Brominated flame retardants (BFRs) are considered to be environmental pollutants due to their toxicity, persistence and ubiquity in the environment. Little information is known about the presence of brominated flame retardants in South Africa's water systems. Therefore, this study examined and compared different extraction methods (liquid-liquid (LL) vs. solid phase (SP) for water, Soxhlet extraction (SE) vs. ultrasonic for sediment) for extraction efficiencies in the determination of polybrominated diphenyl ethers (PBDEs) and polybrominated biphenyls (PBBs) in water and sediment from Jukskei River. Clean-up of sample extracts was performed using disposable Pasteur pipettes containing neutral, acidified and basic silica gel. Final extracts, after concentration and dilution to 200 μL were analyzed by injecting 1 μL in the GC-ECD and GC-MS. Results obtained showed good recoveries for most of the tested analytes in water; for LLE, values ranged between 80.5 ± 10.22% and 126.6 ± 1.94%; SPE, 70.41 ± 2.01%-124.78 ± 3.78% (n = 3) and for sediment (73-114%, with an RSD <17%) using SE. The ultrasonic extraction method gave less than 50% recovery for most of the congeners. The concentrations of the BFRs in water samples were less than the detection limit while the concentrations in sediment ranged from 1.95 to 36.61 ng g(-1) dry weight for Σ(11) BFRs. Dichloromethane and n-hexane : acetone (2 : 1, v/v) gave optimum value of recovery for water and sediment respectively.