The Morigaon district, strategically located within the central Brahmaputra Valley of Assam, represents a paramount case study for analyzing extreme fluvial instability. This research critically evaluates the complex interplay between the region’s unique physiography—comprising extensive low-lying floodplains and a dense network of beels (tectonic wetlands)—and the persistent threat of catastrophic inundation. Situated in the immediate proximity of the Brahmaputra River, the district faces perennial geomorphological volatility, which is significantly amplified by the river’s erratic discharge patterns and heavy sediment load. By synthesizing multi-temporal geospatial analysis, advanced hydrological modeling, and comprehensive historical flood records, this investigation delineates how anthropogenic land-use transitions exert additive pressure on inherent topographical vulnerabilities. The research finds that rapid urban expansion and the encroachment upon buffer zones have severely compromised natural drainage channels, thereby impeding discharge efficiency. Furthermore, the analysis identifies that profound drainage congestion, coupled with the hydraulic phenomenon of backwater effects, serves as the primary driver for prolonged stagnant inundation. These factors, when exacerbated by climate-induced rainfall variability, transform minor seasonal pulses into large-scale humanitarian crises. Consequently, this paper argues that the hydro-ecological resilience of Morigaon is fundamentally tethered to the mitigation of upstream morphological modifications. By elucidating these mechanisms, the study provides a robust framework for evidence-based policy formulation, emphasizing the necessity of integrated flood management strategies to safeguard vulnerable populations from the intensifying hydro-meteorological hazards characteristic of the Brahmaputra riparian landscape.