The interaction between hydrodynamics and the upstream migration of fish has been investigated in several studies over the past few years, but there has been a relative lack of investigation into the effects of hydraulics on the downstream migration of fish. In Norway, mortality associated with downstream migration is strongly related to hydropower production. However, there is a poor understanding of how fish choose their migratory routes, which limits the development of measures to mitigate the impact of anthropogenic structures on fish migration. The current study aimed to analyze the effect of hydraulics on the choice of downstream migration route of Atlantic salmon smolts (Salmo salar) in the proximity of an intake to a hydropower plant in Norway. We combined computational fluid dynamic modeling with 3-Dimensional acoustic telemetry positioning of a group of tagged smolts to investigate the interaction between fish and the flow dynamics, and to determine the influence of this interaction on fish migratory routes. A Hidden Markov Model was used to predict migratory routes based on the relations found between the hydraulic variables and fish behaviour. Results showed relationships between fish migratory routes and the different components of flow velocity. The knowledge acquired in this study is expected to inform opportunities and decision making in aquatic resources management and engineering design to increase fish survival past hydropower intakes and other anthropogenic structures.