In Europe, marine environmental risks are governed in a complex multi-level system. The role that the marine region could or should play as a level of risk governance has attracted growing attention of late. In this context, reference has been made to the regional sea as one level at which participatory processes in the future governing of European Union’s (EU) marine environment and resources are required. The paper unfolds the particular challenges that one faces when trying to implement stakeholder and citizen participatory deliberation at marine region level. The EU Marine Strategy Framework Directive is highlighted as a key European environmental policy initiative and participatory deliberation at regional sea level is underlined as a requirement for the Directive’s successful implementation. The paper’s account of participatory deliberation is informed by perspectives of inclusive risk governance and reflexive governance. The discussion of the challenges draws on the distinction between horizontal and vertical risk governance. The paper’s main argument is that frequently encountered problems of participatory deliberation are exacerbated when deliberation is to be carried out at the regional sea level, i.e. at a large trans-boundary scale. These problems include the ‘inclusivity-effectiveness dilemma’, a fragmentation of participation efforts and a loose connection to actual decision-making.