The post-smolt phase is considered a critical period for Atlantic salmon (Salmo salar). Hence, identifying migration routes used by post-smolts is needed to protect the habitats they require to successfully complete their life cycle. We used a bio-physical model coupled with output from a water circulation model (FVCOM) to simulate dispersal of Atlantic salmon post-smolts in a semi-enclosed bay: Passamaquoddy Bay, New Brunswick, Canada. The model was run with nine post-smolt behaviours and six swimming speeds, and then tested against acoustic telemetry data. While no modelled behaviour entirely captured observed salmon migration routes, we identified some behaviours that could allow salmon to successfully leave the bay and resulted in predictions that matched observations reasonably well (e.g., swimming southwest, negative or tide-varying rheotaxis). We could also rule out several behaviours as unlikely to be used by Atlantic salmon post-smolts in this area (e.g., passive dispersal, orienting based on salinity or temperature, positive rheotaxis). Hence, with suitable behaviours and models, this approach can provide estimates of the essential habitats and migration routes of wild post-smolts.