This study analyzes the flood inundation in low agricultural area caused by rainfall during typhoon periods and how flood inundation areas should be affected. GIS techniques, HEC-HMS and HEC-GeoHMS were used for flood runoff, HEC-RAS was applied in water surface elevation analysis at each cross-section. RMA2, SED2D were applied for runoff characteristics of inundation areas and river bed change and distribution of sediment. As a result, velocity distribution was analyzed 2.6 m/s-3.4 m/s in flood inundation by water level increase. In the case of bed elevation change, most sediments were deposited to the parts that adjoin bank.