Aim The level of imperilment of mediterranean freshwater fish is among the highest recorded for any group of organisms evaluated to date. Here, we describe the geographical patterns in the incidence of threats affecting mediterranean freshwater fish and test whether the effects of specific threats are spatially related to the degree of imperilment of fish faunas. Location The Mediterranean Basin Biome. Methods From the IUCN Red List, we recorded the six main threats to 232 endemic freshwater fish species. We used data on fish distributions from IUCN to characterize the spatial patterns in the incidence of threats (as percentage of species affected) through multivariate statistics. We studied the relationships between threat incidence and two estimators of imperilment (proportion of species threatened and an index of extinction risk) at two spatial scales (10 נ10 km and basins) using partial least squares regressions (PLSR) that incorporated the effects of species richness and mean range size. Results The main axis of variation in the incidence of threats to freshwater fish split areas mainly affected by invasive species from those areas where species are threatened by pollution and agriculture. Wherever invasive species and water extraction were predominant threats, fish assemblages consistently tended to be more imperilled. Main conclusions As far as we know, this is the first large-scale analysis on the spatial relationships between the incidence of threats and level of imperilment of any taxonomic group. Our results highlight the primary role of invasive species and water extraction as drivers of native fish declines in the Mediterranean Basin. Large-scale patterns described here should be generated by local-scale impacts of both threats on fish biodiversity, widely reported in Mediterranean areas. Because all the species under concern are endemic, control of invasive species and reducing overexploitation of freshwater resources should be conservation priorities for mediterranean freshwater systems.