Two main sources of data, meteorological data and land surface characteristics, are essential to effectively run a distributed rainfall-runoff model. The specification and averaging of the land surface characteristics in a suitable way is crucial to obtaining accurate runoff output. Recent advances in remote sensing techniques are often being used to derive better representations of these land surface characteristics. Due to the mismatch in scale between digital land cover maps and numerical grid sizes, issues related to upscaling or downscaling occur regularly. A specific method is typically selected to average and represent the land surface characteristics. This paper examines the amount of flooding by applying the FLO-2D routing model, where vegetation heterogeneity is manipulated using the Manning’s roughness coefficient. Three different upscaling methods, arithmetic, dominant, and aggregation, were tested. To investigate further, the rainfall-runoff model with FLO-2D was facilitated in Yongdam catchment and heavy rainfall events during wet season were selected. The results show aggregation method provides better results, in terms of the amount of peak flow and the relative time taken to achieve it. These rwsults suggest that the aggregation method, which is a reasonably realistic description of area-averaged vegetation nature and characteristics, is more likely to occur in reality.