The ubiquitous presence of micropollutants in surface and groudwater may cause long term effects on aquatic ecology and on human health. Chemical oxidation using permanganate or free chlorine is the commonly used method for treating micropollutants. However, the kinetics and mechanism remain unclear for the permanganate oxidation of micropollutants under different pH conditions. For rapid chlorination reactions, it is still a big challenge to determine their rate constants. In combination of stopped-flow spectrometer, LC-MS, and theoretical analysis, we investigated the kinetics and mechanism of the permanganate oxidation of micropollutants in acidic, neutral, and alkaline aqueous solutions. The rate-limiting step of acidic permanganate oxidation of sulfamethoxazole is the attack of permanganate at N-H bond. The results established that the N-H bond oxidation by MnO4– is a concerted mechanism, whereas the HMnO4 oxidation of N-H bond goes through a stepwise electron-proton transfer. In MS analysis, the protonation site of sulfamethoxazole was located at the nitrogen atom of the isoxazole ring. Formation of the fragment ions were recognized as the results of heterolytic S-N bond and C-S bond cleavage and was attributed to a stepwise rearrangement reaction. In neutral and alkaline aqueous solutions, the rate constants of the reactions between tetracycline and permanganate depended on the species distribution. The reaction in neutral pH condition was the permanganate oxidation of double bond and aromatic ring. The reaction in alkaline medium was the permanganate oxidation of a higher charge complex formed by tetracycline and hydroxide ion. This resulted in the transfer of HOMO from double bond to aromatic ring, leading to the selective oxidation of the phenolate-like moiety. In a more broad pH range, the pH-dependent kinetics was also found to be applicable in the permanganate oxidation of EDTA. Finally, we combined stopped-flow spectrometer, competition kinetics, and colorimetric reagent to propose a novel method to determine the rapid chlorination reactions. A kinetic equation was first derived to estimate the reaction rate constant of N,N-diethyl-p-phenylenediamine (DPD) towards chlorine under a given pH (6.75–8.90) and temperature condition (18–37 oC). By using DPD as a reference probe, we determined the chlorination rate constants of several representative compounds including tetracycline, ammonia, and four α-amino acids. The developed method was validated through comparing the experimentally measured chlorination rate constants of the selected compounds with those obtained or calculated from literature and analyzing with Taft’s correlation as well.