Human-induced river fragmentation is a major threat to migratory fish species. Restoring river connectivity requires the construction of fish passage solutions, such as fishways for upstream and downstream migration. While many studies focussed on the upstream migration of diadromous fishes, and especially of adult Atlantic salmons (Salmo salar), we analyze juvenile behaviour under different hydraulic conditions at reservoir to improve the development of effective bypass systems for downstream passage of salmon smolt. Based on coupling three-dimensional (3D) computational fluid dynamics (CFD) simulations to smolt positions tracked by two-dimensional (2D) telemetry, the present study aimed to explore smolt behaviour in relation to hydraulic cues. More specifically, we explored how hydraulic conditions influence fish behaviour and how fish navigate depending on this behaviour. In 2017, 23 smolts were tracked in the reservoir of Pout es (Allier River, France), associated with different turbine discharge rates. 3D CFD simulations were performed and validated against field measurements in the reservoir upstream of the hydropower plant. The study of fish displacements in relation to flow conditions provided new insights with the use of thrust force, swimming orientation and direction as means to precisely characterize smolt behaviour, which can help in the design of downstream migration passage facilities. At Pout es dam, flow velocity, flow acceleration and turbulent kinetic energy are very low and therefore can lead to fish disorientation. However, results underlined that having a minimum flow velocity of 20 cm/s in reservoirs is sufficient to prevent delay and allow fish navigation.