Catchments form an important terrestrial-aquatic habitat complex for biodiversity conservation and human well-being. Riparian and stream components are debated about how much habitat need to be maintained or restored in rivers subject to habitat degradation and fragmentation. Using brown trout as a focal species we tested the hypothesis that presence of suitable habitat in lotic stream sections can be predicted using habitat modelling. We modelled brown trout habitat at the catchment scale in terms of quality, size, juxtaposition of stream segments using digital elevation data, and presence of dams. The habitat models were validated against presenceabsence data for local brown trout populations. A self-reproducing brown trout population was defined as having three year-classes. We identified the required minimum length (270 m) of a lotic stream section hosting a local brown trout population, corresponding to 3500 m². Adjacent areas of lotic stream habitat between dams had a significant positive effect on brown trout presence. The abundance of brown trout was significantly positively correlated to habitat quality, and negatively to hydropower water regulation. Critical habitat loss thresholds can be used for gap analysis regarding selection of dams to be removed and where restoration measures will be most effective in a catchment.