A new method has been developed for the simultaneous determination of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) at ultratrace levels in water and sediment samples by gas chromatography coupled to high-resolution magnetic sector mass spectrometry (GC-HRMS). GC conditions were optimized in order to perform the separation of both families of contaminants in less than 45 min. Extraction procedures based on solid phase extraction (SPE) and ultrasonic extraction were optimized for water and sediment samples, respectively. For both matrices, the developed methods were validated in terms of linearity, trueness, selectivity, intra-day and inter-day precision, limits of detection (LODs) and quantification (LOQs). Recovery values between 70 and 120% were obtained for all compounds in water (concentration levels assayed: 0.1 and 1.0 ng L⁻¹) and sediments (concentration levels assayed: 1, 5 and 10 μg kg⁻¹). Relative standard deviation (RSD) values were lower than 20% and 19% for intra and inter-day precision, respectively. LODs and LOQs were lower than 0.03 and 0.05 ng L⁻¹ respectively in water, and lower than 0.08 and 0.2 μg kg⁻¹, respectively, in sediments.