Hydropower development is occurring at a rapid, though controversial, pace in the Mekong. We highlight the role of scientific assessment in shaping the Mekong hydropower debate, taking the strategic environmental assessment of the twelve planned mainstream dams as a case study. While environmental impact assessments are designed as science-based decision-making tools, they have often been criticized in practice as a political means to justify already made development decisions. In this case we demonstrate how the Mekong River Commission, operating in a constrained political environment, has instead used environmental impact assessment as a way of providing political space and opening the discussion on dams to a wider public. The main argument of this paper is that scientific assessment can be politically maneuvered to shape governance alliances at both national and transboundary levels, and to a certain extent democratize decision-making processes.