Studies to examine the prevalence of water-related diseases and other health risks in the Lake Victoria region of Uganda were carried out. Surveillance studies were done by the Water Resources Management Department (Directorate of Water Development) and the Fisheries Resources Research Institute. Other sources of data included review and analyses of findings from the Ministry of Health and other studies in the region. Faecal coliform counts in water samples were analysed for indication of faecal contamination. The coliforms were generally very high in most of the sampling sites indicating high contamination of waters. The riparian communities source their water for domestic consumption mainly from the lake. The wet seasons had significantly higher coliform counts than the dry seasons for all lakeshore sites. This seasonal variation in coliform counts correlated positively with waterborne disease incidences that were higher in the wet season. The most prevalent diseases in the landing sites included malaria, dysentery, diarrhoea and bilharzia. Many people in the catchment disposed their wastes in bushes or in polythene bags, contaminating water sources with faecal material and leading to waterborne diseases. Lakeside communities’ vulnerability to water-related diseases was further aggravated by low accessibility to health facilities and personnel. In Lake Victoria, cyanobacteria (potentially toxic to humans and animals) dominate other algal species and contribute a larger fraction (>50%) of the biomass. Algal blooms were found to be frequent in Murchison Bay, a source of drinking water for Kampala and the surrounding urban centres. Algal blooms cause unpleasant odours and tastes in domestic water supplies, clog filters on pumps and machinery, increase chlorine demand, requiring more complex and expensive treatment process. Findings suggest that improvements in water quality, sanitation and hygiene behaviour change can significantly reduce prevalence of water-related diseases.