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 surface water from the Sava and Iška rivers. Sampling was performed between January 2020 to December 2021 using a polypropylene Burkle TM angular beaker attached to a BurkleTM telescopic rod (Bürkle GmbH, Bad Bellingen, DE). The Sava River sampling was performed at Sava Brod and Sava Šentjakob, while the Iška River samples were collected at Iška vas. Besides isotope data, physico-chemical parameters (water temperature and electrical conductivity) were measured on-site at each location using a calibrated UltrameterTM II 6PFCE (MYRON L Company, Carlsbad, CA, USA), with an accuracy of ±0.15 °C, ±1 μS/cm and ±0.02, respectively. In addition, water discharge and temperature data were obtained from the Slovenian Environment Agency (https://www.arso.gov.si/vode/podatki/amp/H3570_t_30.html, website accessed in 11/2022). Altogether, 56 samples of surface water were collected. 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 surface water in the Ljubljana basin. The related groundwater data is also archived at PANGAEA (Žagar et. al. 2022).