In areas with high densities of salmon farming, spillover of the ectoparasitic salmon louse Lepeophtheirus salmonis poses a major threat to wild anadromous salmonids. By combining experimentally salmon louse infestation (mean ± standard deviation = 0.25 ± 0.25 lice g−1 fish) with acoustic telemetry, we studied the behavior of wild first‐time migrating sea trout Salmo trutta (n = 58, fork length = 138–204 mm) from late June to September in a marine area with naturally low infestation pressure. We observed that a similar proportion of sea trout from the control and exposed groups returned to fresh water both temporarily and permanently. However, sea trout from the control group spent nearly twice the amount of time in the fjord before first freshwater detection compared to exposed individuals (32 vs. 17 days), and statistical models indicated a dose–response of louse burden on the timing of freshwater return. This effect was combined with evidence of negative impacts of salmon louse burden on overall marine residency. Sea trout predominantly utilized waters within their natal fjord during the marine migration, with exposed fish spending significantly more time close to their home river than sea trout from the control group. In summary, the behavioral modifications caused by salmon lice could reduce individual marine growth, increase long‐term mortality, and ultimately harm recruitment at the population level.