Rainwater harvesting (RWH) provides household water supply to rural and peri-urban populations that do not have access to centralised water services. The climate in south-west Uganda is particularly well suited to RWH due to bi-annual rainy seasons, which allows for the collection of rainwater to occur over two periods throughout the year. Water quality from RWH, however, depends on how well risk of contamination (ROC), from catchment to consumption, is managed. Using a mixed-methods approach, we assessed the maintenance practices and water quality of 20 RWH installations in Uganda in the dry and rainy seasons. Both domestic and institutional RWH systems were assessed. Sanitary surveys, site inspections, key informant interviews and physiochemical and bacteriological tests were conducted to identify the factors that have an impact on water quality. Water quality test results were compared to guidelines recommended by the World Health Organisation (WHO). We looked at measures that can reduce the ROC across the RWH system. We found that water quality at 75% of the sites met WHO standards. At these sites, end-users reported that they cleaned systems at least twice a year. Where training on system maintenance had been carried out, end-users reported more regular cleaning and maintenance of systems. Sanitary surveys highlighted an absence of first-flush or pre-filtration as the most prevalent ROC. Overall, we found that both access to technical specialists and capacity-building activities led to well-maintained RWH systems that provide acceptable water quality at both a household and community level.