Sea trout (Salmo trutta L.) stock collapses in coastal areas of western Ireland subject to salmon aquaculture were contemporaneous with high abundances of larval sea lice (Lepeophtheirus salmonis Krøyer) on juvenile sea trout. Whereas sea trout remain in near-shore waters throughout their marine migration, Atlantic salmon (Salmo salar L.) smolts typically move quickly offshore into oceanic waters. It might therefore be predicted that salmon smolts would be less vulnerable to coastal stressors, and less likely to be negatively affected by infestations of sea lice early in their marine phase. Groups of micro-tagged, hatchery-reared Atlantic salmon smolts were fed either untreated pellets or pellets incorporating the in-feed sea louse treatment SLICE® (emamectin benzoate) prior to eight experimental releases in three marine locations over a 3-year period. In total 74,324 smolts were released and analysis of tag recaptures from returning adult salmon showed that emamectin-treated smolts experienced increased survivorship and were 1.8 times more likely to return compared to control fish. These results suggest that sea lice-induced mortality on adult Atlantic salmon returns in Ireland can be significant, and that sea lice larvae emanating from farmed salmon may influence individual survivorship and population conservation status of wild salmon in these river systems.