Lake Victoria is the second‐largest freshwater lake in the world, with a surface area of 68,800 km2. The lake is rich in natural resources that are essential to the local economy and livelihoods. However, International Union for Conservation of Nature (IUCN) ranks 76% of freshwater species endemic to the Lake Victoria Basin as threatened with extinction. The biodiversity richness of the lake is still diminishing, and the risk of species extinction is increasing. Many species are yet to be identified, and thus the number of species threatened with extinction exceeds what is currently known. Furthermore, the lake is home to species that are found nowhere else on the planet, but its protection is never given the attention it needs. Genetic diversity loss is harmful to future populations and influences sustainability of the ecosystem. The decline in Lake Victoria's biodiversity is primarily attributed to various pressing issues, including water pollution, invasive species, climate change, overexploitation and the challenges stemming from high human population density. These problems are exacerbated by inadequate regulatory enforcement and a lack of comprehensive data and information to inform and guide conservation efforts. If these factors are not addressed, they may have a detrimental impact on Lake Biodiversity. This article aims to document the main threats to aquatic biodiversity as well as potential management strategies for preventing further losses of the aquatic biodiversity in Lake Victoria. The study recommends reviewing, bolstering and reinforcing the rules and regulations governing the extraction, accessibility and discharge of nutrients into the lake. The national governments should work with local governments, non‐governmental organizations and local people to safeguard and conserve the lake's biodiversity. The national governments of the riparian nations should also reserve funds each fiscal year specifically for research that would inform effective management measures to prevent further losses of the lake's biodiversity.