Water supply systems form one of the most fundamental components of building services. In many communities, especially in developing countries like Uganda, most households use the indirect cold water supply system, particularly because of the intermittent water supply problems. However, research has linked the main component of this system, particularly water storage tanks, to the contamination of water. There is a paucity of research regarding which features of these tanks contribute to water contamination. This study investigated the effects of storage tank features and cleaning practices on water quality. The results revealed that the treated water received by households became significantly (α= 0.05) contaminated with faecal coliforms (p= 0.001), total coliforms (p < 0.001), and heterotrophic bacteria (p < 0.001) while in storage tanks. Furthermore, Fe and Mn significantly increased in stored water (with p= 0.001, and p= 0.023, respectively) while residual free chlorine significantly reduced (p < 0.001). The study revealed that tank type, tank connectors, and tank age significantly affect water quality. The study concluded that tank cleaning does not guarantee improvement in the quality of stored water. Further research is recommended to determine the best tank cleaning methods and optimal cleaning frequency.