Summary 1. The Pleistocene glaciations during the Quaternary appear to have resulted in an impoverished groundwater fauna in northern Europe. Re‐colonisation may have occurred either through long‐distance dispersal from unglaciated southern areas or from local refugia. 2. The Belgian groundwater fauna was sampled at multiple sites, and its habitats characterised, to assess whether the composition of present‐day stygobiotic assemblages can be attributed to either of these mechanisms. 3. A total of 202 sampling sites were selected in four hydrogeographic units of the Meuse River catchment. Sites were equally divided among the saturated and unsaturated zones of fractured aquifers (karst) and within the hyporheic and phreatic zones of porous aquifers. Seventeen environmental parameters were determined in parallel. 4. More than 140 species were recorded, including representatives of the Amphipoda, Cladocera, Copepoda, Hydrachnidia, Isopoda, Oligochaeta, Ostracoda, Mollusca, Syncarida and Nematoda. Thirty stygobiont species were identified, of which 10 species were new to the Belgian fauna, raising the total number of stygobiotic species in Belgium to 41. 5. The frequency of occurrences of stygobiotic species was always low, with 37% of the sampled sites lacking stygobionts. A few species were exclusive to one hydrological zone, although no statistically significant differences were detected in species richness at any of the four hierarchial levels considered (Meuse catchment = region, hydrogeographic units, aquifer type and hydrological zone). 6. Overall, results suggest that the stygobiotic fauna of Belgium is species‐poor and mostly comprises widely distributed species with broad ecological tolerances. This supports the view that eurytopic species re‐colonised the area by long‐distance dispersal from refugia in southern Europe. The virtual absence of endemic species further suggests that the scenario of an ancient fauna that survived in local refugia is of minor importance.