The objective of this study was to assess the effect of natural organic matter (NOM) on disinfection efficacy using two types of disinfectants: Cl2 and ClO2. Bacillus subtilis spores were used as a surrogate for monitoring disinfection efficacy. The effect of natural organic matter was tested using two series of experimental assays. Initially, assays were conducted in ultra-pure buffered waters supplemented with various NOM extracts. Second, confirmation assays were performed on three surface waters. In both natural and synthetic waters, the presence of NOM improved disinfection efficacy where chlorine dioxide was used. This phenomenon was significant, as Ct values required for 2 log inactivation of B. subtilis spores were reduced by a factor of 2.3 to 7.1 depending on the NOM source and concentration. However, such a phenomenon was not observed while disinfecting with free chlorine. It is proposed that (i) free radicals are generated following the reaction of chlorine dioxide and NOM and (ii) those radicals can enhance chlorine dioxide disinfection efficacy.