This article focuses on the governing system of the mitigation of eutrophication in the Baltic Sea. Policies and measures of the Baltic Sea coastal countries, the macro--regional (HELCOM) level, and the level of the European Union are described and governance challenges explicated. We found that the main challenges at different governance levels include: differences between coastal countries in terms of environmental conditions including environmental awareness, overlaps of policies between different levels, the lack of adequate spatial and temporal specification of policies, and the lack of policy integration. To help to meet these challenges, we suggest closer involvement of stakeholders and the public, the improvement of the interplay of institutions, and the introduction of a "primus motor" for the governance of the mitigation of eutrophication in the Baltic Sea.