In order to understand effects of acid rain on nitrogen (N) balance of soil-vegetable systems, field experiments were carried out at three sites in Chongqing for one year to monitor N dynamics in soils and vegetables, atmospheric N deposition from rainfall, and N leaching loss. These sites were subjected to acid rain to a varying extent, i.e. heavily polluted area (HPA), lightly polluted area (LPA), and control area (CK). Under the condition of similar field management, acid rain affected normal growth of vegetables and hence N balance in the soil-vegetable systems at the three sites. The N I/O ratio (input/output) was 1.27 and 1.19 in HPA and LPA, respectively, while it was 1.08 (nearly reaching the balance) in CK. The N input from rainfall in HPA was about 3 to 4 times higher than that in LPA and CK. However, the biomass of vegetables in HPA was decreased by up to 40%, when compared with that in CK, thus leading to a significant decrease in N output through crop harvesting. As a result, a large proportion of N was sequestrated in the soils subjected to acid rain, which subsequently enhanced nitrate leaching posing a risk to water environment.