Anadromous salmon and sea trout smolts face challenging migrations from freshwater to the marine environment characterised by high mortality. Therefore, the timing of smolt migration is likely to be critical for survival. Time-series comparing migration of Atlantic salmon and sea trout smolts in the same river, and their response to the same environmental cues, are scarce. Here, we analysed migration timing of ~41 000 Atlantic salmon and sea trout smolts over a 19-year period from the river Guddalselva, western Norway. Trout displayed a longer migration window in earlier years, which decreased over time to become more similar to the salmon migration window. On average, salmon migrated out of the river earlier than trout. Migration of both species was significantly influenced by river water temperature and water discharge, but their relative influence varied across the years. On average, body-length of smolts of both species overlapped, however, size differences were observed within the migration period and among the years. We conclude that salmon and trout smolts in this river are highly synchronised and migrate in response to the same range of linked environmental cues.