Changes in atmospheric deposition have long-term effects on forest ecosystems and streamwater chemistry. Atmospheric deposition changes with forest disturbance. Although many studies have investigated the effects of air pollution, the effects of the long-term changes in atmospheric deposition induced by canopy alteration on streamwater chemistry have not been investigated sufficiently. This study evaluated the changes in atmospheric deposition, separated into dry deposition and canopy leaching components, in a regrowth forest and the resultant effects on streamwater chemistry. The chemical budgets of Cl−, NO3−, SO42−, Na+, NH4+, K+, Mg2+, and Ca2+ were investigated in regrowth and mature Japanese cedar forests from 1998 to 2015 in paired catchments in the Fukuroyamasawa Watershed, central Japan. After forest cutting in 1999, the total deposition of all ions to forest soil decreased; the Cl−, NO3−, SO42−, Na+, and Mg2+ were significantly lower in the regrowth forest than in the mature forest at 14– 15 years due to lower dry deposition, although the canopy had closed. In comparison, the total deposition of K+ and Ca2+ increased with canopy regrowth and was higher in the 15-year-old regrowth forest than the mature forest due to increased canopy leaching. Stream outputs of NO3−, SO42−, K+, Mg2+, and Ca2+ were not affected by the changes in atmospheric deposition, but the stream outputs of Cl− and Na+ decreased gradually for 5–10 years and remained lower (70–90%) at 15 years than those in the mature forest, which is consistent with the lower dry deposition input. The results of this study suggest that not only the canopy alteration but also the edge effects of taller trees of adjacent catchments influence the dry deposition input change, and the long-term streamwater chemistry change in Japanese cedar regrowth forest.