Progress has been made on improving Europe’s water quality. Nevertheless, there is much scepticism as to whether the goals of the European Water Framework Directive will be realised by 2027. Addressing diffuse agricultural sources of pollution remains a persistent problem. The Special Issue “Water Quality and Agricultural Diffuse Pollution in Light of the EU Water Framework Directive” aims to advance the understanding of the different governance arrangements European Member States developed to address this problem. The contributions in this Special Issue focus on governance arrangements in Denmark, England, Flanders/Belgium, Germany, Ireland, Poland, The Netherlands, Norway and Scotland. The contributions address three themes. First, the contributions signal serious concerns with policy integration across policy domains. Second, it appears to be tough to prioritise source-based measures over effect-based measures of all sorts despite the principles embedded in the Directive. Third, scientific knowledge is an important ally for water interests, yet politicisation in power struggles looms. The contributions in the Special Issue offer reflections on the open, participatory, experimentalist governance that the WFD exemplifies. While most authors agree that this path is attractive and appropriate in some respects, questions can be raised as to whether it also avoids confrontations and hampers the effectiveness of policies.