Spatial and temporal variation of atmospheric depositions on the permanent monitoring plots of Level II of the ICP Forest programme in Czech and Slovak forest areas was described in this paper. The atmospheric bulk deposition of sulphur, ammonium and nitrate nitrogen from the years 2000–2016 were assessed and compared with the data obtained on European plots of this programme. The temporal developments of annual depositions in kg.ha−1.year−1 were determined by linear regression and displayed through maps. The most significant change during the reporting period was in the annual sulphur deposition, which was the statistically significant with rather sharp decrease on Slovak plots (P ≤ 0.01, R2 = 0.68) and with milder decrease in the Czech Republic (P ≤ 0.05, R2 = 0.23). There are small spatial and temporal differences in the deposition of the annual nitrate nitrogen depositions. The decrease was statistically more significant in Slovakia (P ≤ 0.01, R2 = 0.53) than in the Czech Republic (P ≤ 0.05, R2 = 0.30). The smallest changes were in annual depositions of ammonium nitrate, although the deposition was statistically significant in Slovakia (P ≤ 0.01, R2 = 0.42). In the Czech Republic dropped only slightly over the whole territory (except in the Beskydy Mts.) during evaluated period. The temporal variations of polluting components revealed significant differences between developments of depositions on the different plots of both republics. The sulphur and nitrogen depositions in the Slovak and Czech Republic persistently ranking among the highest in Europe, what is caused by local and transboundary anthropogenic emission.