While the need to provide clean drinking water is widely recognized as a priority in rural Sub-Saharan Africa, there is a lack of specific data on water quality to build effective drinking water management policies. This discussion paper describes a water quality study undertaken in Northern Uganda, to test the potability and potential contamination of water taken from wells, open water sources and households. Key lessons from the study include the fact that clean well water can be contaminated during transportation to, and storage in, homes. Building on the data from the water quality tests, this paper explores the policy implications for national governments, non-governmental organizations (NGOs) and individuals at the household level. In the absence of more specific, country-by-country studies, the results from this study are applicable across the region due to similarities in water sources and storage practices in rural Africa.