Faecal-oral transmission of pathogenic microorganisms is widespread in rapidly urbanising areas of sub-Saharan Africa where access to adequate sanitation is limited and there is a range of contaminant pathways between faecal sources and the consumption of household water derived from groundwater. High-frequency sampling of a protected spring in Kampala, Uganda, reveals gross but ephemeral contamination by thermotolerant (faecal) bacteria in response to heavy rainfall events (>10 mm-day-1) during the rainy season. At this time, the incidence of diarrhoeal diseases is observed to increase substantially. Dynamical downscaling of climate projections from the HadCM3 general circulation model (SRES A2 forcing scenario) indicates a rise in the frequency of heavy rainfall events over the 20th century in Uganda. Climate change is, therefore, expected to increase the risk of diarrhoeal diseases in Kampala and similar environments. Significant correlations between sanitary risk scores and bacteriological contamination of groundwater-fed sources in Kampala highlight the critical role of improved community hygiene in reducing this risk.