This research proposes a procedure to conduct climate change impact assessment on flood risks aimed at having smooth risk communication with river managers and citizens. The large ensemble database “d4PDF” was applied to flood runoff analysis model used to develop the flood prevention plan by the river manager. This method expresses the climate change impact in expressions that are easy for river managers to understand by applying the climate model product into the flood runoff model used in the official flood prevention planning. The proposed method was verified in the Nagara River basin, which has a basin population of about 830,000 in mainly the downstream area and no large dam in the upstream of main stream. The hydrological observation data were utilized for verification of the flood runoff model calculation results. The results of the flood runoff analysis by the annual maximum rainfall event extracted from d4PDF NHRCM 20 well represented the distribution of annual maximum flood observations. Although the influence of the spatial resolution of the climate model is still unclear, the assessment procedure presented by this research has versatility applicable to other river basins.