Heilongdong Spring Basin (HSB) is located in a semi-arid region in northern China. In the past few decades, it has been influenced by anthropogenic activities. Currently, there is a lack of information about the impact on the hydrogeochemistry and groundwater quality of different aquifers. To address this concern, the present study used conventional hydrochemical diagrams, stable isotope analysis and multivariate statistical techniques to analyze hydrochemical characteristics and controlling factors of shallow and deep groundwater in the study area. The results showed that all groundwater samples were weakly alkaline. The shallow groundwater (SGW) was mainly composed of SO4-Ca and SO4·HCO3-Ca·Mg water types with high TDS values. However, the predominant water types of deep groundwater (DGW) were HCO3-Ca·Mg and HCO3·SO4-Ca·Mg types with relatively low TDS. The large majority of shallow groundwater had poor water quality, which was influenced by natural factors and anthropogenic activities, characterized by high concentrations of SO42−, NO3−, and Cl−. In contrast, the overall water quality of deep groundwater was good, mainly controlled by the natural background. Nonetheless, a few karst groundwater samples of DGW in runoff areas exhibited close hydraulic connections with SGW samples and presented contamination to a certain degree. Our research results provide a scientific basis for the utilization and protection of groundwater in different aquifers in northern China.