The natural abundance of nitrogen and oxygen isotopes in NO₃^– is useful for identifying the source of nitrate in streamwater, because δ¹⁸O values in NO₃^– are typically higher with atmospheric deposition than in NO₃^– formed by microbial nitrification. To evaluate the source dynamics of NO₃^– during storms, we monitored the δ¹⁸O and δ¹⁵N of NO₃^– in streamwater and the spatial variation (rainfall, soil water, and groundwater) of isotopes in forested watersheds in Japan. The mean δ¹⁸O was higher for rain (59‰) than for soil water (–1.2‰) and groundwater (9.4‰). The mean δ¹⁵N of soil water (–2.3‰) was lower than for groundwater (1.4‰). The streamwater δ¹⁸O increased just after the onset of rainfall, and then both δ¹⁸O and δ¹⁵N decreased with discharge and were lowest at the peak flow. The changes in both the δ¹⁸O of streamwater NO₃^– during storms indicated that the atmospheric NO₃^– contribution to the stream increased (2~8%) at the onset of rainfall due to direct channel rainfall input, and then the contribution of nitrified NO₃^– increased at high flow. Moreover, the decreases in δ¹⁸O and δ¹⁵N at peak flow to below the baseline levels implied that groundwater denitrificated NO₃^– as an additional end-member for NO₃^– because the δ¹⁵N and δ¹⁸O values of soil water were clearly lower than those of groundwater.