The present work analysed composition and spatial organisation of the fish assemblages across the Arade basin, a small Mediterranean-type catchment in Southern Portugal. This basin is of high conservation priority because it hosts endemic cyprinid species with highly restricted distribution, namely Squalius aradensis, an undescribed new species of Chondrostoma (u. n. sp. Chondrostoma) closely related with C. lusitanicum, and Barbus sclateri. A total of 12 species were collected in the 39 sites surveyed. Fish assemblages in tributaries were dominated by the Iberian endemic cyprinids, while exotics were dominant in the Arade River. Abiotic variables played an important role in fish assemblage structuring: u. n. sp. Chondrostoma was associated to high water temperature and deeper sites, B. sclateri preferred sites with high dissolved oxygen, and S. aradensis was captured in sites with high current velocity and large dimension substrate. Depth may be particularly important in Mediterranean-type streams, since deeper pools may provide safer refugia against summer drought period. This corresponded to the majority of the Odelouca and Monchique sites and may account for the high abundance and biomass of endemic cyprinids recorded there. The conservation of these two streams, together with Enxerim, should become a priority.