In the safety assessment for a geological disposal of radioactive waste, it is important to establish validation methods for deep groundwater flow system to estimate radionuclide migration to human environment through groundwater flow. It is necessary to validate the groundwater flow property and flow boundary, as multi-groundwater systems including the different groundwater origins are possible to exist at deep underground. This study discussed the method which estimates groundwater mixing condition and groundwater flow process using three principal component analysis(three-dimensional PCA) to groundwater chemistry and isotopic compositions, together with data of groundwater age and trace element in case of Horonobe area where a lot of water chemistry were measured. The results of three-dimensional PCA show that hydrological system can be divided into two areas: three deep groundwater mixing area at depths greater than 200 to 400m, mixing area of deep groundwater and surface water at depths less than 200 to 400m. The residence time of deep groundwater estimated by chlorine isotopic method shows over several hundred thousand years to 1 million years ago. Deep groundwater is suggested to be discharged at surface through Omagari Fault based on the concentrations of trace dissolved constituents. (author)