The early marine migration of 55 Atlantic salmon post-smolts tagged with acoustic transmitters was automatically monitored using 13 to 25 km long arrays of receivers deployed inside the Bay of Fundy, a coastal system on the east coast of Canada. The survival of post-smolts from groups with short- and long-term transmitters in coastal habitat up to 10 km from the river was 92 to 100%, indicating a successful transition to salt water and departure. Migration for 68 to 77% of post-smolts followed a direct route and it was rapid (transit time usually <12 h). Post-smolts initially migrated in a south to south-west direction (i.e. orientation towards the mouth of the bay) and they were aggregated near the coast. Post-smolts with long-term transmitters were monitored 20 km from the river where they continued to be aggregated, moving near the coast through a ‘common corridor’, and their survival to that point was at least 84%. Post-smolts from both groups travelled heading out of the coastal system during ebb tides. Flood tides interrupted migration, and they caused changes in travel direction and delays in departure for post-smolts not leaving by a direct route. Monitoring of coastal habitat inside the Bay of Fundy intercepted 62% of migrating post-smolts with long-term transmitters returning after an initial absence of 2 to 22 days. Returning post-smolts displayed a resident behaviour, using the habitat monitored inside the Bay of Fundy during July and August.