This paper analyses how specific institutional barriers and drivers affect the success of agri-environmental governance and policy innovations in four case study catchments in Germany, Latvia, Poland and Sweden. Possible adaptations of institutional settings are explored, aiming at increased effectiveness of policies and governance in delivering multiple ecosystem benefits along with reduced nutrient emissions and flood management. Factors of success synthesized from existing examples of innovative policy instruments in the EU and further afield are used to identify barriers and opportunities for the implementation of policy innovations in different institutional settings across the Baltic Sea Region (BSR). Key factors of success include close and trusting cooperation in scheme development, utilization of intermediaries in trust building, an active role of civil society and private sector, spatial targeting and coordination of measures, and result-based and long-term approaches. It is concluded that the effectiveness of measures can be increased by (i) adopting a less prescriptive approach to implementation, (ii) strengthening bottom-up participatory stakeholder learning processes, (iii) fostering cross-sectoral planning and funding initiatives, (iv) creating incentives for local collaborative actions, (v) developing cooperative nutrient management initiatives in the BSR and (vi) developing a systematic and coordinated approach to pilot-testing of new concepts and measures.