Among available tools for estimating the ecological impacts of discharge alteration, hydraulic habitat models link hydraulic models of streams with biological models that reflect the preferences of organisms for hydraulics. The simplification of habitat models now enables their application at the catchment scale for estimating the impacts on habitats of discharge and abstraction management. In the Seine-Normandie catchment in France, we propose an original linkage of a distributed hydrological model, a fish species distribution model and hydraulic habitat models. We show that groundwater abstraction in the catchment cause a moderate alteration of low flows (median: 4.1%) and a weak alteration of usable habitats for fish (median: 1.6%). However, the spatial distribution of alterations helps to identify regions where impacts are stronger (habitat alteration around 15%), due to strong abstraction and/or the presence of demanding fish species. An uncertainty analysis indicates that our results should be interpreted at the regional scale only; they allow identifying regions that would deserve more detailed analyses. Our results open many perspectives for taking into account habitat issues in quantitative water management at the catchment scale.