Here is a large list of the academic, government, industry, ngo, and dialogue reference material I am basing this from:
Auditor General of British Columbia. (2004). Salmon Forever: An Assessment of the Provincial Role in Sustaining Wild Salmon – 2004/2005 Report. Victoria, BC: Office of the Auditor General of British Columbia.
Auditor General of Canada. (2004). Chapter 5: Fisheries and Oceans Canada – Salmon Stocks, Habitat, and Aquaculture. In, 2004 Report of the Commissioner of the Environment and Sustainable Development to the House of Commons. Ottawa: Office of the Auditor General.
EVS Environmental Consultants. (2000). An Evaluation of Knowledge and Gaps related to Impacts of Freshwater and Marine Aquaculture on the Aquatic Environment (Final Report). Prepared for the Canadian Department of Fisheries and Oceans.
Gardner, J. and D.L. Peterson. (2003). Making sense of the Aquaculture Debate. Report prepared for the Pacific Fisheries Resource Conservation Council.
Naylor, R.L., R.J. Goldburg, J. Primavera, N. Kautsky, M.C.M. Beveridge, J.Clay, C. Folke, J. Lubchenco, H. Mooney and M. Troell. (2001). Effects of Aquaculture on World Fish Supplies. Ecology. 8:14.
Naylor, R.L., J. Eagle and W. L. Smith. (2003). Salmon aquaculture in the Pacific Northwest: A global industry with local impacts. Environment. 45:18-39.
Naylor, R.L. and M. Burke (2005) Aquaculture and ocean resources: Raising tigers of the sea. Annual Review of Environment and Resources. 30:185-218.
Marshall, D. (2003). Fishy Business: The Economics of Salmon Farming in BC. Prepared by Canadian Centre for Policy Alternatives - BC Office. Vancouver, BC. Pauly, D., V. Christensen, S. Guenette, T. J. Pitcher, U.R. Sumaila, C.J. Walters, R. Watson and D.
Zeller. (2004). Towards sustainability in world fisheries. Nature. 418: 689-695.
Rees, W. (2003). Net-pen salmon farming: failing on two fronts: An eco-footprint analysis. In Gallaugher, P., Wood, L. (Eds.). The World Summit on Salmon, June 10-13, 2003: Proceedings. Continuing Studies in Science, Simon Fraser University, Burnaby, BC: 139-152.
Tacon, A.G.J. (2005). State of information on salmon aquaculture feed and the environment. Prepared for the World Wildlife Fund/Salmon Aquaculture Dialogue.
Bjorn, P.A. and B. Finstad. (2002). Salmon lice, Lepeophtheirus salmonis (Kroyer), infestation in sympatric populations of Arctic char, Salvelinus alpinus (L.), and sea trout, Salmo trutta (L.), in areas near and distant from salmon farms. International Council for the Exploration of the Sea Journal of Marine Science. 59:131-139.
Butler, J.R.A. (2002). Wild salmonids and sea louse infestations on the west coast of Scotland: sources of infestation and implications for the management of marine salmon farms. Pest Management Science. 58:595-608.
Connors, B.M., M. Krkosek & L.M. Dill. (2008) Sea lice escape predation on their host. Biology Letters.
Costello, M.J. (2006). Ecology of sea lice parasitic on farmed and wild fish. Trends in Parasitology. 22(10):475-477.
Dill, L.M., C.J.C. Losos, B.M. Connors, P. Mages. (2009) Comment on Beamish et al. (2007) “A proposed life history strategy for the salmon louse, Lepeophtheirus salmonis in the subarctic Pacific”. Aquaculture. 286:154-155.
Ford, J. S. and Myers, RA (2008) A Global Assessment of Salmon Aquaculture Impacts on Wild Salmonids. PLoS Biol 6(2): e33 doi:10.1371/journal.pbio.0060033 Frazer, L.N., (2009) Sea-cage aquaculture, sea lice, and declines of wild fish. Conservation Biology. 23:599–607.
Gallaugher, P. and C.D. Orr (2000). Aquaculture and the Protection of Wild Salmon. Workshop Proceedings. Speaking for the Salmon. Continuing Studies in Science, Simon Fraser University, Burnaby, BC. [Electronic copy not available]
Gallaugher, P., C.D. Orr, M. Berry, and P. Broomhall (2002). Speaking for the Salmon: Summit of Scientists on Sea Lice. Centre for Coastal Studies, Simon Fraser University, Burnaby, BC.
Gallaugher, P., J. Penikett, and M. Berry (2004a). Speaking for the Salmon: A Community Workshop to Review Preliminary Results of 2003 Studies on Sea Lice and Salmon in the Broughton Archipelago Area of British Columbia. Simon Fraser University, Inner Coast Natural Resource Centre, Alert Bay, BC.
Gallaugher, P., J. Penikett, and L. Wood (2004b). Speaking for the Salmon: Scientists' Roundtable on Sea Lice and Salmon in the Broughton Archipelago Area of British Columbia—Conveners Report. Continuing Studies in Science and Centre for Coastal Studies, Simon Fraser University, Morris J. Wosk Centre for Dialogue, SFU, Vancouver, BC.
Gottesfeld, A. S., B. Proctor, L. D. Rolston and C. Carr-Harris. (2009) Sea lice, Lepeophtheirus salmonis, transfer between wild sympatric adult and juvenile salmon on the north coast of British Columbia, Canada. Journal of Fish Diseases. 32: 45–57.3
Heuch, P.A., P.A. Bjorn, B. Finstad, J.C. Holst, L. Asplin and F. Nilsen. (2005). A review of the Norwegian Action Plan against salmon lice on salmonids: The effects on wild salmonids. Aquaculture. 246:79-92.
Holst, J.C., P. Jakobsen, F. Nilsen and M. Holm. (2000). Sea lice kill the wild salmon: Measures ahead! Aquaculture Report 2000. Institute of Marine Research. Bergen, Norway.