Polycyclic aromatic hydrocarbons (PAHs) are considered to be rapidly biotransformed by organisms, whereas polychlorinated biphenyls (PCBs) are strongly bioaccumulated. In the present study, the estuarine copepod Eurytemora affinis was exposed in a continuous flow-through system to dissolved PAH (500 ng/L) and PCB (300 ng/L) mixtures for 86 h, whereas control groups were placed in a continuous flow-through system with clean water. Both PCB and PAH body residues were measured and compared in exposed and in nonexposed copepods to assess the uptake and the elimination of these two contaminant classes in this copepod species. After the exposure, exposed copepods exhibited concentration factors, based on a dry-weight basis, of 25, 750, and 1,200, respectively, for total PCBs and PAHs. The lower concentrations of PAHs in the nonexposed versus exposed copepods in contrast to small differences for PCBs suggest a higher rate of metabolism of PAHs compared with PCBs and could explain the differences observed in the accumulation. Furthermore, uptake as well as elimination of both PCBs and PAHs were compound selective in E. affinis. Therefore, higher-molecular-weight PCBs and PAHs were preferentially accumulated, while lower-molecular-weight compounds were preferentially eliminated. These results suggest the importance of copepods in the biogeochemical cycles of hydrophobic organic contaminants in estuarine ecosystems.