Recent development of X-Band Radar system in Japan is expected to provide more accurate and higher resolution rainfall estimates, which may lead to improve flood forecasting through rainfall-runoff predictions. However, the effect of enhancement of rainfall observation has not been well investigated quantitatively, mainly due to the luck of systematic evaluation methods. This paper presents a statistical model to analyze uncertainty structures in radar rainfall estimates and stochastic rainfall generator to represent the uncertainty structures including variance and spatial correlation. The proposed method is applied to C-band and X-band radar data in Kinki region, followed by runoff analysis in Hiyoshi dam reservoir catchment. Based on the simulation results, the uncertainty propagation characteristics are described in radar rainfall fields to runoff.