Microbiological water quality monitoring in Niassa province, Northern Mozambique, shows groundwater is not, in general, grossly contaminated though contamination levels are strongly linked to season and to risks observable at the wellhead, especially risks dealing with wellhead hygiene and maintenance. Diarrhea incidence, in general, is greatest in the rainy season suggesting poor wellhead protection as a potential mechanism for well contamination. Comparison of source water and stored water in the home shows that significant deterioration in source water quality can occur once transport and storage in the home is undertaken but that this deterioration is also related to the quality of the source water. This study shows that a structured approach to water quality monitoring, with targeted observations and an examination of the relationships between risk and water quality, is important to identify the priority interventions to be undertaken.