We aimed to verify the effectiveness of semi-permeablemembrane devices (SPMDs) formonitoring hydrophobic organic compounds, such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), that are not easy to detect using conventional grab samples (because of their low concentrations), in water.We used SPMDs and grab samples to monitor PCBs and PBDEs upstream and downstream of a sewage treatment plant (STP) in the Suyeong River in Busan, Korea. Concentrations in three different phases (freely dissolved, apparently dissolved, and particulate) were measured, to investigate the aquatic fate of PCBs and PBDEs. The freely dissolved (SPMD) concentrations were 2–3 times higher than the apparently dissolved and particulate phase (grab sample) concentrations. No meaningful relationships were found between the total PCB and PBDE concentrations of the grab sample and SPMD sample because of the different partitioning behaviors and detection frequencies of the individual chemicals. However, the summed concentrations of specific PCB and PBDE congeners (that were abundant in all samples) in the grab and SPMD samples correlated well (r2 = 0.7451 for PCBs 28 + 52 + 153, r2 = 0.9987 for PBDEs 28 + 47 + 99). The PBDE concentrations measured using SPMDs decreased with increasing distance from the STP, but no apparent dilution effect was found in the grab samples. Our results show that SPMDs could be used to support grab sampling for specific chemicals, or to trace chemical sources (such as STPs) to the aquatic environment.