Flood and riverbank erosion management in the Brahmaputra River basin (BRB) has traditionally relied on structural engineering interventions. However, there is growing evidence of their ineffectiveness and the social-ecological concerns they raise, including emergent systemic risks. This paper presents a social-ecological systems approach, offering a model that acts as a boundary object to integrate knowledge, foster stakeholder collaboration to tackle community vulnerability, and facilitate policy experimentation—key elements for advancing adaptive management. Employing systems thinking and system dynamics-based modelling can bridge the divide between science and policy, especially in areas characterized by data limitations and uncertainties like the BRB. This study adopts a nested approach encompassing three scales: macro (basin-level hydro-geomorphology), meso (flood control policies and infrastructure at administrative levels), and micro (village-level socio-economic conditions). The constructed boundary object promotes cross-scale learning and policy experimentation. Model scenarios of policy alternatives demonstrate that an integrated strategy—leveraging land covered with coarse sediment, innovating land use, and redesigning floodplains—significantly enhances effective land use and minimizes embankment failures. The findings emphasize the reinforcing dynamics between embankment degradation and community protests, highlight the limitations of compensation mechanisms, and reveal the erosion of adaptive capacity under the current control-based policy regime. A crucial insight from this study is that flood management strategies must evolve continually, reflecting scientific advancements, assessing policy impacts, and addressing local adaptation needs. Furthermore, a greater focus on riparian land use within development strategies is essential. The model scenarios advocate transitioning from traditional flood control to a landscape design harmonizing cropping practices and floodplain development with river morphology dynamics. While rooted in the Indian BRB context, the modelling framework provides a basis for adaptive water governance in other sediment-rich, politically sensitive, and hydrologically dynamic transboundary basins.