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Sediment contamination in Taiwan is a critical environmental problem because it threatens human health through food chains and the local ecosystem as well. Er-Ren River (ERR) in southern Taiwan is one of the most polluted and its sediments have been severely contaminated by hydrophobic organic compounds (HOCs). Among all HOCs, polychlorinated biphenyls (PCBs) have been detected at high levels while hexachlorobenzene (HCB) has been most frequently detected. Due to their higher Kow values and lower biodegradability, they can be biomagnified through trophic levels and consequently pose high risks to humans and the ecosystem. This field study is to demonstrate an effective remediation technology on sediments contaminated by Aroclor 1254 and HCB by coupling in situ phase-inversion emulsification and biological reductive dechlorination (ISPIE/BiRD). By using real contaminated sediment with weathered and freshly-added contaminants, a single ISPIE operation can remove about 62% and 60% of weathered Aroclor 1254 and HCB, respectively. For weathered HCB and Aroclor 1254, the total removal could reach as high as 98% in 70 days. Metagenomic results showed that heat selection during ISPIE significantly changed the diversity and species evenness of the microbial community and that the Dehalococcoides were not positively correlated with the PCB removals. Instead, heat-tolerant archaea, Methanosaeta spp., may play much more important roles in the subsequent biological dechlorination. These results strongly support that ISPIE/BiRD is highly feasible on a full-scale field remediation and that this new microbial consortium could be a highly effective tool for bioremediation of HOC-contaminated sediments.