The isotopic data was obtained to provide information on the temporal and spatial variability of surface water and groundwater in the Ljubljana basin. This dataset includes monthly hydrogen (δ²H) and oxygen (δ¹⁸O) sampling data for groundwater from the Ljubljansko polje (LP) and Ljubljansko barje (LB) aquifers, the primary sources of drinking water for the City of Ljubljana. Sampling was performed between January 2020 to December 2021. Groundwater samples were collected from the Kleče, Hrastje, Jarški prod, Šentvid wellfields (LP), and the Brest wellfield (LB). Groundwater sampling was performed at 13 preselected wells from all five wellfields. If the selected well was not operating, the closest well was sampled instead. Overall, 29 different wells were sampled, and 295 samples were collected monthly by the technical stuff of the water distribution company from a pipe directly connected to the specific well. The water was running for five minutes prior to the sampling. In-situ, temperature measurements were also recorded using a Superfast Thermapen 4 digital thermometer (Electronic Temperature Instruments Ltd). All water samples were collected in 60 ml HDPE bottles and stored at 5 °C until analysis. The isotope ratios of samples were performed at the Jožef Stefan Institute using a dual inlet isotope ratio mass spectrometer (DI IRMS, Finnigan MAT DELTA plus Finnigan MAT GmbH, Bremen, Germany) with an automated H₂-H₂O and CO₂-H₂O equilibrator HDOeq48 Equilibration Unit (custom built by M. Jaklitsch). The average sample repeatability was 0.3 ‰ for δ²H and 0.02 ‰ for δ¹⁸O. Deuterium excess (d−excess) was calculated as d−excess [‰] = δ²H − 8 x δ¹⁸O (Dansgaard, 1964). The obtained isotopic data provide information on the temporal and spatial variability of groundwater in the Ljubljana basin. The related surface water data is also archived at PANGAEA (Žagar et. al. 2022).