Freshwater ecosystems face increasing threats from human activities and climate change, thus requiring efforts to reduce impacts and prevent further deterioration. Restoration projects for riverine environments often rely on hydraulic, habitat, and metapopulation models, which depend on their accuracy in capturing the interactions among the different elements. In this regard, a critical challenge is represented by the definition of reliable relationships between fish population dynamics among river reaches in a catchment and habitat characteristics. This study presents an efficient, eco-hydraulically based framework to model the movement bias of brown trout within a river network. The proposed framework integrates the effects of hydraulics and habitat characteristics in terms of the Habitat Suitability Index for various trout age classes. Novel relationships linking fish dynamics to habitat quality are employed to correct the movement bias of fish based on the upstream and downstream habitat conditions. The corrected bias is used to compute the population dynamics at the catchment scale and tested against different flow regimes. Accordingly, the impact of habitat condition changes on the population dynamics is highlighted. The framework simplicity makes it suitable for future integration into existing habitat and metapopulation models, thus offering a practical tool for enhancing riverine restoration planning.