Display omitted •Cl– retards pollutant removal in Co2+/PMS process by shifting radical distribution.•NH4+ reacted with HOCl and induced more severe efficiency loss of Co2+/PMS process.•DOM inhibited the formation of chloramine and alleviated the efficiency loss.•The formation of chlorate and DBPs are not concerns in the presence of ammonia. A significant loss of the treatment efficiency induced by Cl− is a well-recognized drawback of the SO4·−-based AOPs and various mathematical model have been established to achieve quantitative prediction of the treatment efficiency of SO4·−-based AOPs at different levels of Cl−. However, the background water constituents (e.g., ammonia and dissolved organic matter (DOM)) complicate the chemistry of Cl−/SO4·− system and disable these models. This study shows that the degradation of sulfamethoxazole and bisphenol A by Co2+/PMS process decreased with dosing Cl− at fresh water level, due to the shifted distribution of reactive species from SO4·− to Cl2·−, ClO· and HOCl. Besides quenching radicals, HOCl also contributed to pollutant degradation. Though ammonia alone negligibly influence the Co2+/PMS process, ammonia reacts with the in situ formed HOCl in the Cl−/SO4·− process rapidly along with the generation of chloramine which mainly severed as radical scavenger rather than oxidant. Consequently, more severe efficiency loss of the SO4·−-based AOPs occur in the copresence of ammonia and Cl−. Unexpectedly, the efficiency loss was alleviated after dosing DOM, which was attributed to the suppressed formation of chloramine. The occurrence of chlorate and disinfection by-products are not concerns in the Co2+/PMS process when Cl− coexists with ammonia and DOM, because of the decreased formation of HOCl. These results enhance our understanding of the complex chemistry of SO4·−-based AOPs in real water and promote the progress of SO4·−-based AOPs towards the niche applications in water treatment.