Acidic substances, specifically sulfur (S) compounds, derived from atmospheric deposition play a major role in the acidification of forest ecosystems. This study conducted field surveys to clarify a buffering system against seasonal large S inputs in a forested catchment in central Japan that has historically suffered from transboundary air pollution. Results showed that atmospheric S fluxes significantly increased in winter due to north-westerly seasonal winds from the Asian continent; fluxes were 1.1 and 0.3 kmolc ha−1 in the cold and warm seasons, respectively, due to the large effects of sea salt and transboundary air pollution. Despite the large seasonality within atmospheric deposition, SO42– concentrations in stream water (SW) were found to be relatively stable throughout the year. Similarly, S isotopic ratios (δ34S) in rainwater showed clear seasonal variation, increasing to 12‰ in winter and decreasing to 2‰ in summer, whereas the δ34S value of SW was stable year-round at ~9‰. Flux-weighted mean δ34S values for rainfall (RF), throughfall, stemflow, and SW were similar, i.e. 8.5, 9.5, 9.0, and 9.0‰, respectively. Both the δ34S values and the SO42– concentrations in RF and soil solutions appear to converge at values of SW, suggesting that atmospheric deposition is a primary S origin in SW. The sulfur adsorption-desorption in soil appears to mainly buffer the large sulfur input and prevent sudden acidification, whereas a relatively small biological sulfur cycle was suggested by litterfall. Possible disturbances within this buffering system should be carefully monitored under a changing climate.