Abstract. Lake Victoria ecosystem has undergone major ecological changes in the recent decades. Sedimentary diatom analysis and Fe / Mn determined by Energy Dispersive X-ray Fluorescence (EDXRF) have provided phytoplankton (diatom) productivity and the resultant anoxia (Fe / Mn) in Lake Victoria at Napoleon Gulf during the late Holocene (1778 cal yr BP (calibrated years before present) to 2008 AD) with radiocarbon dates determined using Accelerator Mass Spectrometry standard method. The results showed that increased total diatom counts in Napoleon Gulf during the late Holocene correspond with increased Fe / Mn ratio (anoxia) in some of the profiles and not in others and in most cases those that correspond correlate very well with increased eutrophication from nitrate input (Total Nitrogen, TN). Therefore slightly increased anoxia not related to increased diatom productivity was recorded in Lake Victoria at Napoleon Gulf from the period 1778 to 1135 cal yr BP. There was slightly increased diatom productivity at Napoleon Gulf from the period 857 to 758 cal yr BP but it did not increase anoxia in the lake. The period 415 cal yr BP to 2008 AD recorded increased anoxia at Napoleon Gulf related to high diatom productivity especially from 415 to 390 cal yr BP and 191 cal yr BP to 2008 AD.