Lake Victoria is the largest lake in Africa and its outflows strongly influence flows in the White Nile, including the availability of water for hydropower generation, irrigation and water supply. Understanding the water balance is a major challenge since the lake is large enough to influence the local climate and its catchment spans several countries. Hydrometeorological monitoring networks are also sparse in some parts of the basin. In this paper, we consider the history of water balance estimates for the lake and how the science has developed as new information and techniques have become available, including in areas such as seasonal flow forecasting and estimating the potential impacts of dam operations and climate change. These findings are placed into a wider context including the challenges arising from a changing climate and evolving ideas from international research programmes, which lead to some suggestions for future research priorities for Lake Victoria and other sub-Saharan/Rift Valley lakes.