Abstract: 34 surface water samples and 8 sediment samples in the middle and upper stream of Beijiang River basin were obtained, and the concentration levels of 31 flame retardants in the samples were determined by gas chromatography tandem mass spectrometry (GC-MS/MS), including 3 brominated flame retardants (BFRs), i.e., polybrominated diphenyl ethers (PBDEs), hexabromocyclododecane (HBCD), and tetrabromobisphenol A (TBBPA) and 28 organophosphorus flame retardants (OPFRs). Results shows that the concentrations of PBDEs and HBCD in surface water were 4.78-625.52 ng·L^-1 and 225.43-2209.18 ng·L^-1, respectively, while TBBPA was not detected. The concentration of OPFRs in surface water was 85.80-992.82 ng·L^-1, in which TCEP, TPhP, and TDCIPP were the three monomers with the highest concentration. The contents of PBDEs, HBCD, and TBBPA in sediments ranged from ND-11.82 ng·g^-1, 121.13-395.86 ng·g^-1, and ND-3.30 ng·g^-1, respectively, while that of OPFRs was 102.19-748.17 ng·g^-1. Flame retardants mainly came from home decoration and building materials, electrical waste disassembly, and other industries. Sewage plant discharge and atmospheric sedimentation were two possible ways for pollutants to enter the water environment. The results of ecological risk assessment by risk quotients method show that flame retardants in surface water were generally at medium and low level, however, BDE-100 was at high risk level, and four OPFRs monomers including o-TTP, m-TTP, p-TTP, and TPhP were at medium level. The health risk assessment results show that for all flame retardants with known health data, their carcinogenic risk and non-carcinogenic risk indexes were within the acceptable range, and the health risk caused by drinking water intake can be ignored.