Since the 1980s, Japan has been affected by transboundary air pollution from the Asian continent due to northwesterly seasonal winds in the winter. However, after peaks in 2006 and 2011/2012, sulfur dioxide (SO2) and nitrogen oxide (NOx) emissions began decreasing, respectively. To assess the biogeochemical response of forest ecosystems to the changing atmospheric deposition, flux observations of rainfall outside forest canopies (RF), throughfall and stemflow (TF + SF), and stream water (SW) chemistry were conducted in a Japanese cedar plantation in Kajikawa (KJK) on the Sea of Japan coast in central Japan. Fluxes of S and N by RF and TF + SF at KJK significantly decreased during the observation period (2002–2018). The non-sea salt sulfate (SO42−) flux by TF + SF peaked in 2006/2007 and decreased thereafter, which likely reflected the S emission trends. Accordingly, SO42− concentrations in SW at KJK decreased with increasing alkalinity. Similar decreases in SO42− concentrations beginning in 2006, 2007, and 2008 were observed at eight monitoring lakes in Japan. Thus, the SW chemistry at KJK and possibly that of Japanese lakes were sensitive to atmospheric S deposition reductions. However, as of late, the net S export at KJK has been increasing, exhibiting budget discrepancies in 2014/2015 and 2017/2018. Sulfur isotopic analysis suggested that the S deposited from the atmosphere was retained/cycled in the forest before it was gradually discharged into SW. Thus, a slightly weakened reaction of the output due to the internal cycle and residual effects of previous years may have caused the S budget discrepancies. The nitrate (NO3−) concentration in the SW at KJK has also been continuously increasing. N deposition and other factors, such as the maturation of the planted trees, may play an important role in NO3− leaching in plantations.