This study discusses the (SO4-)-S-center dot based process mediated by natural magnetic pyrrhotite (NP) for the degradation of refractory organic micropollutants. Complete degradation of 20 mu M phenol in distilled water (DW) was obtained within 20 min using NPIPS (persulfate) system. Electron paramagnetic resonance spectra indicated aerobic and acidic conditions favored the generation of both (SO4-)-S-center dot and (OH)-O-center dot species, but only (OH)-O-center dot signal was survived at alkaline condition. The leaked Fe2+ and equivalent to Fe(II) of NP collectively work to activate PS and generate surface and bulk (SO4-)-S-center dot and (OH)-O-center dot simultaneously. The identified intermediates indicate the transformation of benzene ring is the key step for phenol degradation by NP/PS system. Moreover, phenol degradation was greatly inhibited in surface water (SW, 29%) and wastewater (WW, 1%), but 25.9% and 17.5% of TOC removal were obtained in the SW and WW during NP/PS treatment, respectively. Additionally, the acute toxicity tests for NP/PS process exhibited a fluctuating trend depending on the water matrix, while the genotoxic activity analysis indicated that the treated phenol solutions were not genotoxic but cytotoxic. Overall, this study provides a solution to abate refractory organic micropollutants in water systems. (C) 2017 Elsevier B.V. All rights reserved.