The objective of this study is to investigate the impacts of anthropogenic and natural processes on the granular aquifer (GA) and the fractured rock aquifer (FRA) in the central region of Guangzhou city. Results indicate that 47.8% and 30.4% of samples in GA are not suitable for drinking and industrial purposes respectively, mainly due to the high concentrations of Fe and NH4+. In contrast, 48.3% and 41.4% of samples in FRA are not suitable for drinking and industrial purposes respectively, mainly due to the high concentrations of Al, NO3-, NH4+, Fe, and Pb. The contributions of Pb, Al, and NO3- to groundwater quality in GA are lower than those in FRA, while the contributions of Na+, Cl-, SO42-, and TDS to groundwater quality in GA and FRA are similar. High concentrations of Pb, Al, Na+, Cl-, SO42-, TDS, and NO3- in groundwater of both GA and FRA are mainly ascribed to human activities such as urbanization and industrialization, while high concentrations of Fe and NH4+ in groundwater of GA are mainly ascribed to natural processes such as reducing environment. More attention should be paid to the protection of groundwater quality in FRA than in GA due to the greater utilization of the groundwater resource in FRA than that in GA.