This study investigates the contribution ratios of different groundwater recharge sources and influence of a dual monsoon system in Kofu basin, central Japan, through the hydrogen and oxygen isotopic analysis of precipitation, river water, and groundwater. The study is focused on the area of the Kamanashigawa and Midaigawa alluvial fans, which are formed by two main rivers. Precipitation isotopic content exhibits significant seasonal variability. Also, river water presents d-excess values higher than annual precipitation at plain areas (9 and 10‰), suggesting that two different air-masses contribute to precipitation, corresponding to the monsoon and pre-monsoon periods. The results of this study allow estimation of relative contributions of different sources to groundwater and influence of a dual monsoon system. The mass-balance analysis of the δ18O to identify the groundwater source indicates the river water contributes 38–100% of the recharge, while precipitation contributes 29–62% in Kamanashigawa alluvial fan. In the case of Midaigawa alluvial fan, river water contributes 77–99% in the northern part; in the southern side, 30–93% of contribution comes from precipitation. The mass-balance analysis of the d-excess indicates pre-monsoon precipitation contributes 46–68% and 39–65% to groundwater of the Kamanashigawa and Midaigawa alluvial fans, respectively.