The production and use of organophosphate esters (OPEs) as substitutes for traditional halogenated flame retardants is increasing, resulting in greater global concern related to their ecological risks to marine environments. In this study, polychlorinated biphenyls (PCBs) and OPEs, representing traditional halogenated and emerging flame retardants, respectively, were studied in multiple environmental matrices in the Beibu Gulf, a typical semi-closed bay in the South China Sea. We investigated the differences in PCB and OPE distributions, sources, risks, and bioremediation potentials. Overall, the concentrations of emerging OPEs were much higher than those of PCBs in both seawater and sediment samples. Sediment samples from the inner bay and bay mouth areas (L sites) accumulated more PCBs, with penta- and hexa-CBs as major homologs. Chlorinated OPEs were prevalent in both seawater and sediment samples from the L sites, whereas tri-phenyl phosphate (TPHP) and tri-n-butyl phosphate (TNBP) were predominant at the outer bay (B sites) sediment samples. Source identification via principal component analysis, land use regression statistics, and δ13C analysis indicate that PCBs were mainly sourced from the atmospheric deposition of sugarcane and waste incineration, whereas sewage inputs, aquaculture, and shipping activity were identified as sources of OPE pollution in the Beibu Gulf. A half-year sediment anaerobic culturing experiment was performed for PCBs and OPEs, and the results only exhibited satisfactory dechlorination for PCBs. However, compared with the low ecological risks of PCBs to marine organisms, OPEs (particularly trichloroethyl phosphate (TCEP) and TPHP) exhibited low to medium threats to algae and crustaceans at most sites. Given their increasing usage, high ecological risks, and low bioremediation potential in enrichment cultures, pollution by emerging OPEs warrants close attention.