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Although sulphur emissions (mainly as SO2) have been continuously decreasing over the last 20 years in most western industrialized countries, localized SO2 problems still exist in conjunction with strong local emission, meteorological, and topographical factors. In this study, the effect of supplementary installed flue gas desulphurization (FGD) units at high-capacity power plants on regional air pollution in the Carpathian Basin is investigated. The dispersion and accumulation of the SO2 air pollutant are studied with the regional three-dimensional on-line atmosphere-chemistry model REMOTE. The changes in the SO2 air pollution are investigated by parallel simulations in a case study, where the single modified parameter is the SO2 emission rate. The results show that FGD units significantly reduce the horizontal and the vertical dispersion of the emitted SO2, and its transboundary transport, too. Beside the SO2 removal efficiency, the dispersion and accumulation also depend on the seasonal weather conditions. During winter, the dispersion and accumulation are higher than in other seasons. Due to this phenomenon, higher SO2 removal efficiency is needed to guarantee similar air quality features like in the other seasons.