Groundwater is an essential resource and habitat of diverse organismic communities. As a consequence, the assessment and monitoring of groundwater require the same routine as for surface waters, i.e. the application of appropriate bioindicators, ecological criteria and innovative concepts. Indicators are, in the best case, easy to measure, with analysis low in price, and highly sensitive to a multitude of disturbances that act at an ecosystem. Here, groundwater ecosystem microorganisms, that are abundant and ubiquitously distributed, serve as promising bioindicators. Because of the immense biodiversity within microbial communities and with respect to a broad routine application, the focus on integrating microbial measures, such as microbial biomass and activity, is recommended, instead of a taxonomic-phylogenetic approach as generally applied for metazoa. It is of advantage that existing groundwater monitoring networks may be used for sampling. The microbial measures we propose are total prokaryotic cell counts (GZZ) as biomass measure, and cellular ATP as activity measure. Additionally, the concentration of assimilable dissolved organic carbon (AOC) can be determined as measure of energy ready available to microbes. By means of different examples, we show that a characteristic B-A or B-A-E fingerprint can be assigned to individual aquifers or groundwater bodies. Such a fingerprint, i.e. the B-A-E Index, allows to distinguish natural (non- or only moderately contaminated) from polluted groundwater or surface water. The pros and cons of this new microbiological-ecological sound assessment and monitoring scheme are discussed.