In this study, 20 groundwater samples and 7 surface water samples were collected and analyzed by HRGC-HRMS to evaluate the levels, congener distributions, and dissolved/solid partitioning of polybrominated diphenyl ethers (PBDEs) in water matrix as well as the removal efficiency of a typical water treatment plant (WTP). The results indicated that the level of PBDEs concentrations ranging from 18.51 to 4212 pg/L and 30.24 to 1021 pg/L were found in groundwater and surface water, respectively. BDE-209 predominated and contributed over 90% of total PBDEs concentrations for all samples analyzed. In addition, the dissolved/solid distribution indicated that 60–80% of PBDEs were measured in solid phase. 97% of total PBDEs was removed in a WTP. Positive matrix factorization (PMF) analysis was conducted for groundwater samples and the results indicated that 3% and 41% of PBDEs were attributed to octa and deca-BDEs commercial mixtures, respectively, while 56% resulted from anaerobic microorganism debromination process. Understanding the PBDEs occurrences, distribution and debromination process as well as their removal efficiency of water treatment plant could provide valuable information on the fate of those compounds in environment.