A conventional 2D numerical model is improved by incorporating three submodels to consider different effects of secondary flow and a module for cohesive sediment transport. The model is applied to a meandering reach of Yangtze River to investigate secondary flow effects on cohesive sediment deposition, and a preferable submodel is selected based on the flow simulation results. Sediment simulation results indicate that the improved model predictions are in better agreement with the measurements in planar distribution of deposition as the increased sediment deposits caused by secondary current on the convex bank have been well predicted. Secondary flow effects on predicted amount of deposition become more obvious during the period when the sediment load is low and velocity redistribution induced by the bed topography is evident. Such effects vary with the settling velocity and critical shear stress for deposition of cohesive sediment. The bed topography effects can be reflected by the secondary flow submodels.