A long-term declining trend of pH values has been observed for several rivers in areas of central Japan that are geologically dominated by acidic rocks such as granite, rhyolite, or chert. We monitored the seasonal variation in water chemistry in one of these rivers: the Araya River in Niigata Prefecture. During the 4-year survey period, we observed temporary acidification during the rainy and snowmelt seasons when the river flow rate abruptly increased. In the rainy season, the decrease in pH may be attributable to the dilution of almost all ions and increased leaching of NO3 (-) from the catchment. In the snowmelt season, decreases in pH were found to be associated with peaks of SO4 (2-), where the SO4 (2-) was possibly derived from that accumulated in the snowpack. The data pertaining to the river showed that it had a sensitive response to meteorological events and was likely to be acid sensitive. The estimated mass balance of the river showed that the SO4 (2-) output exceeded the corresponding input to the Araya River catchment. Mobilization of internal sulfur accumulated in forest ecosystems might have contributed to the observed long-term acidification of this acid-sensitive river.