In the presence of humic substances (HSs), the oxidative conversion of pentachlorophenol (PCP) was found to be efficiently catalyzed by tetra(p-sulfophenyl)porphineiron(III) (Fe(III)-TPPS) using KHSO5 as an oxygen donor. Ortho-tetrachloroquinone (o-TeCQ), 2-hydroxyl-nonachlorodiphenyl ether (2H-NCDE), 4-hydroxyl-nonachlorodiphenyl ether (4H-NCDE), and octachlorodibenzo-p-dioxin (OCDD) were identified as the major byproducts of the reaction. Decreased amounts of these byproducts were produced in the presence of HS. In particular, the addition of HSs with a lower degree of humification resulted in a large decrease in the formation of dimers, such as 2H-NCDE, 4H-NCDE, and OCDD. More than 60% of the chlorine, which was released from PCP, was found in the HS fractions after the reaction. This suggests that chlorinated intermediates from PCP were incorporated into the HS. Pyrolysis-GC/MS and 13C NMR studies confirmed that the binding of the chlorinated intermediates was covalent in nature and that the intermediates were copolymerized with HS via oxidative coupling reactions. A Microtox test demonstrated that the toxicity of the HS fraction containing PCP-derived intermediates was much lower than that of the mixture of PCP and HS in the absence of a catalytic reaction.