Contemporary processes of environmental policymaking in general span over several territorial tiers. This also holds for the system of environmental quality standards (EQS), which are part of a complex multi-level institutional landscape, embracing both international, EU, national and sub-national level. In the end, however, the implementation of these standards is a task for national and sub-national level actors. An example of the institutional complexity of the EQS-system is the Swedish implementation of the EU water framework directive (WFD), where overarching responsibilities are allocated to regional water boards, including the formulation of EQS and programmes of measures. At the same time, new governance arrangements including stakeholder involvement are put in place, where local water councils are involved in the water governance system. However, the actual measures are supposed to be carried out or enforced by other institutions on state, regional or local levels. Thus, the regional water boards have no means to enforce their programmes if other institutions fail. This increased interdependence between different levels of government, where decision-makers and civil servants are constrained by institutions on multiple levels of governance, is addressed and theorised in the growing body of research on multi-level governance. This paper focuses on the processes of setting and implementing EQS for water on the national (Swedish) level. The study of the Swedish institutional framework for implementing the EU water framework directive through EQS will increase our understanding of the role of the national level in such multi-level governance processes. What role does the ‘environmental state’ play in such complex governance structures, and what are the consequences for policy when many different actors on different levels are involved? Is there coherence between related policies on different levels, and how does the formal structure of the policy system contribute to or inhibit policy coherence?