Introduction: In Malawi, the prevalence of diarrhea in children under the age of five is high. One way of reducing diarrheal diseases is the treatment of water with anti-infectives at point of use. In 2002 PSI/Malawi introduced a disinfectant called WaterGuard, which has shown to reduce diarrhea prevalence. However, there were no data on how waterGuard was used at household (HH) level. Objectives: To identify sources, mothers’ practices on collection and storage of drinking water; to determine the proportion of mothers using waterGuard as per prescribed instructions on the bottle and to identify factors that affect use of waterGuard. Methodology: A cross-sectional survey of data collected by Scotland Chikwawa Health Initiative from mothers of under five was conducted. For each HH sampled, drinking water was tested for residual chlorine. In total, 349 questionnaires and four Focus Group Discussions were included. Results and conclusion: All except 0.3% use improved water source. About three quarters of mothers collected drinking water on a daily basis. Of 238 mothers using waterGuard, 45% used the recommended doses for treating drinking water but only 3% had the right amount of residual chlorine. There was an increase in waterGuard use in 2007 and a drop in 2008. Previous waterGuard use and presence of waterGuard in the house were main factors related to use. Recommendations: Periodic free waterGuard distribution to people without access to safe water should be encouraged as it helps people experience the benefits of the product and continue using it.