Over-browsing of forest understory vegetation by sika deer (Cervus nippon ) has been a serious problem in Japan. Many studies have reported the direct effects of deer over-browsing such as abundance and diversity, however indirect effects such as water quality are still limited. In this study, we compared patterns of stream water NO₃^- discharge during rainfall events between a deer-excluded watershed and an adjacent control watershed in Ashiu Research Forest to elucidate the indirect effects of deer over-browsing on stream water. Although NO₃^- concentrations were not different between two watersheds at the start of deer exclusion, those in the deer-excluded watershed were significantly lower than those in the control watershed after 5 years of deer exclusion. We observed 7 rainfall events from September 2010 to September 2011, and NO₃^- concentrations during all these events were higher in the control watershed, as well as those at baseflow condition. Change patterns of the NO₃^- concentration difference between two watersheds during rainfall event had seasonal variations; we found a positive correlation during growing season and a negative correlation during deciduous season. These results suggest that understory has a significant role to control the discharge pattern of NO₃^- even during rainfall events.