The change in movable beds is related to the mechanisms of sediment transport and hydrodynamics. Numerical modelling with empirical equations and the simplified momentum equation is the common means to analyze the complicated sediment transport processing in river channels. The optimization of parameters is essential to obtain the proper results. Inadequate parameters would cause errors during the simulation process and accumulate the errors with long-time simulation. The optimized parameter combination for numerical modelling, however, is rarely discussed. This study adopted the ensemble method to simulate the change in the river channel, with a single model combined with multiple parameters. The optimized parameter combinations for a given river reach are investigated. Two river basins, located in Taiwan, were used as study cases, to simulate river morphology through the SRH-2D, which was developed by the U.S. Bureau of Reclamation. The input parameters related to the sediment transport module were randomly selected within a reasonable range. The parameter sets with proper results were selected as ensemble members. The concentration of sedimentation and bathymetry elevation was used to conduct the calibration. Both study cases show that 20 ensemble members were good enough to capture the results and save simulation time. However, when the ensemble members increased to 100, there was no significant improvement, but a longer simulation time. The result showed that the peak concentration and the occurrence of time could be predicted by the ensemble size of 20. Moreover, with consideration of the bed elevation as the target, the result showed that this method could quantitatively simulate the change in bed elevation. With both cases, this study showed that the ensemble method is a suitable approach for river morphology numerical modelling. The ensemble size of 20 can effectively obtain the result and reduce the uncertainty for sediment transport simulation.