Freshwater ecosystems are among the most threatened in the world, while providing numerous essential ecosystem services (ES) to humans. Despite their importance, research on freshwater ecosystem services is limited. Here, we examine how freshwater studies could help to advance ES research and vice versa. We summarize major knowledge gaps and suggest solutions focusing on science and policy in Europe. We found several features that are unique to freshwater ecosystems, but often disregarded in ES assessments. Insufficient transfer of knowledge towards stakeholders is also problematic. Knowledge transfer and implementation seems to be less effective towards South-east Europe. Focusing on the strengths of freshwater research regarding connectivity, across borders, involving multiple actors can help to improve ES research towards a more dynamic, landscape-level approach, which we believe can boost the implementation of the ES concept in freshwater policies. Bridging these gaps can contribute to achieve the ambitious targets of the EU’s Green Deal.