The objective of this study is to examine validation of Grid Reconstruction Method, which is developed to simulate drying/wetting in complex natural rivers with wetting and drying domain areas.To verify application of the developed model, the model was applied to natural rivers with wetting and drying domain areas such as Han river and Nakdong river. The simulation results have shown good agreements with observed data and the results for the developed model were more accurate and improved stability of numerical computation than those of RMA-2 model. If the analysis of contaminant advection-diffusion and sediment transport are performed with the study results, the results can be effectively applied to river flow analysis and ecological hydraulics.