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There is increasing evidence that predation by harbour seals on out-migrating salmon smolts may be responsible for the low return of adult coho and Chinook salmon in the Salish Sea. However, little attention has been given to understanding where and when this predation occurs and the extent to which it might be conducted by few or many seals in the population. We equipped 17 harbour seals with data loggers to track seal movements and used accelerometry to infer prey encounter events (PEEs) following the release of ~384000 coho (May 4, 2015) and ~3 million Chinook (May 14, 2015) smolts into the Big Qualicum River. We found a small proportion (5.7%) of all PEEs occurred in the estuary where salmon smolts entered the ocean—and that only one-quarter of the seals actively fed there. PEE counts increased in the estuary after both species of smolts were released. However, the response of the seals was less synchronous and occurred over a greater range of depths following the release of the smaller-bodied and more abundant Chinook smolts. Harbour seals feeding in the estuary appeared to target coho smolts at the beginning of May but appeared to pursue predators of Chinook smolts in mid-May. PEE counts in the estuary increased as tide height rose and were higher at dusk and night—especially during full moonlight. Such fine-scale behavioural information about harbour seals in relation to pulses of out-migrating smolts can be used to design mitigation strategies to reduce predation pressure by seals on salmon populations.