To evaluate temporal variations in nitrogen wet deposition across Japan during 1989–2008, we analyzed results of a chemical transport model (the Models-3 Community Multiscale Air Quality) and observational data. The model successfully reproduced the general patterns of spatial and temporal variations of observed NO3− wet deposition rates. Wet deposition rates of NO3− across Japan increased during 1989–2008, with rates of increase of 2–5%/yr. Sensitivity simulations indicated that the increase of NO3− wet deposition rates was mostly (61%–94%) explained by the increased emissions of atmospheric pollutants in China. Contributions of China's emissions increased from 29%–35% during 1989–1993 to 43%–61% during 2004–2008, suggesting that transboundary pollution had a large impact on NO3− wet deposition in Japan. The contribution of observed NO3− to total nitrogen wet deposition (i.e., NO3− + NH4+) increased in southwestern Japan, and currently, NO3− and NH4+ make similar contributions to nitrogen wet deposition across Japan. Interannual variation of NO3− wet deposition was further evaluated using a meteorological index, area-weighted surface pressure anomaly (ASPA). When ASPA was negative, air masses from the Asian continent were more directly transported to Japan, and NO3− concentrations across Japan became high. Thus, anomalies of NO3− concentrations were negatively correlated with ASPA. Anomalies of NO3− wet deposition rates, however, showed a weak positive correlation with ASPA, reflecting a positive correlation between anomalies in precipitation rates and ASPA. This result strongly suggests that precipitation patterns have a large impact on the interannual variation of NO3− wet deposition across Japan.