Drinking water is frequently recontaminated during transport and storage when water is poured into jerrycans. To address this issue, three strategies aiming at reducing these recontamination risks were implemented at water kiosks in Eastern Uganda. In all three strategies, water at the kiosks was chlorinated to a free residual chlorine (FRC) concentration of 2 mg/L at the tap of the kiosk. In addition, water was collected in different containers for drinking water transport: a) uncleaned jerrycans, b) cleaned jerrycans, and c) cleaned improved containers with a wide mouth and a spigot. Water quality in the containers was compared to that of a control group collecting unchlorinated water in uncleaned jerrycans. Water samples were collected at the tap of the kiosk, from the containers of 135 households after they were filled at the tap, and from the same containers in the households after 24 h of water storage. The samples were analysed for counts of E. coli, total coliforms, and FRC. Household interviews and structured observations were conducted to identify confounding variables and to assess the influence of water, sanitation, and hygiene infrastructure and practices on recontamination.All three intervention strategies contributed to significantly lower E. coli recontamination levels after 24 h than in the control group (Median (Mdn) = 9 CFU/100 mL, Interquartile Range (IQR) = 25). Median E. coli counts and mean FRC consumption were higher in uncleaned jerrycans (Median = 1 CFU/100 mL, IQR = 6, ΔFRC = 1.8 mg/L) than in cleaned jerrycans (Median = 0 CFU/100 mL IQR = 2, ΔFRC = 1.6 mg/L) and the lowest in cleaned improved containers (Median = 0 CFU/100 mL, IQR = 0, ΔFRC = 1.2 mg/L). The FRC concentration at the tap of 2 mg/L was too low to protect water from E. coli recontamination in uncleaned jerrycans over 24 h. Cleaning the jerrycans was inconvenient due to their small openings, therefore, sand was used. The cleaning with sand reduced recontamination with E. coli but did not reduce the count of total coliforms. Improved containers with a larger opening allowed for cleaning with a brush and showed the lowest levels of recontamination for both E. coli and total coliforms. In addition to the intervention strategies, households receiving a higher number of WASH education visits within the previous year had lower recontamination levels of E. coli in stored water (OR = 0.54, p = 0.003).