Studies to examine the prevalence of water-related diseases, cyanobacteria toxins and other health risks at landing beaches in the Ugandan portion of the Lake Victoria basin were carried out. Based on surveillance studies and other data sources in the region, water samples were analysed for indications of faecal contamination. The coliform numbers were generally high for most sampling sites, indicating significant water contamination. The wet seasons exhibited significantly higher coliform counts than the dry seasons for all lakeshore sample sites. This seasonal variation in coliform counts correlated positively with the incidence of waterborne diseases, which are typically higher in the wet season. The water supply for domestic consumption for the Lake Victoria riparian communities is mainly the lake itself. The most prevalent diseases associated with the landing sites include malaria, dysentery, diarrhoea and bilharzia. Malaria was most prevalent, followed by dysentery, in all the studied districts. Many people in the catchment dispose of faecal wastes in lakeshore area bushes, or in polythene bags, contaminating water sources with faecal material, and resulting in waterborne diseases. The vulnerability of lakeside communities to water-related diseases is further aggravated by low accessibility to health facilities and personnel. Further, cyanobacteria (potentially toxic to humans and animals) dominate other algal species in Lake Victoria, contributing >50% of the algal biomass. Algal blooms occurred frequently in Murchison Bay, a source of drinking water for the city of Kampala and surrounding urban centres. Algal blooms can cause unpleasant odours and tastes in domestic water supplies, clog pump and machinery filters, increase chlorine demands for water disinfection, and necessitate more complex and expensive treatment processes. The findings of this study suggest improved water quality, changes in sanitation and hygiene behaviour could significantly reduce the prevalence of water-related diseases and cyanotoxins in the Ugandan portion of the Lake Victoria basin.