The effectivenss of pot chlorination to continously treat shallow wells in a peri-urban community in Kisumu, Kenya, was evaluated. A total of 30 shallow wells used by local residents were identified. Half were randomly allocated to be treated by pot chlorination, while the remainder served as the control group. Residual free chlorine (RFC) and the presence of Escherichia coli (E. coli) were measured in all wells before chlorination and at repeated intervals over a 14-day period. Although there was a reduction in E. coli levels in the intervention wells post-chlorination, there was no difference in the percentage of wells in each group meeting WHO drinking water guidelines of 0 E. coli CFUs/100 ml on day 7 (p = 0.444) or day 14 (p = 0.188). While the intervention was associated with a statistically significant improvement in the percentage of chlorinated wells meeting the WHO guidelines for RFC of at least 0.5 mg/l (41.7%) compared to control wells on day 7 (p = 0.010), by day 14 there was no detectable difference between the two groups (p = 0.444). Pot chlorination of the shallow wells in this study did not improve the microbiological quality of well water to WHO drinking water standards and was not effective in maintaining the recommended RFC required for continuous disinfection.