Microbial communities are microorganisms (viruses, bacteria, fungi, algae) at the base of the food web pyramid, representing about 50 % of the total biomass on Earth. They are responsible for thebiogeochemical cycles that shape the environment of earth and of its aquatic systems, influencing the health of each trophic and ultimately human health, too.In Europe, the good quality of surface waters is established under the Water Frame Directiv (WFD) based either on the chemical monitoring, or on the ecological status and pathogen detection indrinking and bathing waters.However, methods and techniques currently used for monitoring water quality and to detect potential biohazards present several limitations due to the need of highly skilled technicians; the long time for obtaining results, and the lack of tools for an integrated monitoring and evaluation of all different biological and non biological parameters relevant to guide preventive/remediation actions by the water authorities.MicroCokit, a close collaboration of academic groups with pan-European governmental laboratories and leading private enterprise, has been conceived to foster the transfer of knowledge among the partners with the final goal to bring to market faster, more sensitive and robust tools as bioindicators of water quality.The tools will be developed according to three different kind of bioindicators, 1) Microbial community bioindicator; ii) Pathogen indicator; iii) Early warning bioindicators for bacteria,cyanobacteria, and diatoms. The end-products will be of two kinds: a ready to use plate containing defined primers for quantitative Real Time PCR (qPCR) targeting the developed bioindicators and probes for Fluorescence in situ hybridization technique (FISH).The participation of two private enterprises already active in the field of molecular biology diagnostics, will facilitate the translation of this innovative ideas and tools into real products that will benefit European society.