This study investigates if and how present institutional structures and interactions between scientific assessment and environmental management are sufficient for implementing the ecosystem approach to management (EAM) in the case of Baltic Sea eutrophication. Concerning governance structures, a number of institutions and policies focus on issues relating to eutrophication. In many cases, the policies are mutually supportive rather than contradictory, as seen, for example, in the case of the mutually supportive BSAP and MSFD. The opposite is true, however, when it comes to the linkages with some other policy areas, in particular regarding agricultural policy, where the EU CAP subsidises intensive agriculture with at best minor consideration of environmental objectives, thereby undermining EAM. Enhanced policy coherence and stricter policies on concrete measures to combat eutrophication seem well needed in order to reach stated environmental objectives.  When it comes to assessment-management interactions, the science- policy interface has worked well in periods, but the more specific that policies have become, for example, in the BSAP case, the more question marks have been raised about science by affected stakeholders. At present, outright controversies exist, and EAM is far from realised in eutrophication policy in the Baltic Sea region. Besides coping with remaining uncertainties by improving the knowledge on problems and solutions– not least in terms of the socio-economic impacts of eutrophication – it may therefore be valuable to develop venues for improved stakeholder participation.