In this perspective article, we provide recommendations for strengthening the policy framework for protecting the Baltic Sea from agricultural nutrient pollution. The most striking weakness is the lax implementation of prescribed abatement measures, particularly concerning manure management, in most countries. Institutions of the EU should also be leveraged for achieving Baltic Sea Action Plan (BSAP) goals. In contrast to the Helsinki Convention, the European Union has economic, political and legal mandates to further implementation and compliance. Equally important is the need for strengthening of local institutions, particularly Water Boards and independent agricultural advisory services in the eastern Baltic Sea Region countries. There is also an urgent need for implementation of voluntary land-use measures where EU funding available to farmers is more broadly and effectively used by providing it on the basis of estimated abatement performance, which can be realized through modelling. The enormous potential for funding performance-based schemes, manure management infrastructure and advisory services through the EU’s Common Agricultural Policy are currently underutilized.