The present study generated nationwide assessment maps for the impact of climate change on agricultural water resources throughout Japan, by using climate scenarios derived from global climate models and DWCM-AgWU, a hydrological model that incorporated irrigation water management. In addition, we analyzed the uncertainty of the assessment maps, investigating the ranges of the assessment indices in 11 climate scenarios used. For the assessment of drought discharge, we generated the assessment maps for two rice growth stages (puddling and heading) that are highly vulnerable to water shortages. The maps generated in this study provide a framework for assessing the impact of climate change on agricultural water resources in Japan and reveal the vulnerable regions to climate change. The uncertainty analysis suggested that the assessment uncertainty depended on the hydrological processes used to calculate assessment indices and on the magnitude of their natural annual variability. For a deeper understanding of the uncertainty in hydrological assessments it is necessary to investigate the impact on the assessment uncertainty of the natural variability of hydrological processes especially relating to extreme events.