Featured Application: This study examined the tolerance of Escherichia coli isolates, a fecal indicator of water contamination, to chlorine as a common water disinfectant and the effectiveness of chlorine at different concentrations in eliminating E. coli in wastewater effluent. Data obtained can be used as baseline monitoring data for future epidemiological surveillances that could further enhance the control of E. coli and some bacteria species of public health concern in wastewater treatment plants and ensure protection of public and environmental health.Abstract: This study investigated the survival of Escherichia coli (E. coli) recovered from secondary effluents of two wastewater treatment plants in the Eastern Cape Province, South Africa, in the presence of different chlorine concentrations. The bacterial survival, chlorine lethal dose and inactivation kinetics at lethal doses were examined. The bacterial isolates were identified by 16S rRNA gene sequencing. Comparison of the nucleotide sequences of 16S rRNA gene of bacteria with known taxa in the GenBank revealed the bacterial isolates to belong to Escherichia coli. At the recommended free chlorine of 0.5 mg/L, reduction of E. coli isolates (n = 20) initial bacterial concentration of 8.35-8.75 log was within a range of 3.88-6.0 log at chlorine residuals of 0.14-0.44 mg/L after 30 min. At higher doses, a marked reduction (p < 0.05) in the viability of E. coli isolates was achieved with a greater than 7.3 log inactivation of the bacterial population. Inactivation kinetics revealed a high rate of bacterial kill over time (R 2 > 0.9) at chlorine dose of 1.5 mg/L. This study indicates poor removal of bacteria at free chlorine at 0.5 mg/L and a greater efficacy of 1.5 mg/L in checking E. coli tolerance.