A mass loading and mass balance analysis was performed on selected polybromodiphenyl ethers (PBDEs) in the first full-scale indirect potable reuse treatment plant in the United States. Chemical analysis of PBDEs was performed using an environmentally friendly sample preparation technique, called stir-bar sorptive extraction (SBSE), coupled with thermal desorption and gas chromatography/mass spectrometry (GC/MS). The three most dominant PBDEs found in all the samples were: BDE-47, BDE-99 and BDE-100. In the wastewater influent, the concentrations of studied PBDEs ranged from 94 to 775 ng/L, and in the effluent, the levels were below the detection limit. Concentrations in sludge ranged from 50 to 182 ng/g. In general, a removal efficiency of 92–96% of the PBDEs in the plant was accomplished through primary and secondary processes. The tertiary treatment process was able to effectively reduce the aforementioned PBDEs to less than 10 ng/L (>96% removal efficiency) in the effluent. If PBDEs remain in the treated wastewater effluent, they may pose environmental and health impacts through aquifer recharge, irrigation, and sludge final disposal.