Flame retardants have evoked public concerns owing to their extensive usage in consumer products and potential adverse effects on human health. In this study, a rapid and sensitive solid-phase extraction-ultra-high-performance liquid chromatography-tandem mass spectrometry (SPE-UPLC-MS/MS) method was developed to determine hexabromocyclododecane (HBCD), tetrabromobisphenol-A (TBBPA), six bromophenols (BPs), and nine organophosphate flame retardants (OPFRs) in water. Because of the differences in elution conditions and ionization modes for group 1 (HBCD, TBBPA, and the BPs) and group 2 (OPFRs), we had to run them twice under the different conditions to analyse group 1 and group 2 using UPLC-MS/MS. The method detection limits were 0.1-2.5 ng/L, linearity range was 0.1-100.0 ng/L for group 1 (HBCD, TBBPA, and the BPs). The method detection limit was 0.10 ng/L, and the linearity range was 0.25-250 ng/L for the OPFRs. First, the pH values of the water samples were adjusted to the range of 2-3. Then, the acidified water samples were extracted by hydrophilic-lipophilic-balance solid phase extraction (HLB-SPE) cartridges, which were eluted with 12 mL of acetonitrile. Finally, the recoveries of HBCD, TBBPA, and the BPs were 76.2-98.1%, and the relative standard deviations (RSDs, n = 5) were 2.0-28.5%. Regarding the OPFRs, the recoveries were 72.4-110.3%, and the RSDs were 0.6-6.9%. The stability experiment showed that the concentration differences were less than 15%, meeting the requirement for quality control samples. This proposed method was successfully applied to surface water, ground water, raw water, finished water, tap water, and bottled water samples.