In this work, we investigated the emerging pollutants in Taiwanese groundwater for the first time and correlated their presence with possible contamination sources. Fifty target pharmaceuticals and perfluorinated chemicals in groundwater were mostly present at ng L(-1) concentrations, except for 17α-ethynylestradiol, sulfamethoxazole, and acetaminophen (maximums of 1822, 1820, and 1036 ng L(-1), respectively). Perfluorinated compounds were detected with the highest frequencies in groundwater at almost all of the sample sites, especially short-chained perfluorinated carboxylates, which were easily transferred to the groundwater. The results indicate that the compounds found to have high detection frequencies and concentrations in groundwater are similar to those found in other countries around the world. Most common pharmaceuticals that contain hydrophilic groups, such as sulfonamide antibiotics and caffeine, are easily transported through surface waters to groundwater. The results also indicated that the persistent natures of emerging contaminants with high detection frequencies in surface water and groundwater, such as perfluorooctanesulfonate (risk quotient >1), caffeine, and carbamazepine, should be further studied and evaluated.