Abstract Atlantic salmon, Salmo salar L., smolts were exposed to environmental levels of the pesticide atrazine in a hatchery, tagged with acoustic transmitters and released into fresh water at the peak of the smolt run. The subsequent movements of the smolts were monitored within the freshwater and immediate coastal zones using an array of acoustic receivers. In laboratory-based studies, exposure to a 0.1 μg L−1 concentration of atrazine over a 72-h period significantly reduced gill Na+K+ATPase activity but not plasma thyroxine (T4) and triiodothyronine (T3) levels compared with the control group, and on transfer to 33‰ saltwater resulted in 100% mortality. However, exposure to atrazine did not have a significant effect on the subsequent movements of the smolts in the freshwater, estuarine and marine environments. The results are discussed in relation to the impact of diffuse pollution on salmon populations.