The conservation of groundwater ecosystems requires an assessment and evaluation scheme that shows the state of the ecosystem. Consequently, faunal and microbial criteria are required for groundwater monitoring, in addition to physico-chemical analyses. To proof the adequacy of the application of groundwater organisms for the biological assessment of groundwater quality, an extensive sampling collection of various groundwater systems was accomplished between 2002 and 2009 in Germany. Key aspects were the examination of the indicator potential of groundwater communities towards surface-groundwater interactions and anthropogenic impacts, as well as the analysis of stygofaunal distribution patterns, as a base and reference for a faunal assessment scheme of groundwater systems. The sampling design considered local, regional, and biogeographic conditions. To test the indicator potential of groundwater organisms on a local and regional scale, groundwater systems in Nordrhein-Westfalen (NRW) and Baden-Württemberg (BW) were examined. The faunal and microbial data from unconsolidated aquifers (Erftgebiet, NRW) show the sensitivity of groundwater organisms against land use effects, e.g. extensive agriculture. Data analyses revealed positive correlations of organic material (estimated amount of detritus, TOC) and nitrate with faunal abundance, species richness, diversity and the proportions of stygoxene species. Moreover, the bacterial abundance and diversity in the groundwater of the Erftgebiet was high compared to oligotrophic groundwater systems, indicating an effect of surface influence due to agricultural land use. The groundwater colonization in the Alb-Donau-Kreis (BW) was analyzed for regional effects (landscape, type of aquifer, hydrogeology) and local effects (comparing single wells). The results show that the fauna reflects the strength of the hydrological exchange on different spatial scales. Furthermore, the fauna reflects the interaction of regional and local conditions. Accordingly, the diversity and abundance of groundwater organisms was influenced by the high connectivity of the karst and unconsolidated alluvial aquifers, the type of land use, covering layers of soil, the age of groundwater, and the sampling depths. In general, faunal and microbial data of the Alb-Donau-Kreis are characteristic for oligotrophic, oligoalimonic groundwaters. The large scale analyses of stygofaunal distribution patterns revealed significant biogeographical differences of the communities. These community patterns of the groundwater fauna do not coincide with existing classification schemes defined for surface landscapes or freshwater systems. The largest differences between faunal surface and subsurface distribution patterns were found between the groundwater of northern and southern Germany and the foothills of the central mountain ranges - all of them regions shaped by the last ice ages. In accordance with the faunal data assessed in groundwater, four different stygoregions were defined that are populated by distinct faunal assemblages. These are 1) the "Northern lowlands", 2) the "Central mountain ranges", 3) the "South-western mountain ranges", and 4) the "Southern mountain ranges and northern alps". The study corroborates that stygofaunal and microbial communities are an adequate tool for the qualitative assessment and monitoring of groundwater ecosystems. The best indicators to detect anthropogenic impacts on groundwater ecosystems are the faunal diversity, abundance, the proportions of stygobitic (obligate groundwater species) and stygoxene species (species not obligate for groundwater), and the bacterial abundance. The development of an ecologically based groundwater assessment and management, is crucial for the conservation of our groundwater ecosystems and thus, healthy drinking water. The defintion of "stygoregions" is an important base for the development of an assessment and reference scheme for groundwater ecosystems. The assessment of the ecological state of groundwater systems must be conducted on local scale, because the strength of the local hydrological influence determines the amount of food and oxygen as well as stygoxene animals within the aquifer, and thus shapes the local groundwater communities. Nevertheless, information of the biogeographic and regional conditions is needed as a reference for the type of species and abundances that potentially can occur in certain groundwater systems.