Is biodiversity being left behind? Freshwater ecosystems hold unparalleled species diversity, but are amongst the most threatened in Europe. Prioritizing short-term, often localized benefits in ecosystem provisioning services (such as hydropower) is degrading habitats and damaging cultural and regulatory services such as carbon storage, making it impossible for Europe to meet policy goals under the Habitats and Water Framework Directives. The brief calls for ‘biodiversity-conscious priority setting,’ considering the full range of services that freshwater ecosystems provide, as well as improving the knowledge of ecosystems’ status and threats, to use EU funding resources to the greatest advantage.