The article reflects on the main issues, research methodologies and achievements of the project HydroEcoNex, a transboundary project carried out by a consortium of research institutes, NGO and a university – Institute of Zoology, International association of river keepers “Eco-Tiras” (Republic of Moldova), ”Dunărea de Jos” University of Galati (Romania), as well as Ukrainian Scientific Center of Ecology of the Sea and Hydrometeorological Center for Black and Azov Seas. Among the main obtained results are the development of a common methodology with various set of indicators for assessing hydropower impact and climate change, assessment of lost ecosystem services, sharing of generated knowledge to students and researchers, endowment of the research laboratories with advanced research equipment.