ABSTRACT: The article deals with the surface and groundwater, elucidation of water origin in National Nature Reserve Šúr, assessment of qualitative and quantitative indicators of water. In the area there are situated 12 observation boreholes, every two weeks there are measured groundwater level, pH, electric conductivity of water and water temperature. These data were evaluated statistically and graphically. There were collected water samples for chemical analysis of water from surface and groundwater from which physico-chemical parameters of water were determined. The results showed that part of water in the National Nature Reserve Šúr comes from the Quaternary sediments and from the Malé Karpaty Mountains and part of the water comes from the Neogene sediments. The water from the Neogene sediments has high contents of chlorides, sulphates and calcium. The water from the HGŠ-1 borehole at the Šúr Biological Station is clearly of the Neogene origin, which was also confirmed by isotopic analyzes of hydrogen and oxygen.