Assessment of temporal trends and rates of change in hydrochemical parameters and forest cover has been conducted to elucidate key drivers of surface water acidification in glacial lakes in the Czech Republic. Since 1984, the key driver in acidification reversal was sulphate (SO4) concentration (median decrease of −3.58 μeq L−1 yr−1) which fell in line with reductions in sulphur (S) deposition. Reduction of nitrogen (N) deposition was followed by proportional reduction in nitrate (NO3) leaching although decline in NO3 concentrations was more pronounced at two sites, the Čertovo Lake (CT) and Prášilské Lake (PR) until 2006; only Žďárské pond showed effective catchment N immobilization. Coherent decline of chloride concentration was detected across all sites. The decrease of strong mineral acids was partly compensated by decrease of inorganic aluminium (Alin), especially at sites most acidified in the beginning of observations (ANC1984–1986 between −160 and −90 μeq L−1 at CT, Černé Lake—CN and Plešné lake—PL) and by reductions of base cations and increases of pH. All lakes (CN, CT, PL, PR and LK) moved to the ANC range between −29 and 30 μeq L−1 (2010–2012) where sensitivity of pH to further reductions in acid anions may be expected. Concurrently, charge of weak organic acids (OAs) increased and partly balanced the strong mineral acid decrease as a consequence of (i) significant DOC (dissolved organic carbon) increase (median change of 0.13 mgC L−1 yr−1 since 1993) and (ii) deprotonation of weak OAs caused by pH rise. Since 2000s, bark beetle induced forest decline accelerated NO3 leaching at most of the catchments (by 200 % at LK, PL and PR). However, elevated N leaching was effectively neutralized by base cations (K, Mg, Ca) originating from decaying fresh litter, thus acidification recovery was not reversed, but slowed down. After cessation of NO3 leaching we hypothesise that collapsed tree canopy across catchments (from 12 to 87 % compared to 1984) will cause lower total acid input in precipitation (S + N) and regrowth of vegetation may stimulate higher N immobilization (in biomass and soil); processes which could lead to further increase of ANC and pH, key indicators for biological recovery.