The great lakes of Africa, Lakes Victoria, Malawi, and Tanganyika, are located in East Africa in the vicinity of the Great Rift Valleys and hold approximately 27% of the world’s freshwater. Lake Victoria is set between the Rift Valleys and is bounded by uplifted mountains and highlands associated with rifting. Compared to the other lakes, it is geologically younger (less than half a million years) and much shallower with markedly lower water clarity; Secchi depths average between 0.5 and 2.4m (Lung'ayia et al., 2001). Lakes Tanganyika and Malawi are older (millions of years), deeper, meromictic lakes set within the rift valleys. These deep lakes have exceptional water quality and water clarity, with Secchi depths that often exceed 12m (Guildford et al., 2007; Verburg et al., 2003).
The East African Great Lakes are known for their species flocks of endemic cichlid fishes that are a substantial portion the lakes’ native icthyofauna. Each lake, however, has a unique fish community, in part due to differing geological histories as well environmental and ecological effects.
The African Great Lakes support beneficial uses including hydroelectric power, inland water transport, industries, tourism, wildlife, and fishery sectors (Bootsma and Hecky, 1993; Ogutu-Ohwayo et al., 1997). Increasing population has led to widespread deforestation for fuel and timber, and increased agricultural land use leading to accelerated erosion, sedimentation and nutrient loading. There is also increased pressure on the domestic water supply and increased discharge of waste and pollutants into the lakes (Ogutu-Ohwayo et al., 1997). The combined agricultural and urbanization land use surrounding the lakes varies between 30−70% (Scheren et al., 2000; World Resources Institute, 2003a). Much of the land surrounding lakes Tanganyika and Malawi is steep, limiting human occupation and agricultural use resulting in reduced anthropogenic impacts in these areas of the watersheds (Hecky et al., 2003). Where steep rift valley slopes are occupied by humans, soil erosion is a serious problem (Cohen et al., 1996).