Moving towards sustainable ecosystem governance practices is potentially a complex and time consuming endeavour. The RISKGOV project identified three main governance challenges linked to implementing an ecosystem approach to management in the medium to long term time span (i.e. years to decades), that, if adequately addressed by actors and stakeholders, could help improve the governance of environmental problems and risks in the Baltic Sea ecosystem. Firstly, fostering a move towards reflexive and adaptive governance structures and processes by improving regulatory coordination, cross sector collaboration and forming spaces for interaction and dialogue. Secondly, strengthening the regional and ecosystem basis of knowledge generation and management is needed, including integration of various forms of scientific knowledge, stakeholder input, and increased attention to interdependencies among environmental problems and risks to better address uncertainties and disagreements. Thirdly, to develop a more integrated system of stakeholder input and communication, e.g. in the form of a “regional marine advisory council”, to face issues of inclusiveness, create a common concern for the Baltic ecosystem, improve the motivation and capacity, and improve coordination across scales and sectors.