The drafting of a new Global Biodiversity Framework for the Convention on Biological Diversity (CBD) and Biodiversity Strategy for the European Union (EU) render 2020 a critical crossroad for biodiversity conservation. Freshwater biodiversity is disproportionately threatened and poorly studied relative to marine and terrestrial biota, despite providing numerous essential ecosystem services. The urgency of the mounting freshwater biodiversity crisis necessitates approaches catered to the unique ecology and threats of freshwater life, which are not adequately addressed by current strategies. We present a set of 15 special recommendations for freshwater biodiversity to guide the CBD’s post-2020 framework and the 2020 EU strategy based on European case studies, both challenges and successes. Our recommendations cover key outcomes and guiding concepts, enabling conditions and methods of implementation, planning and accountability modalities, and cross-cutting issues. They address topics including invasive species, integrated water resources management, strategic conservation planning, data management, and emerging technologies for freshwater monitoring, among others. These recommendations will enhance the ability of global and European post-2020 biodiversity agreements to halt and reverse the rapid global decline of freshwater biodiversity.