The distribution of perfluoroalkyl acids (PFAAs), one class of persistent organic pollutants, in groundwater, especially in confined aquifers remains poorly understood. In this study, we investigated the occurrence of 12 PFAAs through a water cycle from the Huai River Basin to the Yellow Sea, including confined aquifers, unconfined aquifers, rivers, and coastal waters. We found the ubiquity of PFAAs in all types of samples, including those from confined aquifers (2.7-6.8 ng/L). Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) were the major PFAAs in all samples, accounting for an average of 49.1% (0.8-84.8%) and 33.3% (6.3-92.2%) of total PFAAs, respectively. Comparing the concentration of PFOA with that of PFOS, we found a higher concentration of PFOA in rivers and a higher concentration of PFOS in confined aquifers. Short-chain perfluoropentanoic acid accounted for an average of 10.3% (1.9-24.6%) of total PFAAs in rivers and coastal waters. Branched isomers of both PFOA and PFOS were detected in most samples (36/42 and 39/42, respectively). One-way analysis of variance indicated a significant difference in the profiles of PFAAs among the different types of water samples. Principal component analysis suggested that rainwater and recent uses of PFAAs could be the major sources of PFAAs in confined aquifers, while recent and current uses of PFAAs could be the major source of PFAAs in unconfined aquifers, rivers and coastal waters. The risk quotients of PFOA and PFOS in groundwater and rivers were 2-3 orders of magnitude lower than unity, indicating no immediate risks via drinking water consumption.