Hydro-morphological modeling of large braided rivers such as the Jamuna presents major challenges due to the dynamic nature of flow resistance. Traditional approaches typically adopt a single Manning’s or Chezy’s coefficient for the entire domain, but this oversimplification often leads to significant deviations between simulated and observed conditions. Alluvial resistance formulations provide an improvement by linking roughness with local flow depth; however, these remain insufficient to reproduce the strong seasonal variability observed in river hydraulics and morphology. In this study, a 30 km hydro-morphological model of the Jamuna River was developed, extending from 20 km upstream of the Jamuna Bridge to Char Pauli, 10 km downstream. To better represent the temporal variability of resistance, a novel method was applied by establishing a relationship between the alluvial resistance parameter “a” and observed water levels at Sirajganj. A time-varying function for resistance was derived and incorporated into the model. Simulation results demonstrate that this approach significantly improves the agreement with observed water levels at East and West Guide Bund of the Jamuna Bridge, while also yielding good correspondence with morphological platform adjustments and cross-sectional changes. The findings highlight that incorporating time-varying alluvial resistance offers a more realistic representation of seasonal hydro-morphological dynamics, thereby enhancing the predictive capability of large river models. This method provides a promising step toward robust modeling frameworks for braided rivers under varying flow regimes.