Leaky water supply and sewer mains can become unmanaged sources of urban groundwater recharge and contamination posing environmental and health risks. Stable isotopes of water and hydrochemical tracer were applied to quantify water and sewage leakages in a shallow aquifer of a large Ukrainian city. Binary and ternary mixing models were used based on the d-excess and chloride concentrations of tap water, rural and urban groundwater to estimate fractions of natural recharge, urban seepage, volumes of water supply and sewage leakages in urban springs. Water supply leakages that recharge aquifer were ~ 3% (6.5 Mm 3 a − 1) of the total water supply and strongly correlated with failures on the water infrastructure. Sewage leakages (1.4 Mm 3 a − 1) to the aquifer were less in amount than water supply leakages, but induced nitrate and associated contaminants pollution risk of urban groundwater. The proposed method is useful for the pilot evaluation of urban groundwater recharge and contamination and can be applied in other regions worldwide to support the decision-making in water management.