Large volumes of oil sands process-affected water (OSPW) are produced in northern Alberta by the surface mining oil sands industry. Naphthenic acids (NAs) are a complex mixture of persistent organic acids that are believed to contribute to the toxicity of OSPW. In situ microbial biodegradation strategies are slow and not effective at eliminating chronic aquatic toxicity, thus there is a need to examine alternative remediation techniques. NAs with multiple rings and alkyl branching are most recalcitrant to microbial biodegradation, but here we hypothesized that these same structural features may lead to preferential degradation in the ozonation process. Total NA degradation increased with increasing pH for commercial NA solutions, suggesting a hydroxyl radical mechanism and that naturally alkaline OSPW would unlikely require pH adjustment prior to treatment. For commercial NAs and OSPW, NAs with more rings and more carbon (and more H atoms) were depleted most rapidly in the process. Relative rate measurements with binary mixtures of model NA compounds not only confirmed this structure reactivity but also indicated that alkyl branching patterns were an additional factor determining NA reactivity. The results demonstrate that ozonation is complementary to microbial biodegradation, and the process remains a promising water reclamation strategy for the oil sands industry.