SUMMARY 1. Fish in Mediterranean streams survive through the summer in residual surface waters, encompassing a broad range of abiotic and biotic conditions. Yet, the extent to which fish assemblages may be shaped by functional heterogeneity in dry‐season refugia is largely unknown. This study addresses this issue, by examining fish assemblage and population attributes, and predation patterns in residual summer habitats (12 pools and six runs) across a Mediterranean catchment in south‐west Portugal. 2. Species richness was fairly constant among runs but increased with pool size, with the addition of exotics and rare natives to large pools resulting in nested subsets. The four most common species (chub, nase, loach and eel) were considered generalists in terms of their use of dry‐season refugia. Conversely, rare species presented more specialised habitats, with barbel and exotics favouring pools and stickleback favouring runs. 3. Age and size of the two most common species varied among dry‐season habitats. Age 0 chub were restricted to runs, where spawning stages (age 2 and older fish) were also more represented. Age 0 nase also concentrated in runs, but the individuals collected in pools exhibited greater growth. Conversely, age 2 and older nase were proportionally more abundant in pools, but with greater growth and better condition in runs. 4. The otter was the main fish predator, consuming fish of all species and size classes, irrespective of habitat. Otter activity concentrated in pools, where predation risk for cyprinids seemed to be much higher than in runs. 5. Dry‐season refugia apparently vary in functional importance for different fish species and life stages, acting as complementary units in the landscape. Therefore, the presence of both pool and run refugia trough the summer dry season may play a critical role in promoting the persistence of native species in Mediterranean streams.