The impact of disinfection efficacy in natural waters was evaluated by performing disinfection assays using four untreated surface waters of various qualities and ultra-pure buffered waters as a baseline condition for comparison. Bacillus subtilis spores were spiked in these waters and disinfection assays were conducted at 22 degrees C using either free chlorine or chlorine dioxide. Assays using indigenous aerobic spores were also completed. The inactivation kinetics in natural and ultra-pure buffered waters were not statistically different (at p = 0.05) while using free chlorine, as long as disinfectant decay was taken into account. Filtering natural waters through a 0.45 microm did not improve the sporicidal efficacy of chlorine. For three out of the four waters tested, the efficacy of chlorine dioxide was greater in natural waters compared to that observed in ultra-pure buffered waters. Such results are consistent with previous observations using ultra-pure waters supplemented with NOM-extract from the Suwannee River. Similar to free chlorine results, the impact of filtration (0.45 microm) on the efficacy of chlorine dioxide was not statistically significant.