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Water stable isotopes were used to investigate hydrological pathways and interactions between surface water and groundwater in the Zagreb aquifer system (Croatia). δ2H and δ18O values indicate a spatial variability of the influence of individual groundwater sources inside the aquifer – local precipitation and the Sava River water. Fractions of surface water in groundwater strongly depend on fluctuations of the river water level and less on the distance from the Sava River. These data extend our understanding of groundwater flow in the Zagreb aquifer system, interactions between Sava River water, local precipitation and groundwater. The results of the research allow more precise monitoring plans and definition of the sanitary protection zones of the well fields in the future.