The study assessed whether using clean containers that had been disinfected with chlorine at a water kiosk in the Kangemi slum in Nairobi reduced recontamination of treated water during drinking transport and storage. At the same time, the impacts of container handling and hygiene conditions at the household level on water quality changes during storage were evaluated. Data were collected during interviews with 135 households using either new, clean Maji Safi containers (MSCs) that had been disinfected with chlorine or normal uncleaned jerrycans (NJCs). Bacteriological water quality and free chlorine levels in both types of containers were measured after container filling at the kiosk and in the same containers after 24 h storage in households. The use of MSCs significantly reduced the risk of recontaminating the treated water. After water filling at the kiosk, none of the MSCs contained Escherichia coli bacteria, and 2.8% were contaminated after 24 h storage. In contrast, 6.2% of NJCs were contaminated after filling, and 15.2% after 24 h storage. Multivariate logistic regression indicated that the use of a clean water container and sufficient chlorine and the frequency of cleaning the container in the household mitigated recontamination. We suggest further investigation of water container designs that facilitate cleaning.