The Brahmaputra in India is a paradox; it has been a source of apprehension, jubilation, prosperity, aspiration and misery in different times among different cultures. Flood control in the basin has been part of two different debates within their respective epistemic boundaries. On one hand it is argued, using the ‘dynamic geomorphology’ framework, as a reaction of a new polity to a crisis following the 1950 earthquake with its positive feedback to flood problem gaining attention from late 90s. While on the other hand, the ‘political economy’ framework explains it, as a legacy of an institutional practice to control the river for serving elitist goals. The present study of the social-ecological regime shift, from a prosperous paddy cultivated agro-ecosystem to sediment deposited waste land, in north bank of Upper Brahmaputra Valley, unravels the complex relations between narratives of the problem and purposeful action under the influence of wider discourses and social learning. There has been a continuation of engineering solutions without deeper understanding of their influence on social dynamics, typifications of community behavior with an ignorance of cultural legacies, and lack of prioritization of adaptation needs in the novel social-ecological condition. The conceptual frameworks explaining nuances of flood control in the basin context have also been feeding into distinct discourses influencing policy response and praxis in the problem situation of Upper Brahmaputra Valley. While the discontented resource using community, motivated by actors influenced by identity and space politics, mobilized towards political autonomy. Such influences of opposing discourses in the context may reinforce the narrative of trust gap between the Indian polity and its North East Region. However a latent capacity of flexibility exists within the community in the problem situation and evidences of a capacity for self-organization was observed in this study. The study finally identifies the need of trans-disciplinary research for seeking desirable and feasible solutions in Brahmaputra basin. It also stresses on the need of integrated approaches in ongoing capacity development programs in India under climate change discourse as a mean to enrich such programs and also facilitate credibility and legitimacy of policy interventions. It further argues for inclusion of autonomous councils in Assam for disaster management planning through enabling them as bridging organizations.