Canada’s Mackenzie River Basin (MRB) is one of the largest relatively pristine ecosystems in North America. Home to indigenous peoples for millennia, the basin is also the site of increasing resource development, notably fossil fuels, hydroelectric power resources, minerals, and forests. Three provinces, three territories, the Canadian federal government, and Aboriginal governments (under Canada’s constitution, indigenous peoples are referred to as “Aboriginal”) have responsibilities for water in the basin, making the MRB a significant setting for cooperative, transboundary water governance. A framework agreement that provides broad principles and establishes a river basin organization, the MRB Board, has been in place since 1997. However, significant progress on completing bilateral agreements under the 1997 Mackenzie River Basin Transboundary Waters Master Agreement has only occurred since 2010. We considered the performance of the MRB Board relative to its coordination function, accountability, legitimacy, and overall environmental effectiveness. This allowed us to address the extent to which governance based on river basin boundaries, a bioregional approach, could contribute to adaptive governance in the MRB. Insights were based on analysis of key documents and published studies, 19 key informant interviews, and additional interactions with parties involved in basin governance. We found that the MRB Board’s composition, its lack of funding and staffing, and the unwillingness of the governments to empower it to play the role envisioned in the Master Agreement mean that as constituted, the board faces challenges in implementing a basin-wide vision. This appears to be by design. The MRB governments have instead used the bilateral agreements under the Master Agreement as the primary mechanism through which transboundary governance will occur. A commitment to coordinating across the bilateral agreements is needed to enhance the prospects for adaptive governance in the basin.