Synergistic effects of ozone (O3) and peroxymonosulfate (PMS, HSO5−) for isothiazolinone biocides degradation was studied. The synergistic ozonation process (O3/PMS) increased the efficiency of methyl-isothiazolinone (MIT) and chloro-methyl-isothiazolinone (CMIT) degradation to 91.0% and 81.8%, respectively, within 90 s at pH 7.0. This is 30.6% and 62.5% higher than the corresponding ozonation efficiency, respectively. Total radical formation value (Rct,R) for the O3/PMS process was 24.6 times that of ozonation alone. Calculated second-order rate constants for the reactions between isothiazolinone biocides and ▪ (kSO4-,MIT and kSO4-,CMIT) were 8.15 × 109 and 4.49 × 109 M−1 s−1, respectively. Relative contributions of O3, hydroxyl radical (OH) and ▪ oxidation to MIT and CMIT removal were estimated, which were 15%, 45%, and 40% for O3, OH and ▪ oxidation to MIT, and 1%, 67%, and 32% for O3, OH and ▪ oxidation to CMIT at pH 7.0, respectively. Factors influencing the O3/PMS process, namely the solution pH, chloride ions (Cl−), and bicarbonate (HCO3−), were evaluated. Increasing the solution pH markedly accelerated O3 decay and OH and ▪ formation, thus weakening the relative contribution of O3 oxidation while enhancing that of OH and ▪. Cl− had a negligible effect on MIT and CMIT degradation. Under the dual effect of bicarbonate (HCO3−) as inhibitor and promoter, low concentrations (1–2 mM) of bicarbonate weakly promoted MIT and CMIT degradation, while high concentrations (10–20 mM) induced strong inhibition. Lastly, oxidation performance of O3 and O3/PMS processes for MIT and CMIT degradation in different water matrices was compared.