Journal of Fish Biology (2012) 81, 1626–1645 doi:10.1111/j.1095-8649.2012.03419.x, available online at wileyonlinelibrary.com Estuarine survival and migratory behaviour of Atlantic salmon Salmo salar smolts E. A. Halfyard*†‡, A. J. F. Gibson§, D. E. Ruzzante*, M. J. W. Stokesbury‡‖ and F. G. Whoriskey*‡ *Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H4J1 Canada, ‡Ocean Tracking Network, c/o Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H4JI Canada, §Fisheries and Oceans Canada, 1 Challenger Drive, Dartmouth, NS, B2Y2A2 Canada and ‖Department of Biology, Acadia University, 33 Westwood Avenue, Wolfville, NS, B4P2R6 Canada (Received 6 February 2012, Accepted 24 June 2012) To estimate mortality rates, assess the spatio-temporal dynamics of natural mortality and examine migratory behaviour during the fresh to saltwater transition, 185 wild Atlantic salmon Salmo salar smolts were implanted with coded acoustic transmitters. Seaward migration of tagged S. salar from four river systems in an area of Nova Scotia, Canada known as the Southern Upland was monitored using fixed receivers and active telemetry over 3 years. Cumulative survival through the river, inner estuary, outer estuary and bay habitats averaged 59·6% (range = 39·4–73·5%). When standardized to distance travelled, survival rates followed two patterns: (1) constant rates of survival independent of habitat or (2) low survival most frequently associated with inner estuary habitats. In rivers where survival was independent of habitat, residency periods were also independent of habitat, post-smolts exhibited few upstream movements, took a more direct route to the ocean and reached the ocean rapidly. Alternatively, in rivers where survival was habitat specific, residency was also habitat spe- cific with overall increased residency, more frequent upstream movements and delayed arrival to the open ocean. The sudden disappearance of most (75–100%) smolts and post-smolts assumed dead during the course of this study warrants further examination into the role of avian predators as a mortality vector.  2012 The Authors Journal of Fish Biology  2012 The Fisheries Society of the British Isles Key words: acoustic telemetry; migration; mortality; residency; Southern Upland, Nova Scotia. INTRODUCTION Atlantic salmon Salmo salar L. 1758 populations of the north-west Atlantic Ocean have been in decline over the past two centuries (WWF, 2001); however, a precipitous fall beginning in about 1990 (Hawkins, 2000; Potter et al., 2003) resulted in the extirpation of many populations, particularly those at the southern end of the distribution range (Parrish et al., 1998; COSEWIC, 2011; www.cosewic.gc.ca). In Canada’s Maritime provinces, S. salar populations have also markedly declined (Gibson et al., 2006), most notably in the Inner Bay of Fundy and Nova Scotia’s Southern Upland, both considered distinct designatable units by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). In the 65 rivers of the †Author to whom correspondence should be addressed. Tel.: +1 902 494 2357; email: eahalfyard@dal.ca 1626  2012 The Authors Journal of Fish Biology  2012 The Fisheries Society of the British Isles