Tackling diffuse pollution from agriculture is a key challenge for governments seeking to implement the European Union's Water Framework Directive (WFD). In the research literature, how best to integrate and align effective measures for tackling diffuse pollution, within the context of the EU's multilevel governance structure, remains an open question. This paper focuses on the first and second implementation cycles of the WFD to explore how national governance arrangements either facilitated or hindered the adoption of effective policies, especially with regards to the delivery of agricultural and water policies on the ground. It draws on data collected through systematic document analysis and interviews with key experts, policymakers and interest groups, and presents a comparative analysis of two case studies: England and Scotland. The case studies show that Scotland's joined-up governance structure, which enabled policymakers and interest groups to work together and to build trust and cooperation, facilitated the adoption of stricter measures for tackling diffuse pollution. In contrast, in England institutional fragmentation prevented a meaningful engagement of all parties and acted as a barrier. The analysis unpacks the design of policy mixes and the conditions that allow national governments to pursue more holistic and integrated governance approaches to overcome opposition from interest groups and gain their support.