Summary The conservation of freshwater ecosystems has lagged behind that of marine and terrestrial ecosystems and often requires the integration of large‐scale approaches and transboundary considerations. This study aims to set the foundations of a spatial conservation strategy by identifying the most important catchments for the conservation of freshwater biodiversity in Europe. Using data on 1296 species of fish, mollusc, odonate and aquatic plant, and the key biodiversity area criteria (species Red List status, range restriction and uniqueness of species assemblages), we identified a network of Critical Catchments for the conservation of freshwater biodiversity. Applying spatial prioritisation, we show how the prioritised network differs from the ideal case of protecting all Critical Catchments and how it changes when protected areas are included, and we also identify gaps between the prioritised network and existing protected areas. Critical Catchments (n = 8423) covered 45% of the area of Europe, with 766 qualifying (‘trigger’) species located primarily in southern Europe. The prioritised network, limited to 17% of the area of Europe, comprised 3492 catchments mostly in southern and eastern Europe and species targets were met for at least 96% of the trigger species. We found the majority of Critical Catchments to be inadequately covered by protected areas. However, our prioritised network presents a possible solution to augment protected areas to meet policy targets while also achieving good species coverage. Policy implications. While Critical Catchments cover almost half of Europe, priority catchments are mostly in southern and eastern Europe where the current level of protection is not sufficient. This study presents a foundation for a Europe‐wide systematic conservation plan to ensure the persistence of freshwater biodiversity. Our study provides a powerful new tool for optimising investment on the conservation of freshwater biodiversity and for meeting targets set forth in international biodiversity policies, conventions and strategies.

Freshwater ecosystems host disproportionately high numbers of species relative to their surface area yet are poorly protected globally. We used data on the distribution of 1631 species of aquatic plant, mollusc, odonate and fish in 18,816 river and lake catchments in Europe to establish spatial conservation priorities based on the occurrence of threatened, range-restricted and endemic species using the Marxan systematic conservation planning tool. We found that priorities were highest for rivers and ancient lakes in S Europe, large rivers and lakes in E and N Europe, smaller lakes in NW Europe and karst/limestone areas in the Balkans, S France and central Europe. The a priori inclusion of well-protected catchments resulted in geographically more balanced priorities and better coverage of threatened (critically endangered, endangered and vulnerable) species. The a priori exclusion of well-protected catchments showed that priority areas that need further conservation interventions are in S and E Europe. We developed three ways to evaluate the correspondence between conservation priority and current protection by assessing whether a cathment has more (or less) priority given its protection level relative to all other catchments. Each method found that priority relative to protection was high in S and E Europe and generally low in NW Europe. The inclusion of hydrological connectivity had little influence on these patterns but decreased the coverage of threatened species, indicating a trade-off between connectivity and conservation of threatened species. Our results suggest that catchments in S and E Europe need urgent conservation attention (protected areas, restoration, management, species protection) in the face of imminent threats such as river regulation, dam construction, hydropower development and climate change. Our study presents continental-scale conservation priorities for freshwater ecosystems in ecologically meaningful planning units and will thus be important in freshwater biodiversity conservation policy and practice, and water management in Europe.