In this study, the stable isotope values of oxygen and hydrogen were used to identify the seasonal contribution ratios of precipitation to groundwater recharge in the Hualien River basin of eastern Taiwan. The differences and correlations of isotopes in various water bodies were examined to evaluate the groundwater recharge sources for the Hualian River basin and the interrelations between groundwater and surface water. Proportions of recharge sources were calculated based on the results of the mass balance analysis of the isotope composition of hydrogen and oxygen in the basin. Mountain river water accounted for 83% and plain rainfall accounted for 17% of the groundwater recharge in the Huanlian River basin. Using the mean d-values, a comparison of d-values of precipitation and groundwater indicates the groundwater consists of 75.5% wet seasonal sources and 24.5% dry seasonal sources, representing a distinct seasonal variation of groundwater recharge in the study area. Comparisons between hydrogen and oxygen isotopes in rainwater showed that differences in the amount of rainfall resulted in depleted oxygen and hydrogen isotopes for precipitation in wet seasons as compared to dry seasons. The river water contained more depleted hydrogen and oxygen isotopes than was the case for precipitation, implying that the river water mainly came from the upstream catchment. In addition, the hydrogen and oxygen isotopes in the groundwater slightly deviated from the hydrogen and oxygen isotopic meteoric water line in Huanlian. Therefore, the groundwater in this basin might be a mixture of river water and precipitation, resulting in the effect of the river water recharge being greater than that of rainfall infiltration.