Ecosystem services provided by lakes and rivers are facing serious threats under the pressure of anthropogenic impacts, climate change, biodiversity loss and invasion of exotic species. The assessment of these changes is still defined by traditional criteria, which include time-consuming and expensive approaches (e.g. classical identification of aquatic species). The main aim of the project Eco-AlpsWater is to complement the traditional monitoring approaches used in the Alpine region (Water Framework Directive 2000/60/EC-EU WFD and, in Switzerland, the Water Protection Ordinance-WPO) with advanced and innovative technologies, providing support based on robust knowledge to the water management plans. The new approach will make use of Next Generation Sequencing (NGS) to analyze environmental DNA in waterbodies (which allow rapid species identification at low costs, from fish to bacteria), and smart technologies (automation in data processing, data storage, information retrieval). Along with the identification of gaps in the monitoring approaches across the Alpine regions, the new technologies will allow to define new improved experimental monitoring protocols to be applied in selected areas (including large perialpine lakes and smaller waterbodies, and key rivers). The transnational approach is essential to foster interactions and fill the scientific divide between academia and governance agencies, putting into practice the EUSALP agenda, i.e. capacity building of research institutions, networks and infrastructure with an Alpine Region dimension; and the preservation and valorization of natural resources at a transnational scale. Main outputs include new innovative metagenomic tools and smart bioinformatic technologies to monitor water ecological status and biodiversity; upgrading of traditional WFD/WPO methods with innovative technologies; guidelines for the definition of ecological status and restoration plans using next generation monitoring approaches.