The protection, preservation and restoration of aquatic ecosystems and their functions is of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD; 2000/60/EC) and the Marine Strategy Framework Directive (2008/56/EC). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch thus obtained determines the extent of potential management actions. The current approach to biodiversity assessment and monitoring is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to variation of individual taxonomic expertise of the analysts. Novel genomic tools can circumvent many of the aforesaid problems and could complement traditional bioassessment and biomonitoring strategies. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of DNAqua-Net is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices and metrics for routine application for biodiversity assessments and biomonitoring of European water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.