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Habitat loss and degradation are causing collapses in freshwater fish in the Mediterranean region, where habitat restoration actions are still hampered by poor understanding of fish habitat selection and fitness. Here, we combined field surveys and laboratorial experiments to investigate how water velocity, body size and intra-specific interactions influence habitat selection and foraging success by the highly endangered Mira chub Squalius torgalensis. Velocity negatively affected habitat selection and fitness of chub via its negative effects on prey capture rate. Small chub occupied lower velocity ranges than large chub, and both captured the most prey at the range of velocities selected in the stream. Size-based intra-specific interactions also affected capture success, with small chub capturing proportionally less prey in the presence of large chub. Our results suggest that, during base-flow conditions, restoring low and moderate velocities up to 26 cm/s will help ensure suitable habitat and improve the fitness of small and large chub occurring in interacting groups. Integrated approaches uncovering factors directly related to habitat selection and individual fitness should guide habitat restoration for fish in Mediterranean streams and may help identify critical habitat features for other endangered species.