Governing marine environments is a highly complex and challenging enterprise. This applies particularly to the heavily exploited Baltic Sea for which despite extensive governance arrangements and a substantial scientific knowledge base, it is unlikely that the policy objective of ‘good environmental status’ is reached. Based on a review of governance arrangements linked to five large-scale environmental issues (eutrophication, overfishing, invasive alien species, chemical pollution and oil spills from shipping), this chapter aims to identify pathways and concrete ideas for institutional reform that may improve goal fulfilment. The results show that governance challenges differ substantially between environmental issues, implying a need for case-specific management reforms. For example, coping with extreme uncertainty is a key challenge in the chemical pollution case, whereas it seems more pertinent in the eutrophication case to address the complexity of nutrient pollution sources by adapting objectives and measures amongst sectoral policies to be in line with environmental ones. Furthermore, cross-case comparisons reveal a set of common vital functions (i.e. coordination, integration, interdisciplinarity, precaution, deliberation, communication and adaptability) that are needed in order to facilitate effective and efficient environmental governance in the long term. To promote these functions in Baltic Sea environmental governance, the chapter suggests pathways and institutional reforms aimed at improving multilevel and multisectoral integration, science-policy interactions and stakeholder participation. To further develop these ideas, it is proposed amongst other things that priority is given to setting up an international ‘Baltic Sea Policy Review Mechanism’, formed by cross-body and cross-stakeholder participation.