Regularities in species richness are widely observed but controversy continues over its mechanistic explanation. Because richness patterns are usually a compound measure derived from taxonomically diverse species with different ecological requirements, these analyses may confound diverse causes of species numbers. Here we investigate species richness in the aquatic beetle fauna of Europe, separating major taxonomic groups and two major ecological types, species occurring in standing and running water bodies. We collated species distributions for 800+ species of water beetles in 15 regions across western Europe. Species number in any of these regions was related to three variables: total area size, geographic connectedness of the area, and latitude. Pooled species numbers were accurately predicted, but correlations were different for species associated with either running or standing water. The former were mostly correlated with latitude, while the latter were only correlated with the measure of connectedness or with area size. These differences were generally also observed in each of the four phylogenetically independent lineages of aquatic Coleoptera when analysed separately. We propose that effects of habitat, in this case possibly mediated by different long term persistence of running and standing water bodies, impose constraints at the population or local level which, if effective over larger temporal and spatial scales, determine global patterns of species richness.