Parasite spillback from domestic animals can distort the balance between host and parasites in surrounding wildlife, with potential detrimental effects on wild populations. In aquatic environments, parasite spillback from aquaculture to wild salmon is one of the most contentious sustainability debates. In a 19 year time series of release group studies of Atlantic salmon, we demonstrated that (i) the effect of subjecting out-migrating salmon smolts to parasite treatment on marine survival has been reduced over a time, (ii) the relation between salmon lice levels in the out-migration route of the salmon and effect of treatment against the parasite is weak, but also (iii) the return rates in both treated and untreated groups of salmon are negatively correlated with salmon lice levels, and (iv) returns of wild salmon to the region are similarly negatively correlated with salmon lice levels during the out-migration year. Our study suggests that salmon lice can have a large effect on wild salmon populations that is not revealed with randomized control trials using antiparasitic drugs. This should be better accounted for when considering the impacts of farms on wild salmon populations.