Understanding the links between instream ecology and hydrology has become a critical task in contemporary river research and management. Habitat selection behaviour is a central dimension in applied ecology because it is a primary way that mobile organisms adapt to changing environmental conditions. Here, we analyzed brown trout habitat selection during two consecutive years in rivers presenting contrasting flow conditions to test the following hypotheses: (1) given that adaptation to flow regimes occurs as a response to the interaction between frequency, magnitude and predictability of mortality-causing events, habitat selection would vary across populations subject to different disturbance regimes; (2) because adaptations are directed towards enduring both intra-annual and interannual variations in flow, habitat selection would shift across years as a response to changing flow conditions and (3) such responses to yearly flow fluctuations would depend on the historical long-term hydrologic regime. We found that trout from rivers with highly variable flow and more frequent, longer and stronger extreme flow events were more willing to occupy positions in high-velocity habitats and showed stronger requirements for velocity refuges, whereas trout inhabiting more stable and benign flow environments selected visually-covered habitats to minimize biotic interactions. Results also revealed that trout shifted habitat selection patterns across years differing in flow conditions irrespective of river typology, but this shift was markedly stronger in rivers with higher flow variability and extremity. Overall, observed ecological patterns have strong implications for predicting the consequences of flow alteration for species adapted to particular flow regimes. Copyright © 2013 John Wiley & Sons, Ltd.