A GIS-based paddy inundation simulation system which is capable of simulating temporal and spatial inundation processes was established and applied in this paper. The system is composed of HEC-GeoHMS, and HEC-GeoRAS modules which interface the GIS and flood runoff models, and HEC-HMS, and HEC-RAS models which estimate the flood runoff. It was used to simulate storm runoff and inundation for a small rural watershed, the Baran HP#7, which is 10.69 $km^2$ in size. The simulated peak runoff, time to peak, and total direct runoff for eight storms were compared with the observed data. The results showed that the coefficient of determination ($R^2$) for the observed peak runoff was 0.99 and an error, RMSE, 11.862 $m^3$/s for calibration stages. In the model verification, $R^2$ was 0.99 and RMSE 1.296 $m^3$/s. Paddy inundation for each paddy growing stages in study watershed were estimated using verified inundation simulation system when probability rainfall was applied.