To examine the effects of pine wilt disease on SO42- dynamics in a forested ecosystem, we analyzed the soil solution, groundwater, and streamwater in the Kiryu Experimental Basin, central Japan. The NO3- concentrations in the soil surface layer showed a remarkable seasonality, with peak concentration in the fall. The SO42- concentrations in an area affected by pine wilt disease increased after NO3- concentrations peaked. The delay between maximum SO42- to NO3- concentrations may be explained by anion adsorption on variable charges in humus under low pH conditions resulting from nitrification. Concentrations of SO42- increased with groundwater depth, while the levels of NO3- tended to decrease with groundwater depth. The vertical distribution of the SO42- and NO3- concentrations in groundwater affected the seasonal changes in stream SO42- and NO3- concentrations, as groundwater levels changed. It is reasonable to assume that nitrogen dynamics and hydrological processes play important roles in the retention and discharge of SO42- from disturbed forest soil systems.