thumb|The Makgadikgadi Salt Pans in Botswana mark the remnants of the lake today. They are one of the most important breeding sites in Southern Africa for [[Lesser flamingo|lesser and greater flamingos]]
Lake Makgadikgadi (, ) was a paleolake that existed in what is now the Kalahari Desert in Botswana from 2,000,000 years BP to 10,000 years BP. It may have once covered an area of from and was deep. The Okavango, Upper Zambezi, and Cuando rivers once all emptied into the lake. Its remains are seen in the Makgadikgadi salt pans, one of the largest salt pans in the world.
DNA research suggests (though this remains a matter of controversy) that the lake region is the homeland of Homo sapiens, where humans first evolved as a distinct species about 200,000 years ago, before expanding to other parts of Africa about 70,000 years later.
Northern Botswana has a series of deep, underlying fault lines running beneath its sands. These faults are thought to be the southernmost extensions of the same system of parallel fault lines that are pulling away from each other and have formed East Africa's Great Rift Valley. Parts of the courses of both the Linyanti River and Chobe River mark the line of these faults today.
A drier climatic period followed, which increased evaporation and decreased the flow of the rivers that fed the lake. By about 10,000 years ago the drying of Lake Makgadikgadi was in an advanced stage. Sediment and debris from the Okavango River and windblown sand were gradually filling the lake.
The conclusion is disputed by Chris Stringer, head of human origins at the Natural History Museum in London, and Sarah Tishkoff, a geneticist at the University of Pennsylvania.
Excavations of early Homo sapiens activities have been found at Ga-Mohana Hill in Northern Cape dated to 105,000 years ago (105 kya).
Ecology
Lake Makgadikgadi is theorised to have been the birthplace of the vast number of cichlids that once swam the Congo, Zambezi, Okavango and Limpopo rivers—as many as 100 to 400 new species, of which approximately 25 survive today. The lake's sheer size may have provided the ancestors of these fish with an extremely wide range of new ecological niches to exploit and thus could have served as the stimulus for the evolution of the new species, which they may have done in record time before the lake drained completely. The theory further says that the new species, after having evolved within the confines of the lake, could have escaped with the lakewater as it drained, and populated the rivers of the region to evolve into the cichlids that exist today.
In current times this land is desiccated most of the year and is a seasonal wetland in the rainy summer months.
Legacy
Today the only remains of Lake Makgadikgadi are the Okavango Delta, the Nxai Pan, Lake Ngami, Lake Xau, the Mababe Depression, and the two main Makgadikgadi pans: the Sua Pan and the Nwetwe Pan.
The Makgadikgadi Salt Pans are among the largest in the world and are formed from the last remnants of this great lake. The Okavango Delta is a very large, swampy inland delta formed where the Okavango River reaches the former bed of the lake. It is now an endorheic basin in which all the water reaching the basin is ultimately evaporated and transpired.
The other south draining rivers that once fed the lake have now all been captured by the Zambezi.