The main purpose of this study was to understand the interactions between precipitation, surface water, and groundwater in the Zagreb aquifer system using water stable isotopes. The Zagreb aquifer is of the unconfined type and strongly hydraulically connected to the Sava River. As the groundwater is the main source of drinking water for one million inhabitants, it is essential to investigate each detail of the recharge processes of the aquifer to ensure adequate protection of the groundwater. Measuring the content of water stable isotopes in surface waters and groundwater enabled the creation of two- and three-component mixing models based on the isotopic mass balance for the purpose of the quantification of each recharge component. The mixing models gave ambiguous results. Observation wells equally distant from the Sava River did not have the same recharge component ratio. This indicated that there were more factors (in addition to the distance from the river) that were affecting groundwater recharge, and the properties of the unsaturated zone and surface cover data were therefore also taken into consideration. The thickness of the unsaturated zone and the characteristics of different soil types were identified as important factors in the recharge of the Zagreb aquifer. The areas with high thickness of the unsaturated zone and well-permeable soil had a very similar recharge component ratio to the areas with small thickness of the unsaturated zone but low-permeable soil.