There is limited information on contaminations of per- and polyfluoroalkyl substances (PFASs) in the water source affected by agricultural activities. The contamination of PFASs was investigated in the sources of agricultural groundwater and nearby surface water from an important vegetable production base supply for Beijing and Tianjin, located in North China. Σ13PFAS concentrations ranged from 0.321 to 8.285 ng/L, with an average concentration of 2.022 ng/L in the groundwater and 19.673 ng/L in the surface water. With the increase in the carbon chain length, the mean concentrations of PFASs in groundwater generally showed a decreasing trend. The dominated congeners of short-chain perfluorobutanesulfonate and perfluorooctanoate acid (PFOA) were detected in all groundwater samples, with mean concentrations of 0.944 and 0.654 ng/L. The difference was that PFOA and perfluorooctanesulfonate (PFOS) were the dominant congeners in nearby surface water, with concentrations of 7.585 and 3.421 ng/L. Thus, the concentrations of PFOA and PFOS in the surface water were about 8.5 times higher than those in the groundwater, indicating that Σ13PFAS concentrations might decrease with the water migration from the overground to the underground. In addition, significant correlations were observed between PFASs and DOC/TN related to agricultural activities, suggesting a certain relationship existed between PFAS conger distributions and organic carbon/nutrients in water. Health risk assessment indicated that the PFAS exposure caused insignificantly immediate harm to residents in the studied area. This survey provided information on the sources, spatial distribution, and potential migration characteristics of PFASs in a typical agricultural area of North China.