The aims of this study were to examine the levels of perfluorinated compounds (PFCs) in groundwater around improperly developed municipal and industrial waste disposal sites, including estimating non-cancer risk and cancer risk from ingestion of the groundwater. A total of 27 groundwater samples were collected from two cities in Thailand, Ayutthaya and Chonburi. Seven target compounds were extracted by solid phase extraction (SPE) and analyzed by high-performance liquid chromatography–tandem mass spectrometer (HPLC–MS/MS). The results showed that the total PFCs in groundwater around municipal waste disposal sites (MWDSs) varied from 1.68 to 7.75 ng/L. In groundwater around the industrial waste disposal site (IWDS), total PFCs varied from 2.64 to 42.01 ng/L, which were significantly different from those found in groundwater around the MWDSs at p < 0.01. PFOS and PFOA were ubiquitous in both areas, while perfluorohexane sulfonate (PFHxS) was frequently found in the samples around IWDS. The findings possibly suggest that PFHxS has been introduced for use as an alternative substance for most current C8 and higher due to it having shorter chain length and shorter half-lives. The results for both non-cancer risk and cancer risk in all samples were acceptable.