Changes in rainfall patterns due to climate change may accelerate the runoff of sulfur (S) and nitrogen (N), which are anthropogenically emitted as air pollutants and deposited and accumulated in forest soils. In this study, intensive observations were conducted in a forested catchment on the Sea of Japan side to clarify changes in stream water quality and runoff processes during rainfall events. The pH, electrical conductivity, and sulfate (SO ₄ ²⁻) concentration in the stream water decreased with increasing flow rate, whereas the nitrate (NO ₃ ⁻) concentration increased. The SO ₄ ²⁻ concentration was negatively correlated with the flow rate, and the NO ₃ ⁻ concentration was positively correlated with the cumulative precipitation amount of each event and remarkably increased when it exceeded 10 mm. Hydrograph separations using the water isotopic parameter (deuterium excess, d-excess = δ ²H – 8 × δ ¹⁸O) showed that most of the stream flow during the rain events was derived from pre-storm water, whereas the portion derived from rainwater increased at rainfall intensities stronger than 10 mm h ⁻¹. The S isotope ratio (δ ³⁴S) in the stream water fluctuated minimally compared to the d-excess value during rainfall events, suggesting relatively minor contributions of precipitation SO ₄ ²⁻ to stream water via direct inflow. The SO ₄ ²⁻ well homogenized in soil layers mainly contributed to the discharge during the rainfall events. Future climate change may further accelerate S and N runoff from forest catchments and disrupt material cycles in the ecosystem if warming causes more intense rainfall.