Good water quality is a priority for the efficient functioning of the state. EU member states must achieve the goal of “good status” of all waters, protecting aquatic ecology, unique habitats, drinking water resources, and protecting bathing water. Current traditional water sampling techniques are long-lasting, limited by the availability of taxonomic experts and difficult to sustain in long-term monitoring, and imply the collection of potentially damaging micro-organisms. The aim of the project is to develop a non-invasive, molecularly effective nucleic acid-based tool-test needed to detect the presence and abundance of species in order to improve the monitoring of water quality, which is of global interest to civilisation.