To examine the cause of isotopic difference among gross rainfall, throughfall and stemflow, water sampling with high temporal resolution was conducted in a Japanese cedar forest during a typhoon event. In this event, δ¹⁸O variation of throughfall was similar to that of gross rainfall except for the beginning of the rainfall event. However, isotopic fluctuations of stemflow differed from those of gross rainfall and throughfall throughout the event, although the temporal trend of stemflow volume was similar to that of gross rainfall and throughfall volumes. Comparisons between the observed δ¹⁸O of stemflow and that estimated by a model simulation suggests that isotopic difference between stemflow and gross rainfall or throughfall is caused principally by mixing of waters within canopy and stem storage along their flow paths with secondary effects of evaporation and isotopic exchange with ambient water vapor.