The variation of species richness across latitude is one of the most fascinating phenomena in biodiversity. However, there is still much ongoing debate around the underlying mechanisms determining the patterns of biodiversity across our planet. Furthermore, there is a clear bias in macroecology and biogeography towards investigations of terrestrial systems. We analyzed the variation in α- and β-diversity across latitude for all European freshwater animals (> 14,000 species) using data of α-diversity within 25 pre-defined biogeographic freshwater regions. Across all species we found no monotonous decrease of species richness with latitude, but a peak in central Europe. The regions differ in size, but the peak was not due to an area effect. However, the relationship between species richness and latitude was not concordant across the three basic habitat types: Species living in groundwater and running water habitats showed a monotonous decrease of species richness with increasing latitude, whereas species of standing water habitats exhibited a hump-shaped relationship. This difference calls for an explanation considering habitat conditions as well as traits of species adapted to these habitats. In general, standing water bodies are less persistent than running or groundwater habitats. Therefore species of standing water habitats evolved more efficient strategies for dispersal than species adapted to running or groundwater habitats. Our finding that standing waters showed lower levels of β-diversity among biogeographic regions corroborates this line of arguments.