1. Classification of groundwater habitats and communities at different spatial scales is emphasised as a basic requirement for the implementation of groundwater ecology into legislation. Such a classification would also facilitate prediction of groundwater biodiversity, abundance and community structure, but is not currently available.
2. To identify the factors influencing the distribution of stygofauna at the landscape scale, the groundwater fauna of Baden–Württemberg in South-western Germany was sampled from November 2001 to December 2002. A total of 304 boreholes were sampled twice with a phreatic net. Boreholes were originally selected to represent the full range of geographic, geological and hydrographic variation within the sampling area. However, bores in porous aquifers were overrepresented because the monitoring networks that could be used in this study were originally designed for hydrogeological purposes.
3. In total, 105 taxa (including 60 stygobionts) were found. Most of the stygobionts were rare, with 52% of them occurring in less than 1% of the boreholes. Stygobiotic taxonomic richness in a region or so-called geological unit was directly correlated with the number of bores sampled. Species richness accumulation curves indicated that the real taxonomic richness of Baden–Württemberg is considerably higher than the recorded number of 60 stygobiotic taxa. This finding is in accordance with studies from other regions and suggests that groundwater biodiversity generally is strongly underestimated, probably resulting mainly from huge heterogeneity of groundwater systems and reliance on broad-scale hydrological monitoring networks.
4. To identify regional distribution patterns, the sampling area was separated into regional geological units, each comprising all aquifers of identical geology in a particular region (size: hundred to several thousand square kilometres). Distribution patterns of the aquatic subterranean fauna (including non-stygobionts) were found to be influenced to some degree by the geographical position of the bores, and to a large extent by hydrogeological aquifer type rather than by affiliation of aquifers to a given geological unit. Four types of aquifers could be distinguished: Compact aquifers (aquitards) with reduced pore spaces, and porous, fractured and karstic aquifers.
5. Communities of porous and karstic aquifers were found to be more similar to each other than the communities of compact and fractured aquifers. Therefore, for the purpose of recording groundwater biodiversity and defining undisturbed groundwater habitats, we suggest focusing more strongly than in the past on aquifer hydraulic conductivity and, in particular, on compact and fractured aquifers.