The recent advances in nanotechnology and the corresponding increase in the use of nanomaterials in products in every sector of society have resulted in uncertainties regarding environmental impacts. The detection of nanoparticles in virtually all water domains, including the oceans, surface waters, groundwater, atmospheric water, and even treated drinking water, demonstrates a distribution near ubiquity. The novel and potentially reactive characteristics of nanomaterials have lead to predictions on potential undesirable ramifications of exposure to these materials on human health. The effect of these nanomaterials on microbes is an important consideration due to the role of microbes as the basis of food webs and the primary agents for global biogeochemical cycles. Bacteria are the dominant organisms in aquifers, and their occurrence and activity is related to the biogeochemical conditions, there is often a complex relation between water quality and microbial communities (Lehman, 2007). The long-term monitoring of autochthonous endokarst microbial communities during years or decades may be an interesting approach to assess the general water quality and to detect potential changes in ecosystem functioning due to chronic low level contamination or climate change (Pronk et al., 2009). Microorganisms should be used in biomonitoring for several compelling reasons. (1) A cosmopolitan distribution facilitates comparisons of test results in geographically different regions. (2) Problems of scale are diminished. (3) Replicability is as good as, or better than, tests with larger organisms. (4) Environmental realism is higher than in tests using larger organisms... (6) Testing with microorganisms is less likely to antagonize animal rights activists (Cairns, 2005). Microscale testing methods and the earliest pollution prevention are the most cost-effective (Wells et al., 1998). The goal of our investigation was to develop the background for microscale integrated information systems related to subterranean water quality. The main objectives are: to find some indicator groups of ubiquitous microbial organisms suitable for multispecies toxicity testing and global integrated ecological standards for assessing water quality. Other objectives are: assessment of toxicity and risk of NanoParticles and nanomaterials to humans and the environment, modelling and data management: including the creation and implementation of a common database in cooperation with the PCCP, EU NanoSafety Cluster and other UNESCO Programmes.