Although many studies have shown that trout farm effluents can affect water quality and macro-invertebrate populations downstream of the farm, few studies have investigated effects on fish. Previous work has suggested that trout farm effluents can affect salmonid parr and embryos but there is no data as to whether they affect salmonid smolts. In this experiment, Atlantic salmon smolts were caged upstream and downstream of trout farm effluents for 3 days on two UK Rivers and compared against hatchery controls in two years (2005–2006). No persistent effects on plasma osmolality, plasma sodium, plasma chloride, condition factor and hepato-somatic indices were observed, although there were variations in responses between years. No effects of the effluents were observed on gill Na+K+ATPase activity or plasma thyroid hormones. There was evidence that fish placed downstream of the fish farms had modified plasma potassium regulation, although the relative influence of the fish farm effluents on the physiology compared to other compounds in the river has not been determined. Only one of the smolts (5%) caged downstream of the effluents died and there was little effect on plasma ionoregulatory and osmoregulatory indices, but mortalities increased when the smolts were given a 48 h seawater challenge. However, it is possible that other compounds within the river in addition to the fish farm effluents may have influenced the survival of the smolts.