About 5 million years ago, the Antarctic polar ice caps started to form. This resulted in Southern Africa becoming increasingly dry until about 3 million years ago an extended dry period started. During this dry period strong easterly winds blew across the middle Kalahari and formed elongated dunes the ran from east to west.
As Southern Africa became wetter, the water of the rivers of the area were channelled by these dunes and they flowed into Lake Makgadikgadi. It was also during this period that the Okavango and Zambezi rivers started to flow.
About 1 million years ago, the earth crust under Southern Africa experienced an upheaval which changed the course of these rivers. This fault, known as the Kalahari-Zimbabwe axis caused the rivers to flow into a large basin called Lake Makgadikgadi, which soon filled up. Lake Makgadikgadi became one of Africa’s largest lakes. This damming resulted in the formation of a series of swamps.
The formation of yet another fault, the Gumare fault, caused a reduction in the elevation of the land, caused the water of the Okavango River to spread out over a much larger area of land. As the Okavango River left the Angolan highlands and entered the arid flatness of the Kalahari, it slowed and dropped a million tons of sand and debris, channels became blocked and the water sought other courses, continuing to deposit its sediments wherever it travelled creating the characteristic fan shape of the Delta. Eventually the lake was filled to capacity and the water had to find a way to the ocean. Therefore, about 20 000 years ago the waters of this great lake were forced northwards and then eastwards. This caused the middle and lower Zambezi to connect, which resulted in the formation of Victoria Falls. With the water now able to flow out of the lake, a partial draining of the lake occurred. A drier climatic period followed which caused an increase in evaporation and a decrease in the river flow.
By about 10 000 years ago the drying of the Makgadikgadi Lake was in an advanced stage. Windblown sand, as well as the Okavango River depositing increasing amounts of sediment and debris in the lake, were gradually filling the lake.
Two parallel faults direct the way the Okavango enters the Kalahari Basin in an area called the Panhandle it then fans out into several channels. Some of these channels permanently have water, namely the Boro, the Thaoge and Ngugha channels. Deep water occurs in only these few channels, while vast areas of reed beds are covered by only a few inches of water.
The Okavango River channels are blocked by two southern faults, the Kunyere and the Thalamakane. More than 95% of the Okavango’s water evaporates before it reaches the Thamalakane fault/river. The Thalamakane Fault acts as a 150-mile-long natural dam: Here the channels abruptly change direction and join to form one river, the Boteti, which flows eastwards through a break in the fault towards the Makgadikgadi Pan. A small channel, the Nghabe River, continues southwest toward Lake Ngami, serving as both inlet and outlet depending on the strength and direction of the annual floods.
The Okavango is unique in that it forms a freshwater Delta, simply because it has several outlets. Even though their outflow comprises only three percent of the Okavango’s inflow, this is enough to carry away most of the salts and keep the Delta’s waters fresh. In fact there are 2 groups of outlets: west to Lake Ngami, and south and east to the Makgadikgadi Pan via the Boteti River.
Today the only remains of the Ancient Lake Makgadikgadi (apart from the Okavango Delta) are Nxai Pan, Lake Ngami, Lake Xau, the Mababe Depression, and the two main pans of Makgadikgadi (Sua and Ntwetwe Pans).