Concentrations and fluxes of sulphur and nitrogen compounds in bulk precipitation and in throughfall were evaluated and compared for two experimental sites in the Czech Republic: one situated at Rájec (Drahanská upland, 610 m a.s.l.) and the second one at Bílý Kříž (Moravian-Silesian Beskids, 908 m a.s.l.) both with similar stands of young Norway spruce. The three-year study performed during 2006–2008, revealed statistically significant differences in nitrate nitrogen concentrations in bulk precipitations and in ammonium nitrogen concentrations both in bulk precipitation and in throughfall between the two sites. Higher nitrogen compounds concentrations in bulk precipitation were found at Rájec. Differences between the two sites in sulphur concentrations were not found out neither in bulk precipitation nor in throughfall waters. Total sulphur deposition amounted to 8.1, 8.3 and 6.7 kg S·ha^–1 at Rájec and to 14.8, 16.9 and 15.4 kg S·ha^–1 at Beskids for the three years studied, respectively. Total inorganic nitrogen throughfall flux amounted to 12.1, 11.6 and 11.6 at Rájec and 13.8, 18.9 and 15.0 kg·ha^–1 at Bílý Kříž for the years 2006, 2007 and 2008, respectively.