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Assessment of the Recovery Potential for the Outer Bay of Fundy Population of Atlantic Salmon: Threats to Populations

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Assessment of the Recovery Potential for the Outer Bay of Fundy Population of Atlantic Salmon: Threats to Populations Canadian Science Advisory Secretariat (CSAS) Research Document 2014/006 Maritimes Region Assessment of the Recovery Potential for the Outer Bay of Fundy Population of Atlantic Salmon: Threats to Populations C.N. Clarke1, S.M. Ratelle2, and R.A. Jones1 Fisheries and Oceans Canada Science Branch, Maritimes Region 1Gulf Fisheries Centre P.O. Box 5030 Moncton, NB E1C 9B6 2Mactaquac Biodiversity Facility French Village, NB E3E 2C6 November 2014 Foreword This series documents the scientific basis for the evaluation of aquatic resources and ecosystems in Canada. As such, it addresses the issues of the day in the time frames required and the documents it contains are not intended as definitive statements on the subjects addressed but rather as progress reports on ongoing investigations. Research documents are produced in the official language in which they are provided to the Secretariat. Published by: Fisheries and Oceans Canada Canadian Science Advisory Secretariat 200 Kent Street Ottawa ON K1A 0E6 http://www.dfo-mpo.gc.ca/csas-sccs/ [email protected] © Her Majesty the Queen in Right of Canada, 2014 ISSN 1919-5044 Correct citation for this publication: Clarke, C.N., Ratelle, S.M., and Jones, R.A. 2014. Assessment of the Recovery Potential for the Outer Bay of Fundy Population of Atlantic Salmon: Threats to Populations. DFO Can. Sci. Advis. Sec. Res. Doc. 2014/006. v + 103 p. TABLE OF CONTENTS Abstract...................................................................................................................................... iv Résumé ...................................................................................................................................... v Introduction ................................................................................................................................. 1 Potential Sources of Mortality ......................................................................................................2 Freshwater Water Threats .......................................................................................................2 Acidification .........................................................................................................................3 Climate - Extreme Water Temperature Events .................................................................... 3 Silt and Sediments ..............................................................................................................4 Pollutants, Chemical, and Wastewater ................................................................................ 5 Military Activities ..................................................................................................................8 Other Power Generation ......................................................................................................9 Invasive/Non-native Species Occurrence and Stocking ..................................................... 10 Atlantic Salmon Stocking ................................................................................................... 12 Other Native Salmonid Stocking ........................................................................................ 16 Hydro Dams and Obstructions ........................................................................................... 16 Roads, Culverts and Other Crossing Infrastructure ........................................................... 22 Urbanization ......................................................................................................................23 Agriculture .........................................................................................................................24 Forestry .............................................................................................................................25 Mining ...............................................................................................................................26 Directed Fisheries - Freshwater (Recreational, Aboriginal, Commercial, Illegal) ................ 27 By-catch - Freshwater (Recreational, Aboriginal, Commercial) .......................................... 28 Freshwater Threats Summary ............................................................................................... 29 Marine Threats ......................................................................................................................29 Salmon Aquaculture .......................................................................................................... 29 Shifts in Marine Environment ............................................................................................. 33 Parasite and Disease ........................................................................................................ 36 Depressed Population Phenomena ................................................................................... 38 Shipping Traffic ................................................................................................................. 39 Directed Fisheries and By-catch - Marine/Estuarine .......................................................... 39 Marine Threats Summary ...................................................................................................... 41 Threats Applicable to Freshwater, Estuarine, and Marine Environments ............................... 42 Scientific Research ............................................................................................................ 42 Proposed Cumulative Threat Impact Assessment ..................................................................... 43 Acknowledgements ...................................................................................................................44 Literature Cited .........................................................................................................................44 Tables .......................................................................................................................................63 Figures ......................................................................................................................................82 Appendicies ..............................................................................................................................97 Appendix 1 ............................................................................................................................97 Appendix 2 .......................................................................................................................... 101 iii ABSTRACT This research document provides a compilation of information and review of major threats currently thought to impact the persistence of wild Atlantic Salmon in the Outer Bay of Fundy (OBoF) Designatable Unit (DU). Over 90% of the wild salmon and accessible habitat in this unit lie in the Saint John River (SJR) and its tributaries which, aside from the St. Lawrence, compose the largest river in northeastern North America. Thus, the status of the entire DU population weighs heavily on the status of the SJR. The impacts of threats to Atlantic Salmon vary in dimensions of space, time, and severity. As such, attempts have been made to provide dimensional context for each threat although limitations of available information were encountered. Nearly all threats discussed here have been documented for their effect on salmon populations; however, many have not been directly reported for their effects on OBoF Atlantic Salmon. The information presented here intends to provide only a summary of knowledge on the extent and magnitude each threat poses to this population in either the freshwater or marine environment. Most of this information contributed to the development of a Recovery Potential Assessment (RPA) Science Advisory Report (SAR) for the OBoF Atlantic Salmon population (or DU 16; DFO 2014). To the extent available data permits, each threat has been assessed a rank of concern relative to other threats to the population. Threats thought to be most limiting population recovery ranked as highest concern. Following past science advice for improving threats assessments for species at risk, a proposed approach is presented for assessing accumulated threat impact on each river. The threat of highest concern in the freshwater environment, and for the entire DU, stems from the gauntlet of hydro dams facing migrating salmon. The most significant structure is the Mactaquac hydro-generation dam on the SJR, above which lies 36% of the entire DU habitat relying on manual operations to truck salmon above the dam to complete upstream migrations. Aside from the obvious barriers to upstream migration, hydro dams on the SJR affect flow and temperature regimes, which are critical to/for migration cues, alter food web and aquatic community structure, and harbour a growing abundance and diversity of non-native predators to salmon within reservoirs and tailraces. Smolts migrating from systems upstream of Mactaquac Dam have been shown to experience up to 45% additive mortality when passing through three major hydro dams. Marine threats of highest concern include: depressed population phenomena, salmonid aquaculture operations and shifts in oceanic conditions caused by changes in climate. Effects of depressed population phenomena are often difficult to quantify but are expected to contribute to the negative effects caused by most other individual threats. Shifts
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