This study represents the first isotopic characterization of groundwater nitrate to identify the sources of excessive nitrate in the urban aquifer and provides a reference for the potential implementation of executive programs on groundwater quality and protection. Nitrate concentration exceeded the limits for nitrate in drinking water in most of the wells (110 out of 261). Isotopic composition of the oxygen and nitrogen of NO3− in groundwater indicated sewage as the primary source of nitrate contamination. Denitrification was identified as a non-significant process in the aquifer. Concentrations of anions (Cl−, SO42− and PO43−) and NO3− showed strong correlations confirming potential wastewater influence. Most of the groundwater was weakly acidic, and the chemistry of the groundwater was rather affected by urbanization and land-use than by aquifer rock interactions. The absence of a reliable sewer collecting system, particularly in the central and southern parts of the study area, directly resulted in the poor water quality. Considering the lack of natural attenuation processes in the groundwater, management options need to be considered for reducing nitrogen input into groundwater.