Treatment in a wastewater stabilization pond (WSP) relies on natural purification processes, which can be sensitive to both location and climate. This study investigated the effects of three environmental factors, pH, dissolved oxygen (DO) and temperature, on disinfection efficiency in a WSP system consisting of three facultative cells, and operated in a temperate climate region, in Eastern Ontario, Canada. Indicator organism (Escherichia coli (E. coli)) removal in WSP systems is driven by a combination of different factors. Elevated pH and DO concentrations, which are attributed to the presence of algae, are important factors for effective disinfection. Therefore, the presence of algae in natural wastewater treatment systems can contribute appreciably to disinfection. Consequently, based on algal concentrations, removal efficiencies of pathogenic microorganisms during wastewater treatment over the course of a year can be highly variable, where higher removal efficiencies would be expected in summer and fall seasons.