Lake Victoria, the second largest freshwater body in the world is affected by rise in eutrophication. This is mainly due to anthropogenic activities happening in the catchment. In this study, distribution of six elements (Cu, Zn, N, C, P, and Si) in sediments were studied from the five sites in Kenya namely Kisumu (DK2, OK2), Busia (KK2), Siaya (SPK2 and Kapsabet (KP1A). The elemental flux values were correlated with historical changes in the catchment to see if it can influence the eutrophication in Lake Victoria. Flux calculated for these elements show a strong correlation with anthropogenic activities associated with land-use changes ushered after building of the railroads, agricultural practices and urban development in the catchment. The spatial and temporal changes in distribution of these elements have a distinct signature on the metal flux. The metal flux are correlated with change in trophic conditions in the lake. There is also a distinct difference in metal flux into the lake derived from urban versus rural areas.