Summary: 1. Using species distribution data from 111 aquifers distributed in nine European regions, we examined the pairwise relationships between local species richness (LSR), dissimilarity in species composition among localities, and regional species richness (RSR). In addition, we quantified the relative contribution of three nested spatial units – aquifers, catchments and regions – to the overall richness of groundwater crustaceans.2. The average number of species in karst and porous aquifers (LSR) varied significantly among regions and was dependent upon the richness of the regional species pool (RSR). LSR–RSR relationships differed between habitats: species richness in karstic local communities increased linearly with richness of the surrounding region, whereas that of porous local communities levelled off beyond a certain value of RSR.3. Dissimilarity in species composition among aquifers of a region increased significantly with increasing regional richness because of stronger habitat specialisation and a decrease in the geographic range of species among karst aquifers. Species turnover among karst aquifers was positively related to RSR, whereas this relationship was not significant for porous aquifers.4. The contribution of a given spatial unit to total richness increased as size of the spatial unit increased, although 72% of the overall richness was attributed to among‐region diversity. Differences in community composition between similar habitats in different regions were typically more pronounced than between nearby communities from different habitats.5. We conclude by calling for biodiversity assessment methods and conservation strategies that explicitly integrate the importance of turnover in community composition and habitat dissimilarity at multiple spatial scales.