The Intergovernmental Panel on Climate Change (2014) predicts by the end of this century ~1 4 degrees_C warming and an uncertain trend in future rainfall in the Great Lakes region of East Africa, perhaps 10% lower than present in the Malawi/Nyassa basin and 10% higher in the lake basins to the north. Radar altimetry records of lake level trends available since 1992 display decadal scale variability of 1-2 m, with an overall trend in the last decade towards lower levels in Lakes Malawi/Nyassa and Rukwa, and higher levels in the lakes to the north of Rukwa. As the human population grows in the Great Lakes region, the need arises for enhanced food production. The potential for accomplishing this is quite high, albeit through an expansion of irrigation and fertilizer application. These would pose serious threats to the Great Lakes, with potential for lakes shifting from open- to closed-basin configuration and the development of extensive anoxic dead zones where fish no longer survive and toxic algae blooms threaten the health of lakeshore communities. If the Great Lakes are to survive, East Africa's economy must shift from one supported predominantly by agricultural export to an economy based on another key driver, such as manufacturing or information processing.