Our paper is intended to assess the long-term impact of acid atmospheric deposition on the chemistry of ground waters in the Krušné hory Mts., and to explore to what extent forest cover participates in the development of chemical composition of relevant waters. The study was based on the results of long-term monitoring and assessment of mass flow in the Jezeří experimental catchment (1996-2007), and also on the results of investigation of a network of 26 experimental catchments in the Krušné hory Mts. that were affected by prolonged atmospheric deposition of high levels of sulfur and nitrogen. The monitoring of ground water quality and the health of forests at these catchments was not continuous. However, areal systematic sampling of waters characterizing the periods 1959-65, 1965-74, 1979-89 and 2000-02 enabled us to reconstruct the development of ground waters chemistry in the Krušné hory region during the last 40 years. The changes in chemical composition of waters were compared with data on atmospheric deposition. The obtained results proved the worst quality of ground waters to have occurred in the 1980s, which was manifested by the depletion of HCO₃ contents, a decrease in pH and increase in SO₄ and NO₃ concentrations. Significant damage to the forest cover was recorded during this period of time. The results indicate that in the presence of a coniferous forest the negative impacts of acid atmospheric deposition on groundwater quality are greater. Simultaneously, the deterioration in the quality of groundwater, indicated by increased concentrations of aluminum, plays a part in damaging the health of the forest.