Baltic Sea blue mussels, Mytilus edulis, were exposed to polybrominated diphenyl ethers (PBDEs, IUPAC congeners 47, 99, and 153) and polychlorinated biphenyls (PCBs, congeners 31, 52, 77, 118, and 153) in a flow‐through experimental setup for 44 d. After the exposure phase, the mussels were allowed to depurate in natural brackish water for 26 d. After analyses, uptake clearance rate coefficients (ku), depuration rate coefficients (kd), and bioaccumulation factors (BAF) were calculated. A rapid uptake of all PBDEs and PCBs was observed, especially for PBDE congeners 47 and 99 (ku 120 and 170 L/day/g dry weight, respectively). The depuration rate decreased with increasing hydrophobicity as expected for the PCBs, but for the PBDEs, depuration rate coefficients appeared to be of the same magnitude for all three congeners independently of log Kow. The BAFs obtained for PBDE 47 and PBDE 99 (1.3 × 106 and 1.4 × 106 ml/g dry weight, respectively) were higher than for all other substances in the study, severalfold higher than for PCBs of similar hydrophobicity. The presented data indicate that the bioaccumulation potential of PBDEs, extensively used as flame retardants, is similar or higher than that of PCBs for filter feeding organisms such as blue mussels.