The Učja aquifer, located in the E-W-orientated Učja Valley in NW Slovenia, presents a potential cross-border water resource. Due to the difficult access and steep mountain morphology and complex structural conditions, only basic geological research was done. Despite the fact that the groundwater is already used as a source of drinking water (public and local supply), comprehensive analysis of the aquifer has not yet been carried out. Water for geochemical and isotopic analysis was sampled at 13 locations in the Učja Valley; groundwater was sampled at 12 locations, and the surface water (Učja River) at one location. The sampling sites were located at different elevations and due to accessibility practically all of them were on the southern slopes of the valley. Water measurements, sampling, and analysis were carried out from December 2017 to March 2019. Physico-chemical parameters (pH, temperature, electrical conductivity, oxidation-reduction potential, and dissolved oxygen) were measured on a monthly basis and in-situ at sampling sites using a digital Multimeter 3430 (WTW GmbH, Weilheim, Germany). The missing measurements from some sampling sites are the result of the springs running dry at the time of sampling. Water samples for further geochemical (cations and anions) and isotopic analysis were collected in HDPE bottles for isotopic composition of oxygen (δ¹⁸O), hydrogen (δ²H), total alkalinity (TA), tritium activity (³H), and in Labco glass ampoules for isotopic composition of dissolved inorganic carbon (δ¹³CDIC). Water samples for cations and δ¹³CDIC were filtered using a 0.45 μm pore-sized membrane, and for some analyses water was also chemically treated and stored in a refrigerator until they were analysed. A total of 22 water samples were collected for geochemical analyses (cations, anions), 37 water samples (seasonally) for isotopic analyses δ¹⁸O, δ²H, total alkalinity and δ¹³CDIC, and 10 water samples for ³H. The database comprises information on sampling sites, sampling dates, and the results of field measurements and laboratory analyses.