Juvenile Atlantic salmon (Salmo salar L.) smolts were tracked through two lakes impounded by large hydropower dams, and one natural standing water located in the River Conon system. Eighty smolts were tagged with acoustic transmitters and were tracked for an eight-week period from May to June 2017. High mortality rates were found between the river release location and the three lakes; Loch Garve (25% km-1), Loch Meig (28% km-1) and Loch Achonachie (10% km-1) which was likely the result of predation. Modelling showed that successful lake migration was lower if the lake was impounded, and if individuals were migrating earlier in the study period. Modelling found that successful migration (river release to estuary) was lower if the lake was impounded, and if fish were travelling in smaller release groups.