Numerical modeling of sedimentation and erosion in reservoirs is an active field of reservoir research. However, simulation of the 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 interacting between hydrodynamics and sediment transport are generally challenging to accurately predict. Most researchers assert that the shape of a river channel is mainly determined by the upstream water and sediment, and the physical boundary conditions of the river channel, rather than random events. 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 equilibrium sediment transport equations. The model was verified using experimental data produced by a scaled physical model, and the results indicated that the numerical model is believable. The numerical model was then applied to actual reservoir operations, including reservoir storage, reservoir drawdown, and the continuous flood process, to predict the morphology of reservoir sedimentation and sediment transport rates, and the changes in bed level in the fluctuating backwater area. It was found that the location and morphology of sedimentation affected by the downstream water level result in random evolution of the river bed, and bed-load sedimentation is moved from upstream to downstream as the slope of the longitudinal section of the river bed is reduced. Moreover, the research shows that the river channel sedimentation morphology is changed by the change water level of the downstream reach, causing the dislocation of the beach and channel and random events that will affect the river, which is of certain reference value for waterway regulation.