Microbiologically contaminated water severely impacts public health in low-income countries, where treated water supplies are often inaccessible to much of the population. Groundwater represents a water source that commonly has better microbiological quality than surface water. A 2-month intensive flow and quality monitoring programme of a spring in a densely settled, unsewered parish of Kampala, Uganda, revealed the persistent presence of high chloride and nitrate concentrations that reflect intense loading of sewage in the spring’s catchment. Conversely, thermotolerant coliform bacteria counts in spring water samples remained very low outside of periods of intense rainfall. Laboratory investigations of mechanisms responsible for this behavior, achieved by injecting a pulse of H40/1 bacteriophage tracer into a column packed with locally derived granular laterite, resulted in near-total tracer adsorption. X-ray diffraction (XRD) analysis showed the laterite to consist predominantly of quartz and kaolinite, with minor amounts (<5%) of haematite. Batch studies comparing laterite adsorption capacity with a soil having comparable mineralogy, but with amorphous iron oxide rather than haematite, showed the laterite to have a significantly greater capacity to adsorb bacteriophage. Batch study results using pure haematite confirmed that its occurrence in laterite contributes substantially to micro-organism attenuation observed and serves to protect underlying groundwater.