This study assessed the occurrence, origins, and potential risks of emerging perfluoroalkyl acids (PFAAs) for the first time in drinking water resources of Khyber Pakhtunkhwa, Pakistan. In total, 13 perfluoroalkyl carboxylic acids (PFCAs) with carbon (C) chains C4-C18 and 4 perfluoroalkyl sulfonates (PFSAs) with C chains C4-C10 were tested in both surface and ground drinking water samples using a high-performance liquid chromatography system (HPLC) equipped with an Agilent 6460 Triple Quadrupole liquid chromatography–mass spectrometry (LC–MS) system. The concentrations of ∑PFCAs, ∑PFSAs, and ∑PFAAs in drinking water ranged from 1.46 to 72.85, 0.30–8.03, and 1.76–80.88 ng/L, respectively. Perfluorobutanoic acid (PFBA), perfluorohexanoic acid (PFHxA), and perfluoropentanoic acid (PFPeA) were the dominant analytes in surface water followed by ground water, while the concentration of perfluorobutane sulfonate (PFBS), perfluorooctanoic acid (PFOA), perfluoroheptanoic acid (PFHpA), perfluorooctane sulfonate (PFOS), perfluorohexane sulfonate (PFHxS), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluoroundecanoic acid (PFUnDA), and perfluorododecanoic acid (PFDoDA) were greater than long-chain PFOA and PFOS. The correlation statistics, which showed a strong correlation (p < 0.05) between the PFAA analytes, potentially indicated the fate of PFAAs in the area's drinking water sources, whereas the hierarchical cluster analysis (HCA) and principal component analysis (PCA) statistics identified industrial, domestic, agricultural, and commercial applications as potential point and non-point sources of PFAA contamination in the area. From risk perspectives, the overall PFAA toxicity in water resources was within the ecological health risk thresholds, where for the human population the hazard quotient (HQ) values of individual PFAAs were < 1, indicating no risk from the drinking water sources; however, the hazard index (HI) from the ∑PFAAs should not be underestimated, as it may significantly result in potential chronic toxicity to exposed adults, followed by children.