This study on long-term (36 years) changes of water chemistry in the Vltava River is based on regular monitoring of the Slapy Reservoir, which has a large heterogenous catchment. Ionic concentrations doubled at constant ratio of cations, while the equivalent ratio of anions of strong acids {ie145-01} to hydrogen carbonate increased more than twice between 1959 and 1990. Nitrate levels increased seven times, reflecting mainly rate of fertilization and atmospheric N deposition. Diffuse sources were dominant in N discharge from the basin (at least 60–80%) throughout the period, in extremely dry years the importance of point sources increased. A sharp decline in the fertilizer application since 1990 due to economic changes in the Czech Republic and also decreased emissions of sulphur in Europe has resulted in the slow recovery of water quality.