There is no lack of public policy and research focus on the ecologically fragile and conflict-prone river basins of South Asia. Although there are success stories in different levels of governance in these river basins, the lack of sustainability in policy and practice is a concern. This chapter uses the conceptual metaphor of institutional “fit,” as used in sustainability science, to illustrate the mismatches between public policy, problem framing, and social-ecological dynamics in the Brahmaputra River basin of the Ganga-Brahmaputra-Meghna interlinked basin. The chapter argues that there is a need for capacity among the South Asian water resource management community of practice for systemic understanding of the interlinkages between river basin ecosystems; management sectors for provisioning water, energy and food; culture; and human aspirations. It ends with a proposition that current practices of dialogue (e.g., Track III dialogue processes for transboundary river basin management), when aided with transdisciplinary research design to integrate different kinds of logic and stakeholder experiences, can offer opportunities for shared understanding, learning, and co-design of solutions and management pathways.