[2][3] Approximately 3 million years ago, strong easterly winds formed long dunes, which ran from east to west across the middle of the Kalahari Desert.

[5] Approximately 2 million years ago, the fault known as the Ovamboland-Kalahari-Zimbabwe axis (which runs from NE to SW from Harare through Bulawayo and ends in the east side of the Kalahari Desert) moved in an epeirogenic flexure, and cut off the drainage route into the Limpopo.

Another is thought to have been the less obvious Gidikwe Sand Ridge lying just to the west of the western border of the present Makgadikgadi National Park.

In October 2019, a team led by Vanessa Hayes proposed that land around Lake Makgadikgadi was the area where modern humans (Homo sapiens) first evolved.

The researchers were able to trace where the earliest maternal lineage of modern Homo sapiens emerged, about 200,000 years ago (200 kya).

[7] 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.

[8][3] Excavations of early Homo sapiens activities have been found at Ga-Mohana Hill in Northern Cape dated to 105,000 years ago (105 kya).

[9] 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.