Interpretation on the mechanism involved in the "Sun-Climate-Water" system provides scientific guidance on the water resource management. Using correlation analysis, principal component analysis and wavelet analysis approaches, the combined influences of solar activity and El Niño Southern Oscillation (ENSO) on precipitation, river flow and groundwater levels in Yoshino River basin, Japan were investigated. And the results indicate the following:① Significant influences of solar activity and ENSO on the hydrological processes mainly concentrate in the periodicities of 11 and 2-7 a, respectively. ② The solar-modulated ENSO plays a critical linkage between solar activity and precipitation/surface water resource. However, this linkage doesn't act in the Sun-ENSO-aquifer system. ③ Both direct and indirect influences of solar activity on hydrological processes in the study area are obtained. The direct influence might act via the function of non-ENSO climate indices, while the indirect influence might act via the process of "ENSO-Western Pacific Subtropical High-East Asian Circulation-Water Movement".