The literature on governance of socio-ecological systems has been growing fast during the last one or two decades. However, sound theoretical underpinnings to these systems have not been sufficiently articulated and tied to existing theory, it is argued in this working paper. To address this shortcoming, this paper aims to elaborate on how the theoretical constructs  problem structure, collective choice theory and adaptive governance can be brought together to form a coherent analytical framework for analyzing trans-boundary environmental problems in marine settings. The argument that collective action problematiques may inhibit successful adaptation to environmental change among sovereign states is fundamental to this model. Given that governments tend to prefer national coping strategies where expected national rather than joint benefits are maximized, mutually beneficial cooperation often does not evolve and regional adaptation turn out piecemeal. It is concluded that in order to improve trans-national environmental governance, a better understanding of underlying drivers and countries’ incentives to take action is a necessary prerequisite.