We quantify main ecosystem services (i.e. the contribution of ecosystems to human well-being) provided by rivers, lakes, coastal waters and connected ecosystems (riparian areas and floodplains) in Europe, including water provisioning, water purification, erosion prevention, flood protection, coastal protection, and recreation. We show European maps of ecosystem service capacity, flow (actual use), sustainability and efficiency. Then we explore the relationship between the services and the ecosystem condition at the European scale, considering the ecological status of aquatic ecosystems, reported under the EU Water Framework Directive, as a measure of the ecosystem integrity and biodiversity. Our results indicate that a higher delivery of the regulating and cultural ecosystem services analysed is mostly correlated with better conditions of aquatic ecosystems. Conversely, the use of provisioning services can result in pressures on the ecosystem. This suggests the importance of maintaining good ecological condition of aquatic ecosystems to ensure the delivery of ecosystem services in the future. These results at the continental scale, although limited to the ecosystem services under analysis, might be relevant to consider when investing in the protection and restoration of aquatic ecosystems called for by the current EU water policy and Biodiversity Strategy and by the United Nations Sustainable Development Goals.