This study deals with the occurrence and removal efficiency of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) as selected persistent organic pollutants (POPs) in municipal wastewater via a compartmentalized anaerobic baffled reactor (ABR). The treatment processes and removal efficiencies using ABR were assessed with application of three hydraulic retention times (8, 16 and 24 hrs). The detected concentration values for PAHs in raw wastewater were varied from 345 to 1960.1 with an average value of 1003.5 μg/l. While those for PCBs were 2.3 to 18.7 with an average value of 8.7 μg/l. The removal efficiencies for PAHs achieved 52, 81 and 86%, whereas for PCBs they recorded 41, 67 and 77% at HRT of 8, 16 and 24 hrs, respectively. POPs contributor to surface water bodies in Egypt and better reduction efficiencies are achievable, the present study highlights the possibility of utilizing ABR for restoring water quality for reuse or safely discharging on the streams.