Abstract – Ultrasonic telemetry and hydrodynamic modelling were used to study the migratory behaviour of 54 wild Atlantic salmon (Salmo salar) smolt captured in freshwater during their downstream migration and tracked in 2 years through a shallow estuary system. A high-density, fixed array of receivers provided detailed spatial and temporal resolution of behaviour in the second year of study. Smolt migration in the river occurred mostly at night and downstream migration was slower during the day. In the estuary, smolt moved seaward on ebbing tides and landward on flooding tides. The effect of current velocity was greater during the night than during the day. We documented for the first time that current velocity and diurnal period only accounted for approximately one-third of the variation in smolt ground speeds in the estuary, indicating that smolt movements were far less passive than previously reported. Smolt energetic status had no effect on smolt swimming behaviour or migratory performance. With an increase in salinity, smolt seaward movements during flooding tides were more frequent, and overall seaward ground velocity increased. The increase in salinity experienced by the smolt during their migration through the leading edge of saltwater intrusion thus induced a behavioural transition from a more passive, fluvial migration to a more active- and seaward-oriented migration.