fish Biologist, NOAA 8 Fisheries Office of Protected Resources on March 29, 2006. 9

Gentry, R.L. and J.F. Gilman. 1990. Responses of northern fur seals to quarrying operations. 10 Marine Mammal Science 6: 151-155. 11

Geosyntec Consultants. 2008. White Paper: BMP Effectiveness Assessment for Highway Runoff 12 in Western Washington. Prepared for WSDOT, Olympia, Washington. March 25, 2008. 13 Available at: http://www.wsdot.wa.gov/NR/rdonlyres/195AF37F-1AA3-43AE-B776-14 B4A616CC5C7B/0/BMP_EffectivHwyRunoffWestWA.pdf. 15

Geraci, J.R. 1990. Physiologic and toxic effects on cetaceans. Pages 167-198 in J.R. Geraci and 16 D.J. St. Aubin, editors. Sea mammals and oil: confronting the risks. Academic Press, 17 New York. 18

Gillam, J. 2009. Personal communication from John Gillam, Planner, City of Portland Bureau of 19 Transportation, on June 11, 2009. 20

Ginetz and Larkin. 1976. Factors affecting rainbow trout (Salmo gairdneri) predation on migrant 21 fry of sockeye salmon (Oncorhynchus nerka). Journal of the Fisheries Research Board of 22 Canada 33: 19-24. 23

Good, T.P., R.S. Waples, and P. Adams (editors). 2005. Updated status of federally listed ESUs 24 of West Coast salmon and steelhead. U.S. Dept. Commerce, NOAA Tech. Memo. 25 NMFS-NWFSC-66, 598 pp. Available at: http://www.nwr.noaa.gov/Publications26 /Biological-Status-Reviews/upload/SR2005-allspecies.pdf. Accessed February 23, 2010. 27

Gray, G.A. and D.W. Rondorf. 1986. Predation on juvenile salmonids in Columbia Basin 28 reservoirs. Pages 178-185 in: G.E. Hall and M.J. Van Den Avyle, eds. Reservoir 29 Fisheries Management: Strategies for the 80s. American Fisheries Society, Bethesda, 30 MD. 327 p. 31

Green, J.E., and S.R. Johnson. 1983. The distribution and abundance of ringed seals in relation to 32 gravel island construction in the Alaskan Beaufort Sea, p. 1–28. In B.J. Gallaway [ed.], 33 Biological Studies and Monitoring at Seal Island, Beaufort Sea, Alaska 1982. LGL 34 Ecological Research Associates, Inc., Bryan, TX for Shell Oil Co., Houston, TX. 35

Gregory, R.S. 1992. The influence of ontogeny, perceived risk of predation, and visual ability on 36 the foraging behavior of juvenile Chinook salmon. Theory and Application of Fish 37 Feeding Ecology 18: 271-284. 38

Gregory, R.S. 1993. Effect of turbidity on the predator avoidance behavior of juvenile Chinook 39 salmon (Oncorhynchus tshawytscha). Can. J. Fish. Aquat. Sci. 50:241–246. 40


June 2010 10-11

Gregory, R.S. and T.G. Northcote. 1993. Surface, planktonic, and benthic foraging by juvenile 1 Chinook salmon (Oncorhynchus tshawytscha) in turbid laboratory conditions. Canadian 2 Journal of Fisheries and Aquatic Sciences 50: 233-240. 3

Gregory, R.S. and C.D. Levings. 1996. The effects of turbidity and vegetation on the risk of 4 juvenile salmonids, Oncorhynchus spp., to predation by adult cutthroat trout, O. clarkii. 5 Environmental Biology of Fishes 47: 279-288. 6

Gregory, R.S. and C.D. Levings. 1998. Turbidity reduces predation on migrating juvenile Pacific 7 salmon. Transactions of the American Fisheries Society 127: 275-285. 8

Gray, G.A. and D.W. Rondorf. 1986. Predation on juvenile salmonids in Columbia Basin 9 reservoirs. Pages 178-185 in: G. E. Hall and M. J. Van Den Avyle, eds. Reservoir 10 Fisheries Management: Strategies for the 80s. American Fisheries Society, Bethesda, 11 MD. 327 p. 12

Gustafson, R.G., T.C. Wainwright, G.A. Winas, F.W. Waknitz, L.T. Parker, and R.S. Waples. 13 1997. Status Review of Sockeye Salmon from Washington and Oregon. NOAA 14 Technical Memorandum NMFSNWFSC-33, Northwest Fisheries Science Center, 15 National Marine Fisheries Service, Seattle, Washington. 16

Hamlet, A.F., P. Mote, and D.P. Lettenmaier. 2003. Climatic Variability and Trends in the PNW 17 and Columbia River Basin from 1750-2003 and Projections of Climate Change Impacts 18 for the 21st Century. JISAO Center for Science in the Earth System Climate Impacts 19 Group and Department of Civil and Environmental Engineering, University of 20 Washington. October, 2003. 21

HammerSteel. 2009. Delmag® Diesel Hammers. Available at. http://www.hammersteel.com22 /delmag/Diesel_hammers.html. Accessed November 3, 2009. 23

Harris, R.E., G.W. Miller, and W.J. Richardson. 2001. Seal responses to airgun sounds during 24 summer seismic surveys in the Alaskan Beaufort Sea. Marine Mammal Science, 17, 25 795-812. 26

Havis, R.N. 1988. Sediment resuspension by selected dredges. EEDP-09-2. U.S. Army Engineer 27 Waterways Experiment Station. Vicksburg, Mississippi. 28

Hay, D.E. and McCarter, P.B. 2000. Status of the eulachon Thaleichthys pacificus in Canada. 29 Department of Fisheries and Oceans Canada, Canadian Stock Assessment Secretariat, 30 Research Document 2000-145. Ottawa, Ontario. 31

Hecht, S.A., D.H. Baldwin, C.A. Mebane, T. Hawkes, S.J. Gross, and N.L. Scholz. 2007. An 32 overview of sensory effects on juvenile salmonids exposed to dissolved copper: applying 33 a benchmark concentration approach to evaluate sublethal neurobehavioral toxicity. U.S. 34 Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-83, 39 pp. 35

Heiser, D.W. and E.L. Finn, Jr. 1970. Observations of juvenile chum and pink salmon in marina 36 and bulkheaded areas. Supplemental progress report, Puget Sound stream studies. 37 Washington Department of Fisheries, Management and Research Division. 38


10-12 June 2010

Herrera Environmental Consultants. 2007. White Paper: Untreated Highway Runoff in Western 1 Washington. Prepared for WSDOT, Olympia, Washington. May 16, 2007. Available at: 2 http://www.wsdot.wa.gov/NR/rdonlyres/B947A199-6784-4BDF-99A7-3 DD2A113DAB74/0/BA_UntreatedHwyRunoffWestWA.pdf. 4

Hickey, B.M., L.J. Pietrafesa, D.A. Jay, and W.C. Boicourt. 1997. The Columbia River plume 5 study: subtidal variability in the velocity and salinity field. Journal of Geophysical 6 Research: 103(C5):10339-10368. 7

Hildebrand, J.A. 2005. Impacts of Anthropogenic Sound in J.E. Reynolds et al. (eds), Marine 8 Mammal Research: Conservation beyond Crisis. The Johns Hopkins University Press, 9 Baltimore, Maryland. Pages 101-124 (2005). Available at: http://www.escholarship.org/10 uc/item/8997q8wj. 11

Hildebrand, J.A. 2009. Anthropogenic and natural sources of ambient noise in the ocean. Marine 12 Ecology Progress Series. Vol. 395: 5–20, 2009. 13

Hillson, T.D. 2002. Re-Introduction of Lower Columbia River Chum Salmon into Duncan Creek 14 Annual Report for 2002, Report to Bonneville Power Administration, Contract No. 15 00007373, Project No. 200105300, BPA Report DOE/BP-00007373 -1. 63 electronic 16 pages. 17

Hillson, T.D. 2003. Re-Introduction of Lower Columbia River Chum Salmon into Duncan Creek 18 Annual Report for 2003, Report to Bonneville Power Administration, Contract No. 19 00007373, Project No. 200105300, BPA Report DOE/BP-00007373-2. 73 electronic 20 pages. 21

Hillson, T.D. 2004. Re-Introduction of Lower Columbia River Chum Salmon into Duncan 22 Creek. Annual Report for 2004, Report to Bonneville Power Administration, Contract 23 No. 00007373, Project No. 200105300, BPA Report DOE/BP-00007373-4. 81 electronic 24 pages. 25

Hillson, T. 2006. Re-Introduction of Lower Columbia River Chum Salmon into Duncan Creek, 26 2004–2005 Annual Report, Project No. 200105300, BPA Report DOE/BP- 00020932. 27 173 electronic pages. 28

Hillson, T. 2009. Washington Department of Fish and Wildlife. Personal Communication. Phone 29 conference with M. Parton, Parametrix, on December 12, 2009. 30

Hollis L., J.C. McGeer, D.G. McDonald, and C.M. Wood. 2000. Protective effects of calcium 31 against chronic waterborne cadmium exposure to juvenile rainbow trout. Environmental 32 Toxicology and Chemistry 19(11):2725-2734. 33

Holmes, E.E. and A.E. York. 2003. Using age structure to detect impacts on threatened 34 populations: a case study using Steller sea lions. Conservation Biology 17:1794-1806. 35

Hood River Watershed Group. 2008. Hood River watershed action plan. Available at 36 http://www.hoodriverswcd.org/ActionPlan.pdf. 37

Howell, P.K. Jones, D. Scarnecchia, L. LaVoy, W. Kendra and D. Ortmann. 1985. Stock 38 Assessment of Columbia River Anadromous Salmonids. Two Volumes. Final Report to 39 Bonneville Power Administration. (Contract No. DE-AI79-84BP12737), Portland, OR. 40


June 2010 10-13

Howell, M.D., M.D. Romano, and T.A. Rien. 2001. Migration Timing and Distribution of Larval 1 Eulachon, Thaleichthys pacificus, in the Lower Columbia River, Spring 2001. WDFW, 2 Vancouver, WA, and ODFW, Clackamas, OR. Available at: http://wdfw.wa.gov/fish3 /creel/smelt/USACE_smelt_emmigration_rep.pdf. Accessed February 10, 2010. 4

Hulse, D., S. Gregory, and J. Baker, Eds. 2002. Willamette River Basin Planning Atlas: 5 Trajectories of Environmental and Ecological Change. Pacific Northwest Ecosystem 6 Research Consortium, Oregon State University, Corvallis, OR. 7

ICTRT (Interior Columbia Technical Recovery Team). 2007a. Current ICTRT draft population 8 status reports. Working Drafts. Available at: http://www.nwfsc.noaa.gov/trt/col/9 trt_current_status_assessments.cfm. Accessed October 10, 2009. 10

ICTRT (Interior Columbia Technical Recovery Team). 2007b. Required survival rate changes to 11 meet Technical Recovery Team abundance and productivity viability criteria for interior 12 Columbia River basin salmon and steelhead populations. 13

Incardona, J. P., M.G. Carls, H. Teraoka, C.A. Sloan, T.K. Collier, and N.L. Scholz. 2005. Aryl 14 hydrocarbon receptor-independent toxicity of weathered crude oil during fish 15 development. Environ. Health Perspect. 113, 1755-1762. 16

Incardona, J. P., T.K. Collier, and N.L. Scholz. 2004. Defects in cardiac function precede 17 morphological abnormalities in fish embryos exposed to polycyclic aromatic 18 hydrocarbons. Toxicol. Appl. Pharmacol. 196, 191-205. 19

Incardona J.P., H.L. Day, T.K. Collier, and N.L. Scholz. 2006. Developmental toxicity of 4-ring 20 polycyclic aromatic hydrocarbons in zebrafish is differentially dependent on AH receptor 21 isoforms and hepatic cytochrome P450 1A metabolism. Toxicol. Appl. Pharmacol. 22 217:308-321. 23

ISAB (Independent Scientific Advisory Board). 2000. The Columbia River Estuary and the 24 Columbia River Basin Fish and Wildlife Program. A Review of the Impacts of the 25 Columbia River’s Hydroelectric System on Estuarine Conditions. Conducted for the 26 Northwest Power Planning Council in conjunction with studies by NOAA Fisheries. 27

Isidori M., M. Lavorgna, M. Palumbo, V. Piccoli, and V. Parrella. 2007. Influence of alklyl 28 phenols and trace elements in toxic, genotoxic, and endocrine disruption activity of 29 wastewater treatment plants. Environmental Toxicology and Chemistry 26(8):1686-1694. 30

JCRMS (Joint Columbia River Management Staff). 2007. 2008 ODFW/WDFW joint staff report 31 concerning stock status and fisheries for sturgeon and smelt. Available at: 32 http://wdfw.wa.gov/fish/crc/crc2008_sturgeon_smelt_js_rpt.pdf. Accessed 33 December 2009. 34

JCRMS. 2009a. 2009 Joint staff report: Stock status and fisheries spring Chinook, summer 35 Chinook, sockeye, steelhead, other species, and miscellaneous regulations. ODFW and 36 WDFW. Available at: http://wdfw.wa.gov/fish/crc/. Accessed December 2009. 37

JCRMS. 2009b. 2009 Joint staff report: Stock status and fisheries fall Chinook, coho, Chinook, 38 chum, summer steelhead, and white sturgeon. ODFW and WDFW. Available at: 39 http://wdfw.wa.gov/fish/crc/. Accessed December 2009. 40


10-14 June 2010

JCRMS. 2009c. 2008 Joint staff report: Stock status and fisheries for sturgeon and smelt. ODFW 1 and WDFW. Available at: http://wdfw.wa.gov/fish/crc/crc2008_sturgeon_smelt_2 js_rpt.pdf. Accessed December 2009. 3

JISAO (Joint Institute for the Study of the Atmosphere and Ocean). 2002. Impacts of climate 4 variability and change in the Pacific Northwest. The JISAO Climate Impacts Group, 5 University of Washington. JISAO Contribution #715. 6

Johnsen, R.C. and C.W. Sims. 1973. Purse seining for juvenile salmon and trout in the Columbia 7 River estuary. Transactions of the American Fisheries Society 102:341–345. 8

Johnson, F.H. 1969. Environmental and species associations of the walleye in Lake 9 Winnibigoshish and connected waters, including observations on food habits and 10 predator-prey relationships. Minnesota Fisheries Investigations 5:5-36. 11

Johnson, O.W., W.S. Grant, R.G. Kope, K. Neely, F.W. Waknitz, and R.S. Waples. 1997. Status 12 review of chum salmon from Washington, Oregon, and California. NMFS Technical 13 Memorandum NMFS-NWFSC-32. National Marine Fisheries Service, Northwest 14 Fisheries Science Center, Seattle, Washington. 15

Johnson, O.W. F.S. Goetz, and G.R. Ploskey. 1998. Unpublished report on salmon light study at 16 Hiram M. Chittenden Locks, US Army Corps of Engineers, Stevenson, Washington. 17

Johnson and O’Neil. 2001. Wildlife-Habitat Relationships in Oregon and Washington. Oregon 18 State University Press. 19

Johnson, L.L., G.M. Ylitalo, M.R. Arkoosh, A.N. Kagley, C.L. Stafford, J.L. Bolton, J. Buzitis, 20 B.F. Anulacion, and T.K. Collier. 2007. Contaminant exposure in outmigrant juvenile 21 salmon from Pacific Northwest estuaries. Environmental Monitoring and Assessment. 22 124:167-194. 23

Johnson, J., J. Poirier and T. Whitesel. 2008. Evaluate factors limiting Columbia River gorge 24 chum salmon Populations. BPA Project 2000-012-00, October 2005 to September 2006. 25 U.S. Fish and Wildlife Service, Columbia River Fish Program Office, Habitat and 26 Population Assessment Team. Vancouver, WA. 27

Johnson, L.L., G.M. Ylitalo, M.S. Myers, B.F. Anulacion, J. Buzitis, W.L. Reichert, and T.K. 28 Collier. 2009. Polycyclic aromatic hydrocarbons and fish health indicators in the marine 29 ecosystem in Kitimat, British Columbia. U.S. Dept. Commer., NOAA Tech. Memo. 30 NMFS-NWFSC-98, 123 pp. 31

Kastak, D., and R.J. Schusterman, R.J. 1996. Temporary threshold shift in a harbor seal (Phoca 32 vitulina). Journal of the Acoustical Society of America, 100, 1905-1908. 33

Kastak, D., R.J. Schusterman, B.L. Southall, and C.J. Reichmuth. 1999. Underwater temporary 34 threshold shift induced by octave-band noise in three species of pinniped. Journal of the 35 Acoustical Society of America, 106, 1142-1148. 36

Kastak, D., B.L. Southall, M.M. Holt, C.R. Kastak, and R.J. Schusterman. 2004. Noise-induced 37 temporary threshold shift in pinnipeds: Effects of noise energy. Journal of the Acoustical 38 Society of America, 116 (4, pt. 2), 2531. 39


June 2010 10-15

Kastak, D., B.L. Southall, R.J. Schusterman, and C. Reichmuth Kastak. 2005. Underwater 1 temporary threshold shift in pinnipeds: Effects of noise level and duration. Journal of the 2 Acoustical Society of America, 118, 3154-3163. 3

Kastak, D., C. Reichmuth, M.M. Holt, J. Mulsow, B.L. Southall, and R.J. Schusterman. 2007. 4 Onset, growth, and recovery of in-air temporary threshold shift in a California sea lion 5 (Zalophus californianus). Journal of the Acoustical Society of America, 122, 2916-2924. 6

Keller, K. 2006. Evaluate spawning of fall Chinook and chum salmon below the four lowermost 7 Columbia River mainstem dams; 2005 Columbia River chum salmon return. 2005-2006 8 annual report. Prepared for Bonneville Power Administration, Portland, Oregon. 9

Krahn, M.M., P.R. Wade, S.T. Kalinowski, M.E. Dahlheim, B.L. Taylor, M.B. Hanson, G.M. 10 Ylitalo, R.B. Angliss, J.E. Stein, and R.S. Waples. 2002. Status review of Southern 11 Resident killer whales (Orcinus orca) under the Endangered Species Act, U.S. Dept. of 12 Commerce, NOAA Tech. Memo., NMFS-NWFSC-54, 133 pp. 13

Krahn, M.M., M.J. Ford, W.F. Perrin, P.R. Wade, R.B. Angliss, M.B. Hanson, B.L. Taylor, G.M. 14 Ylitalo, M.E. Dahlheim, J.E. Stein, and R.S. Waples. 2004. 2004 status review of 15 Southern Resident killer whales (Orincus orca) under the Endangered Species Act, U.S. 16 Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-62, 73 pp. 17

Kruse, S. 1991. The interactions between killer whales and boats in Johnstone Strait, B.C. Pages 18 149-159 in K. Pryor and K.S. Norris, editors. Dolphin societies: discoveries and puzzles. 19 University of California Press, Berkley. 20

Lambourne, D. 2010. Personal communication with Dyanna Lambourne, Marine Mammal 21 Research Biologist, WDFW. February 25, 2010. 22

Langer, O.E., B.G. Shepherd and P.R. Vroom. 1977. Biology of the Nass Eulachon 23 (Thaleichthys pacificus). Fisheries and Environment of Canada. PAC/T-77-10. 24

Langness, O. 2008. Personal communication. E-mail correspondence and telephone 25 conversations between Olaf Langness, Sturgeon and Eulachon Biologist, Washington 26 Department of Fish and Wildlife, and Jennifer Lord and Mike Parton, Parametrix 27 biologists, in November 2008. 28

Langness, O. 2009. Personal communication. E-mail correspondence and telephone 29 conversations between Olaf Langness, Sturgeon and Eulachon Biologist, WDFW, and 30 Jennifer Lord and Mike Parton, Parametrix biologists, in December 2009. 31

LaSalle, M.W. 1988. Physical and chemical alterations associated with dredging: an overview. 32 Pages 1-12 in C.A. Simenstad, ed. Effects of dredging on anadromous Pacific fishes. 33 University of Washington, Seattle, Washington. 34

Laughlin, J. 2005. Underwater Sound Levels Associated With Restoration of the Friday Harbor 35 Ferry Terminal. Friday Harbor Ferry Terminal Restoration Project, Washington State 36 Department of Transportation, Seattle, Washington. 37

Laughlin, J. 2005b. Underwater Sound Levels Associated with Restoration of the Friday Harbor 38 Ferry Terminal. Washington State Department of Transportation Office of Air Quality 39 and Noise. Seattle, Washington. 40


10-16 June 2010

Laughlin, J. 2009. Personal communication. E-mail correspondence from Jim Laughlin, Acoustic 1 Specialist, WSDOT, on October 22, 2009. 2

LCFRB (Lower Columbia Fish Recovery Board). 2004. “Mainstem Lower Columbia River and 3 Columbia River Estuary Subbasin Plan.” In Columbia River Basin Fish and Wildlife 4 Program. Portland, OR. Available at: http://www.lcfrb.gen.wa.us/December%205 Final%20%20Plans/lower_columbia_salmon_recovery_a.htm. Accessed 6 November 6, 2009. 7

LCFRB. 2010. “Mainstem Lower Columbia River and Columbia River Estuary Subbasin Plan 8 Update.” (Draft) In Columbia Basin Fish and Wildlife Program. Portland, OR. Available 9 at: http://www.lcfrb.gen.wa.us/March%202010%20review%20draft%20RP10 /RP%20Frontpage.htm. 11

LCREP (Lower Columbia River Estuary Partnership). 2007a. Columbia River Estuary ESA 12 Recovery Plan Module for Salmon and Steelhead. Prepared for NOAA Fisheries by 13 LCREP. Available at: http://www.nwr.noaa.gov/Salmon-Recovery-Planning/ESA-14 Recovery-Plans/Estuary-Module.cfm. Accessed February 3, 2010. 15

LCREP. 2007b. Lower Columbia River and estuary ecosystem monitoring: Water quality and 16 salmon sampling report. Lower Columbia River Estuary Partnership. Portland, Oregon. 17

Ledgerwood, R.D., F.P. Thrower, and E.M. Dawley. 1991. Diel sampling of migratory juvenile 18 salmonids in the Columbia River estuary. Fishery Bulletin 88:69–78. 19

Ledgerwood R.D., S.W. Naman, B.A. Ryan, B.P. Sandford, C.Z. Banks, and J.W. Ferguson. 20 2004. Detection of PIT-Tagged Juvenile Salmonids in the Columbia River Estuary Using 21 a Pair-Trawl, 2000 and 2001. Contract Report 4328, Northwest Fisheries Science Center, 22 National Marine Fisheries Service, Seattle, Washington. Available at: 23 http://www.nwfsc.noaa.gov/publications/displayallinfo.cfm?docmetadataid=4328. 24 Accessed July 30, 2009. 25

Lee, H. S.L. Laua, M. Kayhanianb, and M.K. Stenstrom. 2004. Seasonal first flush phenomenon 26 of urban stormwater discharges. Water Research 38:19: 4153-4163. 27

LeGore, R.S. and D.M. DesVoigne. 1973. Absence of acute effects of threespine sticklebacks 28 (Gasterosteus aculeatus) and coho salmon (Oncorhynchus kisutch) exposed to 29 resuspended harbor sediment concentrations. J. Fish. Res. Bd. Can. 30(8):1240-1242. 30

Levings, C. D., C. D. McAllister, and B. D. Chang. 1986. Differential use of the Campbell River 31 estuary, British Columbia, by wild and hatchery-reared juvenile Chinook salmon 32 (Oncorhynchus tshawytscha). Can. J. Fish. Aquat. Sci. 43(7):1386-1397. 33

Levy, D.A., and T.G. Northcote. 1982. Juvenile salmon residency in a marsh area of the Fraser 34 River estuary. Can. J. Fish. Aquat. Sci. 39:270-276. 35

Li H., B.J. Teppen, C.T. Johnston, and S.A Boyd. 2004. Thermodynamics of nitroaromatic 36 compound adsorption from water by smectite clay. Environmental Science & Technology 37 38:5433-5442. 38

Lloyd, D.S. 1987. Turbidity as a water quality standard for salmonid habitats in Alaska. North 39 American Journal of Fisheries Management 7: 34-45. 40


June 2010 10-17

Loge, F., M.R. Arkoosh, T.R. Ginn, L.L. Johnson, and T.K. Collier. 2006. Impact of 1 Environmental Stressors on the Dynamics of Disease Transmission. Environmental 2 Science & Technology. 39(18):7329-7336. 3

MacGillivray, A. and R. Racca. 2005. Sound pressure and particle velocity measurements from 4 marine pile driving at Eagle Harbor maintenance facility, Bainbridge Island, WA. 5 Prepared for the Washington State Department of Transportation. 6

Matkowski, S.M.D. 1989. Differential susceptibility of three species of stocked trout to bird 7 predation. North American Journal of Fisheries Management 9:184–187. 8

McCabe, G.T. Jr., R.L. Emmett, W.D. Muir, and T.H. Blahm. 1986. Utilization of the Columbia 9 River estuary by subyearling Chinook salmon. Northwest Science 60:113–124. 10

McComas, R.L., G.A. McMichael, J.A. Vucelick, L. Gilbreath, J.P. Everett, S.G. Smith, T. 11 Carlson, G. Matthews, and J.W. Ferguson. 2008. A Study to Estimate Salmonid Survival 12 through the Columbia River Estuary using Acoustic Tags, 2006. Available at: 13 http://www.nwfsc.noaa.gov/assets/26/6914_05082009_161212_Acoustic-Tag-2006-14 Accessible.pdf. Accessed October 8, 2009. 15

McDonald, J. 1960. The behavior of Pacific salmon fry during their downstream migration to 16 freshwater and saltwater nursery areas. Journal of the Fisheries Research Board of 17 Canada. 17:655-656. As cited in Tabor et al. 2004. 18

McElhany, P. 2005. Columbia River chum salmon ESU. in T.P. Good, R.S. Waples, and P. 19 Adams, eds. Updated status of federally listed ESUs of west coast salmon and steelhead. 20 NOAA, Seattle, Washington. 21

McElhany, P., M. Chilcote, J. Myers, and R. Beamesderfer. 2007. Viability status of Oregon 22 salmon and steelhead populations in the Willamette and Lower Columbia basins. 23 Prepared for Oregon Department of Fish and Wildlife and National Marine Fisheries 24 Service by the National Marine Fisheries Service, Northwest Fisheries Science Center, 25 Seattle, Washington. 26

McIntosh, B.A., J.R. Sedell, R.F. Thurow, S.E. Clarke, and G.L. Chandler. 2000. Historical 27 changes in pool habitats in the Columbia River basin. Ecological Applications 28 10(5):1478-1496. 29

McIntyre J.K., D.H. Baldwin, J.P. Meador, and N.L. Scholz. 2007. Chemosensory deprivation in 30 juvenile coho salmon exposed to dissolved copper under varying water chemistry 31 conditions. Environmental Science & Technology (in press). 32

McMahon, T.E., and S.H. Holanov. 1995. Foraging success of largemouth bass at different light 33 intensities: implications for time and depth of feeding. Journal of Fish Biology. 34 45, 759-767. 35

Metro. 1997. 2040 Growth Concept. Portland, Oregon. Available at: 36 http://www.oregonmetro.gov/index.cfm/go/by.web/id=29882. 37

Metro. 2003. South Corridor Project Water Quality and Hydrology Results Report. Prepared by 38 URS, Portland, Oregon. 39


10-18 June 2010

Myers, K.W., and H.F. Horton. 1982. Temporal use of an Oregon estuary by hatchery and wild 1 juvenile salmon. In V. S. Kennedy (ed.), Estuarine comparisons, p. 388–392. Academic 2 Press, New York. 3

Miles, P.R., C.I. Malme, G.W. Shepard, W.J. Richardson, and J.E. Bird. 1986. Prediction of 4 drilling site-specific interaction of industrial acoustic stimuli and endangered whales: 5 Beaufort Sea (1985),” BBN Report 6185, Outer Continental Shelf Study MMS 86-0046, 6 Minerals Management Service, Anchorage, AK. 7

Miles, P.R., C.I. Malme, and W.J. Richardson. 1987. Prediction of drilling site-specific 8 interaction of industrial acoustic stimuli and endangered whales in the Alaskan Beaufort 9 Sea,” BBN Report 6509, Outer Continental Shelf Study MMS 87-0084, Minerals 10 Management Service, Anchorage, AK. 11

Miller, G.W., V.D. Moulton, R.A. Davis, M. Holst, P. Millman, and A. MacGillivray. 2005. 12 Monitoring seismic effects on marine mammals – southeastern Beaufort Sea, 2001-2002. 13 In S.L. Armsworthy, P.J. Cranford, and K. Lee (Eds.), Offshore oil and gas 14 environmental effects monitoring: Approaches and technologies. Columbus, Ohio: 15 Battelle Press. pp. 511-542. 16

Minor, M. 2009. Personal communication with Michael Minor, Hydroacoustics Specialist, 17 Michael Minor and Associates, Inc. E-mail correspondence on December 6, 2009. 18

Modde, T., A.F. Wasowicz, and D.K. Hepworth. 1996. Cormorant and grebe predation on 19 rainbow trout stocked in a southern Utah reservoir. North American Journal of Fisheries 20 Management 16:388-394. 21

Moody, M.F. 2008. Eulachon Past and Present. Masters Thesis. University of British Columbia. 22 Vancouver, British Columbia, Canada. March 2008. 23

Mote, P., A. Petersen, S. Reeder, H. Shipman, and L.W. Binder. 2008. Sea Level Rise in the 24 Coastal Waters of Washington State. A report by the University of Washington Climate 25 Impacts Group and the Washington State Department of Ecology. 26

Moyle, P.B., P.J. Foley, and R.M. Yoshiyama. 1992. Status of green sturgeon, Acipenser 27 medirostris, in California. Final Report submitted to National Marine Fisheries Service. 28 11 p. University of California, Davis, CA. 29

Mulvihill, E.L., C.A. Francisco, J.B. Glad, K.B. Kaster, and R.E. Wilson. 1980. Biological 30 impacts of minor shoreline structures on the coastal environment: State of the art review, 31 Volume II, data printout. FWS/OBS-77/51. Prepared by Beak Consultants, Inc., Portland, 32 Oregon, with O. Beeman, for National Coastal Ecosystems Team, Office of Biological 33 Services, Fish and Wildlife Service, U.S. Department of the Interior. As cited in 34 Carrasquero 2001. 35

Myers, J.M., R.G. Kope, B.J. Lindley, and R.S. Waples. 1998. Status review of Chinook salmon 36 from Washington, Idaho, Oregon, and California. U.S. Dept. of Commerce, NOAA Tech. 37 Memo, NMFS-NWFSC-35, 443 pp. 38

NAS (National Academy of Sciences). 1973. Water Quality Criteria, 1972. National Academy of 39 Sciences, Washington, D.C. 40


June 2010 10-19

NatureServe Explorer. 2009. Online Encyclopedia. Available at: http://www.natureserve.org1 /explorer/servlet/NatureServe?init=Species. Accessed October 8, 2009. 2

Newman, M.C. and R.H. Jagoe. 1994. Ligands and the bioavailability of metals in aquatic 3 environments. In: Hamelink JL et al. (eds) Bioavailability: Physical, Chemical, and 4 Biological Interactions. CRC Press, Boca Raton, FL 5

Nightingale, B. and C.A. Simenstad. 2001. White Paper: Overwater Structures: Marine Issues. 6 Prepared by Washington State Transportation Center (TRAC). Prepared for Washington 7 State Transportation Commission. June 2001. 8

NMFS (National Marine Fisheries Service). 1992. Recovery Plan for the Steller Sea Lion 9 (Eumetopias jubatus). Prepared by the Steller Sea Lion Recovery Team for the National 10 Marine Fisheries Service, Silver Spring, MD. 92 pp. 11

NMFS. 1996. Making Endangered Species Act Determinations of Effect for Individual or 12 Grouped Actions at the Watershed Scale. National Oceanic and Atmospheric 13 Administration, National Marine Fisheries Service. 14

NMFS. 2000a. Guidelines for Electrofishing Waters Containing Salmonids Listed Under the 15 Endangered Species Act. Available at: http://www.nwr.noaa.gov/ESA-Salmon-16 Regulations-Permits/4d-rules/upload/electro2000.pdf. Accessed November 9, 2009. 17

NMFS. 2000b. White Paper: Predation on salmonids relative to the Federal Columbia River 18 Power System. Northwest Fisheries Science Center. National Marine Fisheries Service, 19 Seattle, Washington. 20

NMFS. 2002. Endangered Species Act Section 7 Consultation and Magnuson-Stevens Act 21 Essential Fish Habitat Consultation: Biological Opinion for the Columbia River Federal 22 Navigation Channel Improvements Project. 23

NMFS. 2003. Regulations governing the taking and importing of marine mammals; Eastern 24 North Pacific Southern Resident killer whales. Federal Register 68:103 (29 May 25 2003):31980-31983. 26

NMFS. 2004. Endangered Species Act – Section 7 Consultation Biological Opinion and 27 Conference Opinion and Magnuson-Stevens Act Essential Fish Habitat Consultation. 28 Reinitiation of Columbia River Federal Navigation Channel Improvements Project. U.S. 29 Army Corps of Engineers – Portland District. February 16, 2005. Reference Number: 30 2004/01612. 31

NMFS. 2005a. Final Assessment of NOAA Fisheries Critical Habitat Analytical Review Teams 32 for 12 Evolutionarily Significant Units of West Coast Salmon and Steelhead. NOAA 33 Fisheries Protected Resources Division, Portland, Oregon. Available at: 34 http://nwr.nmfs.noaa.gov/Salmon-Habitat/Critical-Habitat/2005-Biological-Teams-35 Report.cfm. Accessed October 8, 2009. 36

NMFS. 2005b. Endangered Species Act Section 7 Consultation. Kensington Gold Project 37 Operations. NMFS Protected Resources Division, Alaska Region. March 18, 2005. 38


10-20 June 2010

NMFS. 2005c. Endangered Species Act - Section 7 Consultation Biological Opinion and 1 Conference Opinion and Magnuson-Stevens Act Essential Fish Habitat Consultation 2 Reinitiation of Columbia River Federal Navigation Channel Improvements Project. 3 National Marine Fisheries Service, Northwest Region. Reference Number 2004/01612. 4 February 16, 2005. 5

NMFS. 2006a. Salmon and steelhead recovery planning in the Snake River basin, Chapter 8. 6 Available at: http://www.idahosalmonrecovery.net/recoverplans/srfallchinook.html. 7 Accessed October 10, 2009. 8

NMFS. 2006b. Salmon and steelhead recovery planning in the Snake River basin. Chapter 9. 9 Available at: http://www.idahosalmonrecovery.net/recoverplans/srsockeye.html. 10 Accessed October 10, 2009. 11

NMFS. 2006c. Salmon and steelhead recovery planning in the Snake River basin. Chapter 7. 12 Available at: http://www.idahosalmonrecovery.net/recoverplans/srsteelhead.html. 13 Accessed October 12, 2009. 14

NMFS. 2007. California, Seal and Sea Lion Viewing Guidelines. Available at: 15 http://swr.nmfs.noaa.gov/psd/rookeryhaulouts/casealviewbrochure.pdf. Accessed 16 February 2009. 17

NMFS. 2007. Draft Revised Recovery Plan for the Steller sea lion (Eumetopias jubatus). 18 National Marine Fisheries Service, Silver Spring, MD. 285 pp. 19

NMFS. 2008a. Upper Columbia River Steelhead DPS Information Page. Available at: 20 http://www.nwr.noaa.gov/ESA-Salmon-Listings/Salmon-Populations21 /Steelhead/STUCR.cfm. Accessed March 10, 2009. 22

NMFS. 2008b. Recovery plan for Southern Resident killer whales (Orcinus orca). NMFS, 23 Northwest Region, Seattle, Washington. 24

NMFS. 2008c. Proposed Designation of Critical Habitat for the Southern Distinct Population 25 Segment of North American Green Sturgeon: Draft Biological Report. Available at: 26 http://swr.nmfs.noaa.gov/gs/Final_Draft_GS_BioRpt.pdf. Accessed April 2, 2009. 27

NMFS. 2008d. Biological Opinion and Magnuson-Stevens Fishery Conservation and 28 Management Act Essential Fish Habitat Consultation on Treaty Indian and Non-Indian 29 Fisheries in the Columbia River Basin Subject to the 2008-2017 US v. Oregon 30 Management Agreement. NMFS Northwest Region, Portland, Oregon. 31

NMFS. 2008e. Supplemental Comprehensive Analysis of the Federal Columbia River Power 32 System and Mainstem Effects of the Upper Snake and other Tributary Actions. Available 33 at: http://www.nwr.noaa.gov/Salmon-Hydropower/Columbia-Snake-Basin/upload/Final-34 SCA.pdf. Accessed May 11, 2009. 35

NMFS. 2008f. NMFS Guidance on ESA-Listed Marine Mammal Consultations. Memorandum 36 for Northwest Region Assistant Regional Administrators. Available at: 37 http://www.wsdot.wa.gov/NR/rdonlyres/CB776678-A5A7-4929-94DB-38 2EC74BF63B11/0/BA_ESAMarineMammConsul.pdf. Accessed October 8, 2009. 39

NMFS. 2008g. Anadromous Salmonid Passage Facility Design. NMFS, Northwest Region, 40 Portland, Oregon. 41


June 2010 10-21

NMFS. 2008h. Recovery Plan for the Steller Sea Lion Eastern and Western Distinct Population 1 Segments (Eumetopias jubatus) Revision. Available at: http://www.nmfs.noaa.gov/2 pr/pdfs/recovery/stellersealion.pdf. Accessed October 8, 2009. 3

NMFS. 2008i. NOAA Review of Re-circulated Draft Environmental Impact Statement/ 4 Environmental Impact Report (REDIS/EIR) for Berth 97-109 China Shipping Container 5 Terminal Project. EFH and MMPA Recommendations. July 11, 2008. 6

NMFS. 2008j. Revisions to Standard Local Operating Procedures for Endangered Species to 7 Administer Maintenance or Improvement of Road, Culvert, Bridge and Utility Line 8 Actions Authorized or Carried Out by the USACE in the Oregon (SLOPES IV Roads, 9 Culverts, Bridges and Utility Lines). NMFS, Northwest Region. August 13, 2008. 10

NMFS. 2008k. Summary of scientific conclusions of the review of the status of eulachon 11 (Thaleichthys pacificus) in Washington, Oregon, and California. Biological Review 12 Team, Northwest Fisheries Science Center, Seattle, WA. 229 electronic pages. 13

NMFS. 2009. Guidance Document: Data Collection Methods to Characterize Background and 14 Ambient Sound within Inland Waters of Washington State. NMFS Northwest Fisheries 15 Science Center - Conservation Biology Division and Northwest Regional Office - 16 Protected Resources Division. November 30, 2009. 17

NMFS. 2009. Species List: Endangered Species Act Status of West Coast Salmon and Steelhead. 18 Updated July 1, 2009. 19

NMFS. 2009a. Middle Columbia River Steelhead Distinct Population Segment ESA Recovery 20 Plan. National Marine Fisheries Service Northwest Region. Available at: 21 http://www.nwr.noaa.gov/Salmon-Recovery-Planning/Recovery-Domains/Interior-22 Columbia/Mid-Columbia/Mid-Col-Plan.cfm. Accessed October 9, 2009. 23

NMFS. 2009b. Endangered Species Act – Section 7 Consultation Biological and Conference 24 Opinion & Magnuson-Stevens Fishery Conservation and Management Act Essential Fish 25 Habitat Consultation ConocoPhillips Company’s Piling Replacement Project. Willamette 26 River, Portland, Oregon. 27

NOAA (National Oceanic and Atmospheric Administration) Fisheries. 2003. Biological Opinion 28 and Essential Fish Habitat Consultation for Invasive Species Management at the Gresham 29 Woods Conservation and Restoration Project, Johnson Creek, Multnomah County, 30 Oregon. June 2003. 31

NOAA (National Oceanic and Atmospheric Administration). 2008. Listing endangered and 32 threatened species: Notification of finding on a petition to list Pacific eulachon as an 33 endangered or threatened species under the Endangered Species Act. 73 FR 34 13185-13189. 35

NOAA. 2009. Satellite and information service. National Climatic Data Center. Available at: 36 http://www.ncdc.noaa.gov/oa/climate/stationlocator.html. Accessed December 23, 2009. 37

Noggle, C.C. 1978. Behavioral, physiological and lethal effects of suspended sediment on 38 juvenile salmonids. Master’s thesis. University of Washington, Seattle, Washington. 39


10-22 June 2010

North, J.A., L.C. Burner, B.S. Cunningham,. and five others. 2002. Relationships between bank 1 treatment / nearshore development and anadromous / resident fish in the lower 2 Willamette River. Annual Progress Report, May 2000–June 2001. City of Portland-3 Bureau of Environmental Services, Endangered Species Act Program. Portland, Oregon. 4 130 electronic pages. 5

North, J. 2009. Personal communication. E-mail of December 10, 2009 from John North, 6 Columbia River Fisheries Manager, ODFW, to M. Parton, Parametrix. 7

Northwest Power and Conservation Council. 2004. “Mainstem Lower Columbia River and 8 Columbia River Estuary Subbasin Plan.” In Columbia River Basin Fish and Wildlife 9 Program. Portland, Oregon. 10

NWFSC (Northwest Fisheries Science Center) Environmental Conservation Division. 2001, in 11 draft. Potential impacts of toxic contaminants in salmonids and prey from the Columbia 12 River estuary. 26 pp. 13

ODFW (Oregon Department of Fish and Wildlife) and WDFW. 2001. Washington and Oregon 14 eulachon management plan. Available at: http://wdfw.wa.gov/fish/creel/smelt/wa-15 ore_eulachonmgmt.pdf. Accessed November 2008. 16

ODFW. 2005. Oregon wolf conservation and management plan. Available at: 17 http://www.dfw.state.or.us/Wolves/docs/wolf_plan.pdf. 18

ODFW. 2007a. Annual Progress Report: Spring Chinook salmon in the Willamette and Sandy 19 Rivers. F-163-R-11/12. Salem, Oregon. 20

ODFW. 2007b. Upper Willamette Draft Conservation and Recovery Plan. Chapter 4: Current 21 Status: Viability Assessments. Available at: http://www.dfw.state.or.us/fish/CRP22 /upper_willamette_river_plan.asp. Accessed October 8, 2009. 23

ODFW. 2008a. Fish Division: Management of sea lion predation on threatened and endangered 24 salmonids. Available at: http://www.dfw.state.or.us/fish/SeaLion/faqs.asp. Accessed 25 October 8, 2009. 26

ODFW. 2008b. Field Report: 2008 Pinniped Management Activities at Bonneville Dam. 27

ODFW. 2009. Wolves in Oregon. Available at: http://www.dfw.state.or.us/Wolves/index.asp. 28

ODFW. 2009. Lower Columbia River conservation and recovery plan for Oregon populations of 29 salmon and steelhead (Draft). Available at: http://www.dfw.state.or.us/fish/CR30 /lower_columbia_plan.asp. 31

ODFW. 2010a. Marine Mammal Research Program: Species Information. Available at: 32 http://www.dfw.state.or.us/MRP/mammals/species.asp. Accessed February 18, 2010. 33

ODFW. 2010b. Daily count data were available as records published by ODFW. Available at: 34 http://www.dfw.state.or.us/fish/fish_counts/willamette/Willamette%20Web/09_counts_w35 illamette%20falls.asp. 36

ODFW and WDFW (Washington Department of Fish and Wildlife). 2008a. Joint staff report: 37 stock status and fisheries for spring Chinook, summer Chinook, sockeye, steelhead, and 38 other species, and miscellaneous regulations. Available at: http://www.dfw.state.or.us39 /fish/OSCRP/CRM/reports/08_reports/08_fjsr.pdf. Accessed March 10, 2009. 40


June 2010 10-23

ODFW and WDFW. 2008b. Joint Staff Report: Stock Status and Fisheries for Sturgeon and 1 Smelt. 2

ODOT (Oregon Department of Transportation). 2006. Roadside Development Design Manual. 3 Guidelines for Visual Resource Management, Landscaping, and Hardscaping. Available 4 at: ftp://ftp.odot.state.or.us/techserv/Geo-Environmental/Environmental/Procedural5 %20Manuals/Roadside%20Development/Roadside%20Development%20Design%20Ma6 nual.pdf. Accessed November 9, 2009. 7

ODOT. 2008. Stormwater Treatment Program - BMP Selection Tool. Available at: 8 ftp://ftp.odot.state.or.us/techserv/Geo-Environmental/Stormwater%20Team/BMP_9 Selection_Tool/BMP_Selection_Tool/ODOT_BMP_Selection_Tool_Memo_Final.pdf. 10 Accessed October 22, 2008. 11

ODOT. 2009. Stormwater Management Program: Stormwater quality and flow control guidance 12 on ODOT projects. Technical Bulletin GE-09-02(B). Available at: 13 http://www.oregon.gov/ODOT/HWY/TECHSERV/technicalguidance.sht. Accessed 14 January 9, 2009. 15

Olesiuk, P.F., M.A. Bigg, and G.M. Ellis. 1990. Life history and population dynamics of resident 16 killer whales (Orcinus orca) in the coastal waters of British Columbia and Washington 17 State. Report of the International Whaling Community (special issue). 18

Omernik, J.M. 1987. Ecoregions of the Coterminous United States: Map Supplement. 19 Association of American Geographers, 77(1):118-125. 20

OSPAR. 2009. Assessment of the environmental impact of underwater noise. Convention for the 21 Protection of the Marine Environment of the North-East Atlantic. OSPAR Commission, 22 2009. Publication Number 436/2009. 23

OSU (Oregon State University). 2006. Is It All Hot Air? Climate Change, Global Warming and 24 the Pacific Northwest Institute for Natural Resources Climate Change Workshop. 25

Pacific EcoRisk. 2007. White paper: Potential Effects of Highway Runoff on Priority Fish 26 Species in Western Washington. Prepared for Washington State Department of 27 Transportation. December 2007. Available at: http://www.wsdot.wa.gov/Environment28 /Biology/BA/BAguidance.htm#Stormwater. 29

Packman, J.J., K.J. Comings, and D.B. Booth. Using Turbidity to Determine Total Suspended 30 Solids in Urbanizing Streams in the Puget Lowlands. University of Washington, Seattle, 31 Washington. 32

Palermo, M.R., J.H. Homziak, and A.M. Teeter. 1990. Evaluation of clamshell dredging and 33 barge overflow, Military Ocean Terminal, Sunny Point, North Carolina. U.S. Army 34 Corps of Engineers Waterways Experiment Station, Vicksburg Mississippi. March 1990. 35

Paragamian, V.L. 1989. Seasonal habitat use by walleye in a warm water river system, as 36 determined by radio telemetry. North American Journal of Fisheries Management 9: 37 392-401. 38

Parcel Insight. 2009. Columbia River Crossing, Oregon and Washington Corridor Report. 39 200.40. March 3, 2009. 40


10-24 June 2010

PBS (PBS Engineering and Environmental). 2003. Biological Evaluation: Burnt Bridge Creek 1 Regional Wetland Bank and Greenway Trails Project. PBS Engineering and 2 Environmental, Vancouver, Washington. 3

Pearson, W., N. Kohn, and G. Williams. 2005. Approach to Estimation of Entrainment of Coho 4 Salmon by Dredges in Washington and Oregon. PNNL-15287, Pacific Northwest 5 National Laboratory, Richland, Washington. PFMC (Pacific Fishery Management 6 Council). 1999. Amendment 14 to the Pacific Coast Salmon Plan. Appendix A: 7 Description and Identification of Essential Fish Habitat, Adverse Impacts and 8 Recommended Conservation Measures for Salmon. 9

Pentec (Pentec Environmental). 1997. Movement of Juvenile Salmon through an Industrialized 10 Everett Harbor. Report to the Port of Everett, Everett, Washington. 11

Petersen, J.H. and T.P. Poe. 1993. System wide significance of predation on juvenile salmonids 12 in Columbia and Snake River reservoirs. Annual Report 1992. Bonneville Power 13 Administration, Division of Fish and Wildlife, Portland, Oregon. December 1993. 14

Petersen, James H, Sally T. Sauter, Conrad N. Frost, Steven R. Gray, and Thomas P. Poe. 1993. 15 Indexing juvenile salmonid consumption by northern squawfish in the Columbia River 16 below Bonneville Dam and in John Day Reservoir, 1992. In: System-wide Significance 17 of Predation on Juvenile Salmonids in Columbia and Snake River Reservoirs: Annual 18 Report 1992. Edited by James H. Petersen and Thomas P. Poe. Prepared by U.S. Fish and 19 Wildlife Service, National Fishery Research Center, Columbia River Field Station, Cook, 20 Washington, for U.S. Department of Energy, Bonneville Power Administration. 21

Pflug, D.E. and G.B. Pauley. 1984. Biology of smallmouth bass (Micropterus dolomieui) in Lake 22 Sammamish, Washington. Northwest Science 58:118-130. 23

PFMC (Pacific Fishery Management Council). 1999. Amendment 14 to the Pacific Coast 24 Salmon Plan. Appendix A: Description and Identification of Essential Fish Habitat, 25 Adverse Impacts, and Recommended Conservation Measures for Salmon. Pacific 26 Fisheries Management Council. 27

Phillips, R.W., R.L. Lantz, E.W. Claire, and J.R. Moring. 1975. Some effects of gravel mixtures 28 on emergence of coho salmon and steelhead trout fry. Transactions of the American 29 Fisheries Society 104(3):461-466. 30

Poe, T.P., R.S. Shively, and R.A. Tabor. 1994. Ecological consequences of introduced 31 piscivorous fishes in the lower Columbia and Snake Rivers. Pages 347-360, in D. J. 32 Stouder, K. Fresh, and R. J. Feller (eds.), Theory and Application in Fish Feeding 33 Ecology. Bell W. Baruch Library and Marine Sciences, No. 18, University of South 34 Carolina Press, Columbia, South Carolina. 35

Poole, G.C. and C.H. Berman. 2001. An ecological perspective on in-stream temperature: natural 36 heat dynamics and mechanisms of human-caused thermal degradation. Environmental 37 Management 27(6): 787-802. 38

Popper, A.N., T.J. Carlson, A.D. Hawkins, B.L. Southall, and R.L. Gentry. 2006. Interim criteria 39 for injury of fish exposed to pile driving operations: a white paper. 40


June 2010 10-25

Pribyl, A.L., J.S. Vile, and T.A. Friesen. 2004. Population structure, movement, habitat use, and 1 diet of resident piscivorous fishes in the lower Willamette River. ODFW Columbia River 2 Investigations, Clackamas, Oregon. 3

Prinslow, T.E., E.O. Salo, and B.P. Snyder. 1979. Studies of behavioral effects on a lighted and 4 an unlighted wharf on outmigration salmonids: March-April 1978. Fisheries Research 5 Institute, University of Washington, Seattle, Washington. 6

Probst, W.E., C.F. Rabeni, W.G. Covington, and R.E. Marteney. 1984. Resource use by stream-7 dwelling rock bass and smallmouth bass. Transactions of the American Fisheries Society 8 113:283-294. 9

PSMFC (Pacific States Marine Fisheries Commission). 2003. Presence/Absence Study for 10 Salmonids in Burnt Bridge Creek. Funded by the City of Vancouver. Vancouver, 11 Washington. 12

PTAGIS. 2010. PIT Tag Information System. Available at: http://www.ptagis.org/ptagis. 13 Accessed January 8, 2010. 14

Quinn, T.P. 2005. The Behavior and Ecology of Pacific Salmon and Trout. University of 15 Washington Press, Seattle. 16

Ratte, L.D. and E.O. Salo. 1985. Under-pier ecology of juvenile Pacific salmon in 17 Commencement Bay, Washington. Final report to the City of Tacoma. FRI-UW-8508. 18 University of Washington, Fisheries Research Institute, Seattle, Washington. 19

Rawding, D. and T. Hillson. 2003. Population Estimates for Chum Salmon Spawning in the 20 Mainstem Columbia River. Project No. 2001-05300, BPA Report DOE/BP-00007373-3. 21 47 electronic pages. 22

Redding, J.M., C.B. Schreck, and F.H. Everest. 1987. Physiological effects on coho salmon and 23 steelhead of exposure to suspended solids. Transactions of the American Fisheries 24 Society 116: 737-744. 25

Reijnders, P.J.H. and A. Aguilar. 2002. Pollution and marine mammals. Pages 948-957 in W.F. 26 Perrin, B. Wursig, and J.G.M. Thewissen, editors. Encyclopedia of marine mammals. 27 Academic press, San Diego, California. 28

Richardson, W.J., C.R. Greene, Jr., C.I. Malme, and D.H. Thomson. 1995. Marine Mammals and 29 Noise. Academic Press, San Diego. 576 pp. 30

Riddell, D.J., J.M.Culp, and D.J. Baird. 2005. Sublethal effects of cadmium on prey choice and 31 capture efficiency in juvenile brook trout (Salvelinus fontinalis). Environmental 32 Toxicology and Chemistry 24(7):1751-1758. 33

Rieman, B.E. and J.D. McIntyre. 1993. Demographic and Habitat Requirements for 34 Conservation of Bull Trout. Gen. Tech. Rep. INT-302. Ogden, UT: U.S. Department of 35 Agriculture, Forest Service, Intermountain Research Station, Boise, ID. 38pp. Available 36 at: http://www.fs.fed.us/rm/pubs_int/int_gtr302.pdf. Accessed February 8, 2010. 37

Rieman, B.E. and J.D. McIntyre. 1995. Occurrence of bull trout in naturally fragmented habitat 38 patches of varied size. Transactions of the American Fisheries Society 124(3):285-296. 39 Available at: http://www.fs.fed.us/rm/boise/publications/fisheries/40 rmrs_1995_riemanb001.pdf. Accessed February 8, 2010. 41


10-26 June 2010

Riley Research Associates. 2008. Riley Report/Portland-Vancouver Area Survey. June 18, 2008. 1

Roberts M.G., C.L. Ruch, H. Li, B.J. Teppen, and S.A. Boyd. 2007. Reducing bioavailability and 2 phytotoxicity of 2,4-dinitrotoluene by sorption on k-smectite clay. Environmental 3 Toxicology and Chemistry 26(2):358-360. 4

Roby, D.D., D.E. Lyons, D.P. Craig, K. Collis, and G.H. Visser. 2003. Quantifying the effects of 5 predators on endangered species using a bioenergetics approach: Caspian terns and 6 juvenile salmonids in the Columbia River estuary. Canadian Journal of Zoology 7 81:250-265. 8

Rogers, I.H., I.K. Birtwell, and G.M. Kruzynski. 1990. The pacific eulachon (Thaleichthys 9 pacificus) as a pollution indicator organism in the Fraser River estuary, Vancouver, 10 British Columbia. Science of the Total Environment 97/98: 713-727. 11

Romano, M.D., M.D. Howell, and T.A. Rien. 2002. Use of an Artificial Substrate to Capture 12 Eulachon (Thaleichthys pacificus) Eggs in the Lower Columbia River. Oregon 13 Department of Fish and Wildlife, Clackamas, OR, and Washington Department of Fish 14 and Wildlife, Vancouver, WA. Draft Report. Available at: http://www.dfw.state.or.us/15 fish/OSCRP/CRI/criwebpage/pdf%20Reports/USACE_smelt_substrate_rep.PDF. 16 Accessed November 18, 2009. 17

Roni, P. and L.A. Weitkamp. 1996. Environmental monitoring of the Manchester Naval Fuel 18 Pier replacement, Puget Sound, Washington, 1991-1994. Report to the U.S. Department 19 of Navy, Naval Facilities Engineering Command, Western Division, Contract N62474-20 91-MP-00758, 40 pp. plus appendices. 21

Ross, P.S., G.M. Ellis, M.G. Ikonomou, L.G. Barrett-Lennard, and R.F. Addison. 2000. High 22 PCB concentrations in free-ranging Pacific killer whales, Orcinus orca: effects of age, 23 sex, and dietary preference. Marine Pollution Bulletin 40(6):504-515. 24

Ruggerone, G.T. 1986. Consumption of migrating juvenile salmonids by gulls foraging below a 25 Columbia River dam. Transactions of the American Fisheries Society 115:736-742. 26

Salo, E.O. 1991. Life history of chum salmon (Oncorhynchus keta). In Pacific Salmon Life 27 Histories, C. Groot and L. Margolis (eds), pp. 231–310. University of British Columbia 28 Press, Vancouver, Canada. 29

Salo, E.O., T.E. Prinslow, R.A Campbell, D.W. Smith, and B.P. Snyder. 1979. Trident Dredging 30 Study: the effects of dredging at the U.S. Naval submarine base at Bangor on 31 outmigrating juvenile chum salmon, Oncorhynchus keta, in Hood Canal, Washington. 32 FRI-UW-7918. University of Washington College of Fisheries, Fisheries Research 33 Institute, September 1979. 34

Salo, E.O., N.J. Bax, T.E. Prinslow, C.J. Whitmus, B.P. Snyder, and C.A. Simenstad. 1980. The 35 Effects of Construction of Naval Facilities on the Out-migration of Juvenile Salmonids 36 from Hood Canal, Washington. Final Report to the U.S. Navy. University of Washington 37 Fisheries Research Institute (FRI-UW-8006), Seattle, Washington. 38

Sandahl, J.F., D.H. Baldwin, J.J. Jenkins, and N.L. Scholz. 2007. A sensory system at the 39 interface between urban stormwater runoff and salmon survival. Environmental Science 40 & Technology 41(8):2998-3004. 41


June 2010 10-27

Sandercock, F.K. 1991. The history of coho salmon (Oncorhynchus kisutch). In Pacific Salmon 1 Life History, edited by C. Groot and L. Margolis. Vancouver: UBC Press. 2

Schreck, C.B., H.W. Li, C.S. Sharpe, K.P. Currens, P.L. Hulett, S.L. Stone, and S.B. Yamada. 3 1986. Stock identification of Columbia River Chinook salmon and steelhead trout. Report 4 to U.S. Dep. Energy, Contract DE-A179-83BP13499, Project 83-451, 184 pp. 5

Servizi, J.A. and D.W. Martens. 1987. Some effects of suspended Fraser River sediments on 6 sockeye salmon (Oncorhynchus nerka). p. 254-264. In H.D. Smith, L. Margolis, and C.C. 7 Wood [ed.] Sockeye salmon (Oncorhynchus nerka) population biology and future 8 management. Can. Spec. Publ. Fish. Aquat. Sci. 96. 9

Servizi, J.A. and D.W. Martens. 1992. Sublethal responses of coho salmon (Oncorhynchus 10 kisutch) to suspended sediments. Canadian Journal of Fishery Aquatic Science, Vol. 49: 11 1389-1395. 12

Sheng G., C.T. Johnston, B.J. Teppen, and S.A. Boyd. 2002. Adsorption of dinitrphenol 13 herbicides from water by montmorillonites. Clays and Clay Minerals 50:25-34. 14

Shreffler, D.K., and R.A. Moursund. 1999. Impacts of ferry terminals on juvenile salmon 15 migrating along Puget Sound shorelines. Phase II: Field studies at Port Townsend ferry 16 terminal. WA-RD 480.1, GCA-1723. Prepared for Washington State Transportation 17 Center (TRAC), Seattle, Washington. 18

Sigler, J.W., T.C. Bjornn, and F.H. Everest. 1984. Effects of chronic turbidity on density and 19 growth of steelheads and coho salmon. Transactions of the American Fisheries Society 20 113: 142-150. 21

Simenstad, C.A., K.L. Fresh, and E.O. Salo. 1982. The role of Puget Sound and Washington 22 coastal estuaries in the life history of Pacific salmon: an unappreciated function. 23 p. 343-363. In V.S. Kennedy (ed.). Estuarine comparisons. New York: Academic Press. 24

Simenstad, C.A., C.D. Tanner, R.M. Thom, and L.L. Conquest. 1999. Estuarine Habitat 25 Assessment Protocol. U.S. Environmental Protection Agency, Region 10, Seattle, 26 Washington. 27

Simenstad, Charles A. and Barbara Nightingale. 1999. Impacts of Ferry Terminals on Juvenile 28 Salmon Migrating along Puget Sound Shorelines Phase I: Synthesis of State of 29 Knowledge. Prepared by Washington State Transportation Center (TRAC). Prepared for 30 Washington State Transportation Commission. June 1999. 31

Smith, W.E., and R.W. Saalfeld. 1955. Studies on Columbia River smelt Thaleichthys pacificus 32 (Richardson). Fisheries Research Papers 1(3): 2-23, Washington Department of Fisheries, 33 Olympia, Washington. 34

Southall, B.L., A.E. Bowles, W.T. Ellison, J.J. Finneran, R.L. Gentry, C.R. Greene Jr., D. 35 Kastak, D.R. Ketten, J.H. Miller, P.E. Nachtigall, W.J. Richardson, J.A. Thomas, and 36 P.L. Tyack. 2007. Marine Mammal Noise Exposure Criteria: Initial Scientific 37 Recommendations. Aquatic Mammals 33(4): 411-509. 38


10-28 June 2010

Southard, S.L., R.M. Thom, G.D. Williams, J.D. Toft, C.W. May, G.A. McMichael, J.A. 1 Vucelick, J.T. Newell, J.A. Southard. 2006. Impacts of Ferry Terminals on Juvenile 2 Salmon Movement along Puget Sound Shorelines. Prepared by Batelle Memorial 3 Institute. Prepared for the Washington Department of Transportation. June 2006. 4

Spence, B.C., G.A. Lomnicky, R.M. Hughes, and R.P. Novitzki. 1996. An ecosystem approach 5 to salmonids conservation. 21TR-4501-96-6057. ManTech Environmental Research 6 Services Corp., Corvallis, Oregon (available from NMFS, Portland, Oregon). 7

Sprague, J.B. 1964. Avoidance of copper-zinc solutions by young salmon in the laboratory. J. 8 Water Pollut. Control Fed. Vol. 36:990-1004. 9

Sprague, J.B. 1968. Avoidance reactions of rainbow trout to zinc sulphate solutions. Water 10 Research Pergamon Press. Vol. 2 pp. 367-372. 11

Spromberg, J. A., J. P. Meador. 2006. Relating chronic toxicity responses to population-level 12 effects: A comparison of population-level parameters for three salmon species as a 13 function of low-level toxicity. Ecological Modeling 199(2006):240-252. 14

Stansell, R. 2010. Personal communication. Telephone conversation between Robert Stansell, 15 Fisheries Biologist, U.S. Army Corps of Engineers, and Craig Hansen, Parametrix 16 Biologist, on February 8, 2010. 17

Stansell, R., S. Tackley, W. Nagy, and K. Gibbons. 2009. Evaluation of Pinniped Predation on 18 Adult Salmonids and Other Fish in the Bonneville Dam Tailrace. 2009 Field Report. U.S. 19 Army Corps of Engineers Fisheries Field Unit, Cascade Locks, Oregon. Available at: 20 http://www.nwd-wc.usace.army.mil/tmt/documents/fish/2009/2009_Pinniped_21 Report.pdf. Accessed November 6, 2009. 22

Stober, Q.J., B.D. Ross, C.L. Melby, P.A. Dinnel, T.H. Jagielo, E.O. Salo. 1981. Effects of 23 suspended volcanic sediment on coho and Chinook salmon in the Toutle and Cowlitz 24 Rivers. University of Washington, Fisheries Research Institute, Technical Completion 25 Report FRI-UW-8124. 26

Streamnet. 2009. Streamnet: Fish data for the Northwest. Interactive mapper. Available at: 27 http://www.streamnet.org/. Accessed July 2009. 28

Tabor, R.A., G. Brown, and V. Luiting. 1998. The effect of light intensity on predation of 29 sockeye salmon fry by prickly sculpin and torrent sculpin. U.S. Fish and Wildlife 30 Service, Western Washington Office, Lacey, Washington. May 1998. 31

Tabor, R.A. and R.M. Piaskowski. 2001. Nearshore habitat use by juvenile Chinook salmon in 32 lentic systems of the Lake Washington basin, Annual Report, U.S. Fish and Wildlife 33 Service, Western Washington Office, Lacey, Washington. 34

Tabor, R.A., G.S. Brown, and V.T. Luiting. 2004. The effect of light intensity on sockeye 35 salmon fry migratory behavior and predation by cottids in the Cedar River, Washington. 36 North American Journal of Fisheries Management. 24:128-145. 37

Tackley, S., R. Stansell, and K. Gibbons. 2008. Pinniped predation on adult salmonids and other 38 fish in the Bonneville Dam tailrace, 2005-2007. U.S. Army Corps of Engineers, 39 CENWP-OP-SRF, Bonneville Lock and Dam, Cascade Locks, Oregon. 40


June 2010 10-29

Taylor, W.S. and W.S. Willey. 1997. Port of Seattle fish migration study; Piers 64 & 65 short-1 stay moorage facility: Qualitative fish and avian predator observations. Prepared for Beak 2 Consultants, Seattle, Washington. 3

Teel, D.J., C. Baker, D.R. Kuligowski, T.A. Friesen, and B. Shields. 2009. Genetic stock 4 composition of subyearling Chinook salmon in seasonal floodplain wetlands of the lower 5 Willamette River, Oregon. Transactions of the American Fisheries Society 138(1): 6 211-217. 7

Tennis, M. J. 2009a. Field project leader, Columbia River Sea lions - Pacific States Marine 8 Fisheries Commission (PSMFC). Personal communication. E-mails May 14-15 2009. 9

Tennis, M. J. 2009b. Personal communication. E-mail communication with Matthew Tennis, 10 Field project leader, Columbia River sea lions, Pacific States Marine Fisheries 11 Commission. November 24, 2009. 12

Tetra Tech. 1995. Willamette River Basin Water Quality Study. Prepared for the Oregon 13 Department of Environmental Quality, Salem, Oregon. 14

Tetra Tech. 1996. Lower Columbia River Bi-State Program – The Health of the River, 1990-15 1996. Integrated Technical Report. Prepared for Oregon Department of Environmental 16 Quality and Washington Department of Ecology. 17

Thomas, D.W. 1983. Changes in the Columbia River estuary habitat types over the past century. 18 Columbia River Estuary Data Development Program, Columbia River Estuary Task 19 Force, Astoria, Oregon. 20

Thomsen, F., K. Ludemann, R. Kafemann, and W. Piper. 2006. Effects of offshore wind farm 21 noise on marine mammals and fish. Cowrie, Ltd., Hamburg, Germany. 22

Thomsen, F., S. McCully, D. Wood, F. Pace, and P. White. 2009. A generic investigation into 23 noise profiles of marine dredging in relation to the acoustic sensitivity of the marine 24 fauna in UK waters with particular emphasis on aggregate dredging: PHASE 1 Scoping 25 and review of key issues MEPF Ref No. MEPF/08/P21. Centre for Environment, 26 Fisheries & Aquaculture Science (CEFAS), Suffolk and Institute of Sound and Vibration 27 Research, University of Southampton. February 20, 2009. 28

Thompson, R.B. 1959. Food of the squawfish (Ptychocheilus oregonensis) of the lower 29 Columbia River. U.S. Fish and Wildlife Service, Fishery Bulletin 158:43-58. 30

Toft, J.D., J. Cordell, C. Simenstad, and L. Stamatiou. 2004. Fish distribution, abundance, and 31 behavior at nearshore habitats along City of Seattle marine shorelines, with an emphasis 32 on juvenile salmonids. Technical Report SAFS-UW-0401, School of Aquatic and Fishery 33 Sciences, University of Washington. Prepared for Seattle Public Utilities, City of Seattle, 34 Seattle, Washington. 35

Tomaro, L.M., W. van der Naald, R.R. Brooks, T.A. Jones, and T.A. Friesen. 2007. Evaluation 36 of Chum and Fall Chinook Salmon Spawning Below Bonneville Dam; Annual Report 37 October 2005 - September 2006. Oregon Department of Fish and Wildlife. Prepared for 38 Bonneville Power Administration. Project No. 1999-003-01. 39


10-30 June 2010

USACE (U.S. Army Corps of Engineers). 1989. Columbia River and Tributaries Review Study: 1 Project Data and Operating Limits, North Pacific Division, CRT 69. Available at: 2 http://www.nwd-wc.usace.army.mil/TMT/basin.html. Accessed October 8, 2008. 3

USACE (U.S. Army Corps of Engineers). 1999. Columbia River Channel Improvement Study, 4 Final Integrated Feasibility Report and Environmental Impact Statement. Portland, 5 Oregon. 6

USACE. 2001. Columbia River Channel Improvements Project Biological Assessment. Portland 7 District, Portland, Oregon. 8

USACE. 2008a. 2008 Field Report: Evaluation of Pinniped Predation on Adult Salmonids and 9 Other Fishes in the Bonneville Dam Tailrace. 10

USACE. 2008b. Dredge Material Evaluation and Disposal Procedures. Prepared by the Dredge 11 Material Management Office, U.S. Army Corps of Engineers. July 2008. 12

USACE. 2009 (Accessed). River Sediment Quality Evaluation for the Columbia River Channel 13 Deepening Feasibility Report. Available at: https://www.nwp.usace.army.mil/ec/docs14 /Planning/crcd/main.pdf. 15

USACE (U.S. Army Corps of Engineers), BPA (Bonneville Power Administration), and USBR 16 (U.S. Bureau of Reclamation). 2007. Comprehensive analysis of the Federal Columbia 17 River Power System and mainstem effects of Upper Snake and other tributary actions. 18 Portland, Oregon. Available at: http://www.salmonrecovery.gov/Biological_Opinions19 /FCRPS/BA-CA/CA/CA-Final.pdf. Accessed April 23, 2009. 20

USDA (U.S. Department of Agriculture). 1972. Soil Survey of Clark County, Washington. Soil 21 Conservation Service in cooperation with the Washington Agricultural Experiment 22 Station. November 1972. 23

USDA. 1983. Soil Survey of Multnomah County, Oregon. Soil Conservation Service in 24 cooperation with Oregon Agricultural Experiment. August 1983. 25

USFWS (U.S. Fish and Wildlife Service). 1998. Bull Trout Interim Conservation Guidance. 26 47 pp. 27

USFWS and NMFS. 1998. Endangered species consultation handbook: Procedures for 28 conducting consultation and conference activities under Section 7 of the Endangered 29 Species Act. U.S. Fish and Wildlife and National Marine Fisheries Service. March 1998. 30

USFWS. 2002. Bull Trout (Salvelinus confluentus) Draft Recovery Plan for the Klamath River 31 and Columbia River Distinct Population Segments of Bull Trout. Portland, Oregon. 32 Available at: http://www.fws.gov/pacific/bulltrout/Recovery.html. Accessed 33 March 11, 2009. 34

USFWS. 2010a. County species lists obtained for Hood River County. Available at: 35 http://www.fws.gov/oregonfwo/Species/Lists/Documents/County36 /HOOD%20RIVER%20COUNTY.pdf. Accessed March 1, 2010. 37

USFWS. 2010b. County species lists obtained for Clark County. Available at: 38 http://www.fws.gov/oregonfwo/Species/Lists/Documents/County39 /CLARK%20COUNTY.pdf. Accessed March 1, 2010. 40


June 2010 10-31

USGS (U.S. Geological Survey). 2007. Oregon Water Science Center Data Grapher. Available 1 at: http://or.water.usgs.gov/cgi-bin/grapher/graph_setup.pl?basin_id=tdg& 2 site_id=453439122223900. 3

USGS. 2009. Oregon Water Science Center Data Grapher. Available at: http://or.water.usgs.gov4 /cgi-bin/grapher/graph_setup.pl?basin_id=tdg&site_id=453439122223900. Accessed 5 October 8, 2009. 6

Utter, F., G. Milner, G. Stahl, and D. Teel. 1989. Genetic population structure of Chinook 7 salmon, Oncorhynchus tshawytscha, in the Pacific Northwest. Fisheries Bulletin., U.S. 8 87:239-264. 9

UW (University of Washington). 2009. Columbia Basin data in real time. Data managed by 10 Columbia Basin Research, School of Aquatic & Fishery Sciences, University of 11 Washington, Seattle, WA. Available at: http://www.cbr.washington.edu/dart/. Accessed 12 November 2009 and January 2010. 13

Varanasi, U., E. Casillas, M.R. Arkoosh, T. Hom, D.A. Misitano, D.W. Brown, S-L Chan, T. L. 14 Collier, B.B. McCain and J.E. Stein. 1993. Contaminant exposure and associated 15 biological effects in juvenile Chinook salmon (Oncorhynchus tshawytscha) from urban 16 and nonurban estuaries of Puget Sound. U.S. Dept. of Commerce, NOAA Tech. Memo., 17 NMFS-NWFSC-8, 112p. 18

Vigg, S. and M. Dennis (Eds.). 2009. Lower Columbia River (LCR) Fishery Management and 19 Evaluation Plan (FMEP) and Coho Supplement Annual Report, 2008: Five year 20 Comprehensive Update, 2002–2007. Report prepared by WDFW for NOAA Fisheries. 21 WDFW, Vancouver, WA. 71 electronic pages. 22

Vigg, S. 2009. Proposal 200754200: Shad for Nutrient Enhancement - Demonstration of Fishery 23 Supply, Disease Evaluation, Product Type and Potential Use. Submitted to Northwest 24 Power and Conservation Council. Available at: http://www.nwcouncil.org/fw25 /budget/innovate/proposal.asp?id=961. 26

Vogel, J.L. and D.A. Beauchamp. 1999. Effects of light, prey size, and turbidity on reaction 27 distances of lake trout (Salvelinus namaycush) to salmonid prey. Canadian Journal of 28 Fisheries and Aquatic Sciences 56: 1293-1297. 29

Wahl, D.H. 1995. Effect of habitat selection and behavior on vulnerability to predation of 30 introduced fish. Canadian Journal of Fisheries and Aquatic Science 52:2312-2319. 31

WDFW (Washington Department of Fish and Wildlife). 2007a. Burnt Bridge Creek Fish Passage 32 Inventory and Habitat Assessment. Presented by Susan Cierebiej, Fisheries Biologist. 22 33 October 2007. 34

WDFW. 2007b. Washington Lakes and Rivers Information Systems (WLRIS): Fish Distribution. 35 WDFW, Olympia, Washington. 36

WDFW. 2009a. Draft Wolf Conservation and Management Plan. Available at: 37 http://wdfw.wa.gov/wildlife/management/gray_wolf/mgmt_plan.html. 38

WDFW. 2009b. Gray Wolf Conservation and Management. Available at: http://wdfw.wa.gov39 /wildlife/management/gray_wolf/. 40


10-32 June 2010

WDFW. 2009c. SalmonScape, WDFW Interactive Mapper. Available at: http://198.238.33.671 /mapping/salmonscape/index.html. Accessed July 2009. 2

WDFW. 2009d. Hydraulic Project Approval (HPA). Available at: http://wdfw.wa.gov3 /hab/hpapage.htm. Accessed June 4, 2009. 4

WDFW. 2009e. Adult run timing and presence in the CRC area. Unpublished document. E-mail 5 from C. LeFleur, WDFW, to S. Morrow, CRC, on November 2, 2009. 6

WDFW and ODFW. 2001. Washington and Oregon eulachon management plan. Available at: 7 http://wdfw.wa.gov/fish/creel/smelt/wa-ore_eulachonmgmt.pdf. Accessed 8 November 2008. 9

WDFW and ODFW. 2009. Joint Staff Report: Stock Status and Fisheries for Spring Chinook, 10 Summer Chinook, Sockeye, Steelhead, and Other Species, and Miscellaneous 11 Regulations. Available at: http://wdfw.wa.gov/fish/crc/2009_spring_jsr.pdf. Accessed 12 June 25, 2009. 13

WDFW/HMCC (Washington Department of Fish and Wildlife/Mount Hood Community 14 College). 1999. Burnt Bridge Creek: A Model for Urban Stream Recovery in Clark 15 County. Compiled by the Washington Department of Fish and Wildlife and Mount Hood 16 Community College. 17

WDNR-NHP (Washington Department of Natural Resources, Natural Heritage Program). 2000 18 and 2007. Field Guide to Selected Rare Vascular Plants of Washington. Available at: 19 http://www1.dnr.wa.gov/nhp/refdesk/fguide/htm/fgmain.htm. Accessed April 21, 2009. 20

WDNR-NHP. 2008. Washington Plant Heritage database. Olympia, WA. 21

Wedermeyer, G.A. and D.J. McLeay. 1981. Methods for Determining the Tolerance of Fishes to 22 Environmental Stressors. Pp. 247-268. In: A.D. Pickering [ed.] Stress and fish. Academic 23 Press, Toronto, Ontario. 24

Weinheimer, J.M. 2007. E-mail correspondence with John Weinheimer, District 9 Fish Biologist, 25 Washington Department of Fish and Wildlife. September 7, 2007. 26

Weitkamp, D.E. 1982. Juvenile chum and Chinook salmon behavior at Terminal 91, Seattle, 27 Washington. Prepared for Port of Seattle by Parametrix, Seattle, Washington. 28

Wheeler, A.P. and M.S. Allen. 2003. Habitat and diet partitioning between shoal bass and 29 largemouth bass in the Chipola River, Florida. Transactions of the American Fisheries 30 Society 132:438-449. 31

White, Steven T. 1975. The influence of piers and bulkheads on the aquatic organisms in Lake 32 Washington. Master’s thesis. University of Washington, College of Fisheries, Seattle. As 33 cited in Carrasquero 2001. 34

Wicks, B. J., R. Joensen, Q. Tang, and D. J. Randall. 2002. Swimming and ammonia toxicity in 35 salmonids: the effect of sub lethal ammonia exposure on the swimming performance of 36 coho salmon and the acute toxicity of ammonia in swimming and resting rainbow trout. 37 Aquatic Toxicology 59:55–69. 38


June 2010 10-33

Williams, G.D., and R.M. Thom. 2001. Marine and estuarine shoreline modification issues. 1 Aquatic Habitat Guidelines: An integrated approach to marine, freshwater, and riparian 2 habitat protection and restoration. PNWD-3087. Prepared for Washington Department of 3 Fish and Wildlife, Washington Department of Ecology, and Washington Department of 4 Transportation by Battelle Marine Sciences Laboratory, Sequim, Washington. 5

Williams G.D., R.M. Thom, D.K. Shreffler, J.A. Southard, L.K. O’Rourke, S.L. Sargeant, V.I. 6 Cullinan, R.A. Moursund, and M. Stamey. 2003. Assessing Overwater Structure-Related 7 Predation Risk on Juvenile Salmon: Field Observations and Recommended Protocols. 8 PNNL-14435. Prepared for WSDOT by the Pacific Northwest National Laboratory’s 9 Marine Sciences Laboratory in collaboration with Shreffler Environmental and the 10 University of Washington. 11

Williams, R., A.W. Trites, and D.E. Bain. 2002a. Behavioural responses to killer whales 12 (Orcinus orca) to whale-watching boats: opportunistic observations and experimental 13 approaches. Journal of the Zoological Society of London 256:255-270. 14

Williams, R., D.E. Bain, J.K.B. Ford, and A.W. Trites. 2002b. Behavioral responses of male 15 killer whales to a “leapfrogging vessel.” Journal of Cetacean Research and Management 16 4(3):305-310. 17

Wilson, M.F., R.H. Armstrong, M.C. Hermanns, and K. Koski. 2006. Eulachon: A Review of 18 Biology and an Annotated Bibliography. Alaska Fisheries Science Center. National 19 Marine Fisheries Service. Juneau, Alaska. August 2006. 20

WLCTRT (Willamette/Lower Columbia Technical Recovery Team). 2003. Interim Report on 21 Viability Criteria for Willamette and Lower Columbia Basin Pacific Salmonids. 22 Appendix B: Summary of Core and Genetic Legacy Populations. Available at: 23 http://www.nwfsc.noaa.gov/trt/wlc/viability_criteria.cfm. Accessed October 8, 2009. 24

Wood, C.C. and C.M. Hand. 1985. Food-searching behavior of the common merganser (Mergus 25 merganser) I: functional response to prey and predator density. Canadian Journal of 26 Zoology 63:1260–1270. 27

WRI (Willamette Restoration Initiative). 2004. Draft Willamette Subbasin Plan Prepared for the 28 Northwest Power and Conservation Council. 29

WSDOT (Washington State Department of Transportation). 2005. NPDES Progress Report for 30 the Cedar-Green, Island-Snohomish, and South Puget Sound Water Quality Management 31 Areas. 32

WSDOT. 2006. Roadside Classification Plan. Washington Department of Transportation, 33 Olympia, WA. Available at: http://www.wsdot.wa.gov/Publications/Manuals/M25-34 31.htm. Accessed November 9, 2009. 35

WSDOT. 2008. Biological Assessment for the SR 500 St. Johns Interchange and Fish Passage 36 Project. 37

WSDOT. 2009. Assessment of nighttime roadway lighting effect on Lake Washington fish 38 habitat: Technical Memorandum. Prepared for WSDOT by SR 520 Traffic/Illumination 39 Design Team. January 9, 2009. 40


10-34 June 2010

WSDOT. 2009b. Marine Mammal, Fish, and Marbled Murrelet Injury and Disturbance 1 Thresholds for Marine Construction Activities. Available at: http://www.wsdot.wa.gov2 /NR/rdonlyres/216F21DA-A91B-43F2-8423-CD42885EE0EC/0/BA_3 MarineNoiseThrshlds.pdf. 4

WSF (Washington State Ferries) 2009. Reference Biological assessment: Washington State 5 Ferries Capital, Repair, and Maintenance Projects. Washington State Ferries, Seattle, 6 Washington. 7

Wursig, B. 1990. Cetaceans and oil: ecological perspectives. Pages 129-166 in J.R. Geraci and 8 D.J. St. Aubin, editors. Sea mammals and oil: confronting the risks. Academic Press, 9 New York. 10

Wyatt, Garth. 2009. PGE (Portland General Electric). Personal communication on December 17, 11 2009. 12

Wydoski, R.S. and R.R. Whitney. 2003. Inland fishes of Washington, 2nd ed. University of 13 Washington Press, Seattle, WA. 322 pp. 14

Yelverton, J.T., D.R. Richmond, E.R. Fletcher, and R.K. Jones. 1973. Safe distance from 15 underwater explosions for mammals and birds. Defense Nuclear Agency, Dept. of 16 Defense, Washington. D.C., Tech. Rept. DNA 3114 T. 67 pp. 17

Ylitalo, G.M., C.O. Matikin, J. Buzitis, M.M. Krahn, L.J. Jones, T. Rowles, J.E. Stein. 2001. 18 Influence of life-history parameters on organochlorine concentrations in free-ranging 19 killer whales (Orcinus orca) from Prince William Sound, Alaska. The Science of the 20 Total Environmental 281:183-203. 21

Yonge, D., A. Hossain, M. Barber, S. Chen, and D. Griffin. 2002. Wet Detention Pond Design 22 for Highway Runoff Pollutant Control. National Cooperative Highway Research 23 Program. 24

Zawlocki, K.R. 1981. A Survey of Trace Organics in Highway Runoff in Seattle, Washington. 25 Master’s thesis. University of Washington, Seattle, Washington. 26

Zimmerman, M.P. 1999. Food habits of smallmouth bass, walleyes, and northern pikeminnow in 27 the lower Columbia River basin during outmigration of juvenile anadromous salmonids. 28 Transactions of the American Fisheries Society 128:1036-1054. 29