Atlantic salmon (Salmo salar) migrations in a large hydropower reservoir and the regulated Saint John River by Amanda Babin Master of Science, University of New Brunswick, 2013 Bachelor of Science, Mount Allison University, 2009 A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Graduate Academic Unit of Biology Supervisors: Tommi Linnansaari, Ph.D., Biology Stephan Peake, Ph.D., Biology Examining Board: René Malenfant, Ph.D., Biology Allen Curry, Ph.D., Biology, Forestry and Env. Management Paul Arp, Ph.D., Forestry and Env. Management External Examiner: Joseph Zydlewski, Ph.D., Biology, USGS, University of Maine This dissertation is accepted by the Dean of Graduate Studies THE UNIVERSITY OF NEW BRUNSWICK December, 2019 ©Amanda Babin, 2020 ABSTRACT My research focused on evaluating the impacts of the large Mactaquac Generating Station (MGS) reservoir on the migrations of the endangered Outer Bay of Fundy Atlantic salmon (Salmo salar). Salmon respond to flowing waters to determine the direction, timing, and speed of their migrations. A large reach of the Saint John River (SJR) was impounded by the MGS in 1968, transforming the habitat from a free- flowing river to a lacustrine environment with altered and slower flow. I examined all migratory lifestages of Atlantic salmon in the SJR using acoustic telemetry, including pre-smolts, smolts, adults, and post-spawned adults (kelts), as they navigated these environments. Migration rates were compared between the lentic MGS reservoir and the more lotic reaches upriver and downriver of the MGS to assess whether migration is delayed in the reservoir. Nearly all of the tagged salmon experienced migratory delay within the reservoir (medians: smolts 1.3-6.4 d, kelts 3.5-10.5 d, adults 1.5-5.7 d) due to suppressed migration rates (medians: smolts 5.0-13.3 km d-1 vs. 15.4-29.3 km d-1, kelts 4.4-8.9 km d-1 vs. 14.9-36.8 km d-1, adults 8.5-20.1 km d-1 vs. 19.3-46.9 km d-1). Migration success through the reservoir was higher for downstream migrants (smolts > 81 % and kelts > 82 %) than upstream migrants (adults 47 %). Recommendations informed by these findings with the aim of aiding recovery of this endangered population are given to hydropower and fisheries managers, including: i) changing the spill regime to allow a greater proportion of downstream migrants the option of spillway passage since all but a few smolts and even the earlier kelt migrants were sometimes forced to pass via turbines; ii) constructing a downstream surface- ii bypass facility which is more economically feasible than increasing spill and is supported by the observed variable passage timing; iii) allowing the free-swim of downstream migrants through bypasses in comparison to a trap-and-haul strategy that was not found to increase survival of smolts; and iv) maintaining trap-and-haul operations for adults migrating upstream of the MGS due to the high proportion of fallbacks and increased energy expenditure from superfluous movements in the reversed direction to the intended migration observed in the reservoir. iii DEDICATION To my husband, Kraig Babin, who has been there from the beginning. iv ACKNOWLEDGEMENTS I would first like to thank my principal supervisor, Tommi Linnansaari, for always telling me ‘good job’ at the end of the day, whether we had a successful day tagging fish or a not-so successful day getting the truck stuck in the mud. The extensive fieldwork throughout this project gave me a breadth of practical knowledge and was made better by Tommi’s experience and advice. Thank you to the remainder of my committee, Ross Jones for the extensive help both in planning and in the field, Steve Peake for his work on the Hydroacoustic Technology Inc. system, and the principal investigator, Allen Curry, all of which provided support and contributions to the thesis. I received financial support from the Natural Sciences and Engineering Research Council’s Collaborative Research and Development Programme (CRDPJ: 462708-13) in partnership with NB Power, along with the Atlantic Salmon Conservation Foundation, and the Wildlife Trust Fund. In addition to the funds facilitating my studies, my attendance in international conferences were supported by the UNB Biology Department and the UNB School of Graduate Studies. This work relied heavily on the rest of the MAES team, mainly Mark Gautreau, Ben Wallace, and Sam Andrews, as well as numerous summer students and supporting staff. Maintaining such a large receiver network throughout the river is not easy work, and their efforts are very much appreciated. We also relied heavily on the staff at the Mactaquac Biodiversity Facility, namely Leroy Anderson, John Whitelaw, and Becky Graham. It was always a lot of fun working with the hatchery staff while carefully handling the salmon. The first time I saw an adult salmon, I could hardly work between exclaiming about their beauty. I would v also like to thank the salmon themselves for the opportunity to interfere with individuals to further the understanding of the population as a whole. The First Nations along the river were invaluable in aiding this research project. Austin Paul from Kingsclear First Nation, Brian Polchies and Sandy Sappier from Woodstock First Nation, and John Perley, Jake Molten, and Mike Solomon from Tobique First Nations, all significantly contributed to the capture and care of the salmon. Peter Cronin and Bruce Beaton were instrumental in finding the holding pools and capturing numerous salmon. Robert Hughes, Claude Fitzherbert, and Terry Rooney provided extensive help with salmon tagging and tracking. George Ducheno and Mona Crewdson very kindly offered their private property for access to the water for salmon release. Scott Dixon and George Kelly at the Mactaquac and Beechwood Generating Stations were always available to provide whatever help was needed. Lastly, I would like to thank my family for their life-long support of my education. My grandparents, Archie and Bea Nesseth, and my mother, Colleen Nesseth, instilled a deep respect for continued learning and working to improve the world around me through compassion and understanding. My husband continues to fuel this passion while providing practical tools to do the work, along with emotional support throughout the stressful times. Thanks to all of you for helping make the dream of my six-year-old self come true. vi Table of Contents ABSTRACT ...................................................................................................................... ii DEDICATION ................................................................................................................. iv ACKNOWLEDGEMENTS ...............................................................................................v Table of Contents ............................................................................................................ vii List of Tables.................................................................................................................... xi List of Figures ................................................................................................................ xiii List of Symbols, Nomenclature or Abbreviations..............................................................1 Chapter 1 General Introduction ..........................................................................................3 1.1 Mactaquac Aquatic Ecosystem Study (MAES) ...................................................... 5 1.2 Atlantic salmon migratory ecology ......................................................................... 8 1.3 Use of telemetry in fish ecology studies ............................................................... 13 1.4 Impacts of hydropower generation on salmonids and their migrations ................ 18 1.5 Current state of the Outer Bay of Fundy Atlantic salmon population in the Saint John River ................................................................................................................... 29 1.6 Synthesis, objectives, and chapter overview ......................................................... 38 1.7 References ............................................................................................................. 42 Chapter 2 Detection efficiency of acoustic receivers in a large hydropower reservoir ...68 2.1 Abstract ................................................................................................................. 69 2.2 Introduction ........................................................................................................... 70 2.3 Materials and Methods .......................................................................................... 73 2.4 Results ................................................................................................................... 76 2.5 Discussion ............................................................................................................. 79 vii 2.6 Acknowledgements ............................................................................................... 83 2.7 References ............................................................................................................. 84 Chapter 3 Migration of Atlantic salmon (Salmo salar) smolts in a large hydropower reservoir............................................................................................................................93 3.1 Abstract ................................................................................................................