Sediments accumulated in lake basins consist of various organic and inorganic materials, mostly utilized as proxies for climatic changes and as historical records of the lake connectivity to terrestrial ecosystems and anthropogenic activities. In-lake production, aerial wet and dry deposition and transported materials in running water are the main sources of lake deposits, which may be permanently deposited as bottom sediments or remobilized through erosive forces and turbulence, resuspension, tunneling by organisms, and porewater exchanges with the overlying water mass. Examination of the sediment biodiversity, quality, composition, and stratigraphy is part of the approaches in understanding ecological and climatic changes and other anthropogenic impacts in lakes. There are no detailed studies on the spatial distribution of sediment characteristics within the Nyanza Gulf, especially after the establishment of water hyacinth. The first observations on the nature of the bottom of Lake Victoria were made during 1927-1928 survey, with subsequent detailed geochemical core studies concentrated in the main lake. Roles of sediment organic matter are explained, and data from surficial sediments collected, from about 32 sampling sites between 1994 and 2012, are used to characterize the sediments. Lastly, the potential influences from increased urbanization, eutrophication, presence of water hyacinth (Eichhornia crassipes), and associated floating macrophytes since 1989 and current cage aquaculture in L. Victoria are explored.