Understanding hydrological process of surface water and groundwater is significant for the management of urban water resources. In this study, a total of thirty-seven water samples have been collected from the river (RW, 15 samples), shallow aquifer (SG, 12 samples), and deep aquifer (DG, 10 samples) in Suzhou, Northern Anhui Province, China, and their major ion concentrations and stable H–O isotopes have been measured. The results revealed that Na+ and HCO3− were the dominant cation and anion, respectively, and most of the water samples are classified to be Na-HCO3 type, to a lesser extent, Mg-HCO3 type. K-mean and Q-type clustering analyses ruled out the hydrological relationship between river and groundwater, but there was a significant connectivity between shallow and deep groundwater, which was further confirmed by the hydrogen and oxygen isotopes. The relationship between δ2H and δ18O has shown that precipitation was the main source of the groundwater in the study area. Furthermore, the values of deuterium excess (d-excess) in different water bodies suggested that the groundwater has not been affected by evaporation, which was the main process controlling the isotopic composition of river water.