Habitat selection and seasonal mobility are major components of the biology of fish populations. The aim of this study is to characterise fish habitat use templates at two different spatial scales (over reaches of 2 vs. 35 km) for two native rheophilic cyprinids (Barbus barbus and Squalius cephalus) and for the non-native catfish (Silurus glanis). The study was carried out in the Upper Rhône River characterised by strong and rapid variations of flow and thermal regimes (caused by hydroelectric and nuclear power plants). Results reveal contrasted mobility patterns, habitat uses and home-range sizes between native and non-native fish species, but also a high inter-individual variability. At a local scale, fish modify their habitat selection when discharge changes in selecting "least constraining" conditions. At a larger scale they are able to travel rapidly between their favoured habitats.