Numerical modeling of sedimentation and erosion in reservoirs is an active field of reservoir research. However, simulation of bed-load transport phenomena has rarely been applied to other water bodies, in particular, the fluctuating backwater area. This is because the complex morphological processes between hydrodynamics and sediment transport are generally challenging to accurately predict. In this study, the refinement and application of a two-dimensional shallow-water and bed-load transport model to the fluctuating backwater area is described. The model employs the finite volume method of the Godunov scheme and saturated sediment transport equations. The model was verified against experimental data of a scaled physical model. It was then applied to actual reservoir operation, including reservoir storage, reservoir drawdown and continuous flood process, to predict the morphology of reservoir sedimentation and sediment transport rates and bed level changes in the fluctuating backwater area. It was found that the location and morphology of sedimentation effected by the downstream water level results in random evolution of the river bed, and bed-load sedimentation is transported from upstream to downstream with the slope of the longitudinal section of the river bed generally reduced. Moreover, the sediment is mainly deposited in the main channel and the elevation difference between the riverbank and channel decreases gradually.