222Rn (radon) and 220Rn(thoron) are remarked as useful geochemical tracers for analyzing surface water and groundwater interaction. We applied the methodology of Dimova et al. (2009) to thoron analysis of groundwater in Kurobe, Toyama pref. and Saijo, Ehime pref., Japan. It seemed that radon equilibration in water ? air exchange system spent about 15 min, On the other hand, thoron equilibration was quicker than that of radon. The radon concentration was one order higher in granitic rock areas than that in alluvial deposit area, on the other hand the thoron concentration was not so different. It was suggested that thoron is a good tracer for detecting groundwater discharge in surface water.