Abstract The Brahmaputra River Basin (BRB) in the Himalayan landscape has seen a range of issues at multiple scales related to water sharing and dams, political mobilizations related to ethnic identity and sovereignty, flood and riverbank erosion, and population displacement. Current disciplinary knowledge fails to explain persistent policy paradoxes such as the continuation of embankment breaches while the river channel may be stabilizing as well as sudden shifts in problem situations, from annual floods to landlessness. This study uses system dynamics to integrate existing knowledge of river basin hydro-geomorphology and flood protection policy in the State of Assam in India, with issues experienced by a riparian tribal community in the upstream part of the Assam Valley. Simulation analysis indicates the role of feedback relationships between local governance issues and flood control effectiveness and also illustrates a need for studies integrating the dynamics of land along with flows of water and sediment in river channels. Model testing also illustrates the importance of policy alternatives at different scales: i.e., farm-level changes to cropping pattern, integration of land use and land tenure in sub-national disaster management, and basin-scale zoning and culturally acceptable relocation of people.