There is a global dimension to lake management in Africa and elsewhere that will require a concerted action not only from individual riparian states, but also from regional, continental and global communities. The current global lake threats arise from climate change, regional land degradation and semivolatile contaminants, and share the common feature that the atmosphere is the vector that spreads their impacts over large areas and to many lakes. The Great Lakes of Africa (Malawi, Victoria and Tanganyika) are particularly sensitive to these problems because of their enormous surface areas, slow water flushing rates, and the importance of direct rainfall in their water budgets. Their response times might be slow to yield a detectable change and, unfortunately, their recovery times might also be slow. It is possible for atmospheric effects to act antagonistically to the impacts of catchment change, but antagonistic effects could become synergistic in the future. Improved understanding of the physical dynamics of these lakes, and development of models linking their physical and biogeochemical behaviour to regional, mesoscale climate models, will be necessary to guide lake managers.