Groundwater from a Pleistocene sandy-gravel aquifer is a drinking water resource for the Union brewery, located near the centre of Ljubljana (Slovenia). A large part of the aquifer recharge area is highly urbanized, which represents a great risk for the groundwater quality assurance. The groundwater dating techniques were used to study the contamination risk of this drinking-water resource. The application of chlorofluorocarbons (CFCs), sulphur hexafluoride (SF6) and tritium-helium-3 (3H-3He) age indicator was tested, as they haven’t been used in Slovene urban areas so far. The results reflect that the 3H-3He dating technique is the most suitable for a groundwater age determination in the study urban aquifer, since SF6 and particularly CFCs concentrations could be affected by the local contaminations. They indicated that average groundwater residence times range from 10 to 30 years. Boreholes that are more distant from the Šisenski hrib hill are more vulnerable to contamination due to flow of young groundwater from a direction of the main aquifer,which is exposed to the urban pollution. The presented results were supplemented with chemical investigations of groundwater organic pollutants. An unknown trace organic pollutant with a base ion mass-to-charge ratio 147 was put into focus. Its identification based on chromatographic separation and a mass spectrometric detection with GC-MS, LC-MS and LC-TOF MS techniques. The newly detected trace organic pollutant in sampled groundwater represents together with the 3H and 3He data a new technique to study the flow paths and contaminant transport in the urban aquifer in both, the lateral and vertical directions.