Water safety and climate mitigation measures are global concerns. In this study, climate variability and related health implications were examined. The data included 11,101 outpatient records in the Luwero district from the Ugandan Ministry of Health database, the records of 2,358 outpatients connected with water-related health risks linked to climate variability (diseases such as cholera, typhoid, acute diarrhoea and dysentery) from seven sub-county health centres, monthly mean rainfall data for 30 years (1977–2007), and information from 90 households that harvest rainwater near the local health units. Using a logistic regression, the analysis controlled for the following list of social factors that potentially influence capabilities: personal characteristics (education), cultural norms, the capacity to cope with shocks, seasonal variation, societal favouritism and community segregation. Integrated water management, man-made induced activities and information on effects of climate variability were important in mitigation planning. Young people, including those under the age of 18, were significantly more vulnerable than people of other ages to water-related health risks linked to climate variability. Although both the young and the elderly are susceptible to waterborne illnesses, the findings reveal a link to climate variability, which is inadequately emphasised. We recommend persistence in climate mitigation measures and control against water-related risks.