Canadian Science Advisory Secretariat (CSAS) Research Document 2013/071 Maritimes Region Inner Bay of Fundy (iBoF) Atlantic Salmon (Salmo salar) Marine Habitat: Proposal for Important Habitat T.L. Marshall Co-chair, iBoF Recovery Team (2002-2007) 19 Sandy Cove Lane, RR 1 Pictou, Nova Scotia Canada B0K 1H0 August 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: Marshall, T.L. 2014. Inner Bay of Fundy (iBoF) Atlantic Salmon (Salmo salar) Marine Habitat: Proposal for Important Habitat. DFO Can. Sci. Advis. Sec. Res. Doc. 2013/071. vi + 69 p. Maritimes Region iBoF Atlantic Salmon Marine Habitat TABLE OF CONTENTS ABSTRACT ................................................................................................................................ iv RÉSUMÉ ....................................................................................................................................v INTRODUCTION ....................................................................................................................... 1 CONTEXT .................................................................................................................................. 1 BACKGROUND ......................................................................................................................... 2 REGULARLY FREQUENTED MARINE HABITAT ................................................................. 2 THE GULF OF MAINE ........................................................................................................... 4 Circulation Patterns ............................................................................................................ 4 BAY OF FUNDY .................................................................................................................... 4 Geomorphology .................................................................................................................. 4 Surface Currents ................................................................................................................ 5 Tides .................................................................................................................................. 6 Salinity ............................................................................................................................... 6 Temperature ....................................................................................................................... 7 Productivity ......................................................................................................................... 7 Prey of Atlantic Salmon ...................................................................................................... 7 FRESHWATER AREAS OF CRITICAL HABITAT .................................................................. 9 ESTUARINE AND MARINE AREAS OF OCCUPANCY ............................................................. 9 SMOLT .................................................................................................................................. 9 POST-SMOLTS ....................................................................................................................10 Historical Tagging: 1963-1990 ...........................................................................................10 First Electronic Tagging Study: 1999 .................................................................................11 Second Electronic Tagging Study: 2001-2002 ...................................................................13 Trawling Surveys: 2001-2003 ............................................................................................15 MATURING AND NON-MATURING SALMON ......................................................................17 RETURNING ADULTS ..........................................................................................................17 Bay of Fundy Commercial/Salmon Fisheries .....................................................................18 Inner Bay of Fundy in-River Recreational Fisheries ...........................................................20 KELTS ..................................................................................................................................21 SUMMARY: LIFE STAGE USAGE OF ESTUARINE/MARINE HABITAT ..............................22 Smolts ...............................................................................................................................22 Post-Smolts .......................................................................................................................23 Maturing/Non-Maturing Salmon .........................................................................................24 Returning Adults ................................................................................................................24 Kelts ..................................................................................................................................25 PROPOSAL FOR IMPORTANT HABITAT ............................................................................25 RESEARCH RECOMMENDATIONS ........................................................................................26 ADDITIONAL RESEARCH ....................................................................................................29 ADDITIONAL CONSIDERATIONS ........................................................................................29 ACKNOWLEDGEMENTS .........................................................................................................29 LITERATURE CITED ................................................................................................................30 TABLES ....................................................................................................................................37 FIGURES ..................................................................................................................................42 ANNEX 1 ..................................................................................................................................67 iii Maritimes Region iBoF Atlantic Salmon Marine Habitat ABSTRACT The inner Bay of Fundy (iBoF) Atlantic salmon (Salmo salar) was listed as an endangered species under the Species at Risk Act (SARA) when it came into force in 2004. SARA requires the identification of critical habitat for endangered species. A Recovery Strategy for the iBoF salmon was developed and published on the SAR Public Registry in May 2010, but was only able to identify freshwater critical habitat areas. Because Atlantic salmon require both freshwater, estuaries, and marine habitat to complete their life cycle, the Strategy included a Schedule of Studies to help define additional critical habitat. Previous documentation in support of the estuarine and marine habitats of iBoF salmon reviewed tagging, telemetry and trawling studies of iBoF post-smolts through 2008. The use of Bay habitats by returning/spawning salmon had been and continues to be based on captures of Carlin-tagged fish in now-closed commercial fisheries. These data represent a body of evidence indicating that some areas within the Bay have a long history of use by at least two life stages moving throughout most of the Bay during their marine phase. Unknown was the extent and proportion to which iBoF salmon smolts used the Bay as post-smolt nursery area, their area of occurrence October through winter, and the wintering location of adults and reconditioning kelts. Hence, the probabilities of use for all habitat locations could not be estimated and, therefore, predicted with equal certainty as required under previous guidelines for the identification of Critical Habitat. Recently, however, the guidelines for the identification of critical habitat have been relaxed such that the absence of scientific certainty regarding the function of the Critical Habitat will not preclude its identification to the extent possible using the best available information. This document reviews: i) information contributory to past evidence of extended use of the Bay by iBoF salmon, ii) newly published analyses of the decade-old data from electronically tagged post-smolts and provides iii) inferred temporal occupancy of estuarine and marine habitats through past smolt, post-smolt and adult monitoring activities and as well, relevant commercial and recreational catch data. Overwintering habitat of all stages and summer habitats of distant migrating post-smolts and maturing adults of the iBoF salmon remain undocumented, although publication of the migration paths of several iBoF kelts tagged in November/December and May bearing 4- and 6-month duration pop-up satellite tags is expected to reveal their habitats and by corollary, perhaps those of post-smolts and