Submarine groundwater discharge (SGD) is considered to be the sustainable water resource, and also the important factor of the water cycle. Methods to evaluate the quantity of SGD can be divided into mathematical analysis and in-site survey, and in the case of wide area study, like the Japanese Islands, the macro evaluation by perennial water balance budget is suitable for the initial study. However, the evaluation of runoff using the River Discharge Year Book of Japan has several problems such as the uncertain accuracy of measurement, the existence of an inconsiderable area between the lowest flow gauge and river mouth, and unavailability of river flows in basins except for Class A rivers. In this paper, we calculated perennial water balances of 10 years in 204 regions on the Japanese Islands. It was the first time to make a distribution map of SGD in Japan. As there existed 144 regions where the flow data were insuff icient, the runoff in each area was estimated by the multiple linear regression analysis between the river flows and the recharges, divided by the geology of the basins where it was judged to be similar geologically by cluster analysis using area ratios of 43 geological classifications.