Loss of endemic species represents a symptom of general degrading ecosystem conditions that is the indirect result of biodiversity alteration. Here, we developed a predictive model relating species richness of endemic riverine fishes to measured biological, climatic, and historical variables using data from 118 rivers distributed all over the Northern Hemisphere. In a minimally adequate multiple general least square model, total riverine fish species richness, historical biogeography (Pleistocene glaciations), and comtemporary climate accounted for 63% of the variability in endemic species richness; the strongest correlate being riverine fish species richness. Our findings suggest that (i) endemism and richness patterns are generally similar (fish diversity “hot-spots” areas sustain higher endemic species richness); (ii) glaciation in the Pleistocene have had a significant negative influence on endemic species richness in the more septentrional areas; and (iii) certain basins situated in desertic areas (subtropical dry-zone of deserts) have unusually high numbers of endemics. These last areas should not be overshadowed when setting conservation priorities.