Migration behaviour, route selection and mortality of Atlantic salmon, Salmo salar L., smolts were studied at four different hydroelectric facilities in the River Mustionjoki, Finland, in May 2017. Radio‐tagged smolts were released upstream of the power stations and tracked by stationary antenna‐receiver systems and hand‐held receivers. Tracking revealed a general tendency of smolts to move downstream with the main flow, but also variable behaviour and mortality related to diverse conditions characteristic of each power station. Average migration delay at the power stations ranged between 13.8 and 101.1 h (median: 1.7–61.5 h). Estimated mortality ranges were 0%–50% in the forebays, 4%–64% in the power stations and 2–30%/km during river migration after passage of the dam. This study provided essential information on behaviour and mortality in relation to local conditions at each power station required for successful application of fish bypass systems in a salmon restoration project.