AbstractChanges in rainfall patterns due to climate change may accelerate the runoff of sulfate (SO42−), which is anthropogenically emitted and deposited as an air pollutant, cycled in forest ecosystems, and partly accumulated in forest soils. A forested catchment on the Sea of Japan side in central Japan is significantly affected by transboundary air pollution from the Asian continent due to northwesterly seasonal winds in winter. In this study, intensive 24‐h observations were conducted every hour eight times from 2019 to 2020 to clarify changes in stream water quality and runoff processes during rainfall events. The pH, electrical conductivity, and SO42− concentration in stream water decreased with increasing hourly average discharge rate (L sec−1). The SO42− concentration was negatively correlated with discharge rate. Hydrograph separations using the water isotopic parameter (deuterium excess, d‐excess = δ2H – 8 × δ18O) showed that most of the stream flow during the rain events was derived from pre‐storm water. A significant negative correlation between the d‐excess and stream water discharge was found for all six events where the water isotope analysis was applied. However, the S isotope ratio (δ34S) in stream water was not correlated with discharge rate during rainfall events and was obviously different (>1.5‰) from rainwater δ34S in the same month. This suggests that rainwater SO42− during rainfall events did not directly flow to the stream but was retained in the forest ecosystem. The isotopically well homogenized internal SO42− appeared to be mainly released into the stream during rainfall events. Future climate change may further accelerate SO42− runoff from forest catchments and disrupt material cycles in the ecosystem if warming causes more intense rainfall.