A mid to late Tertiary lake, Palaeolake Etosha, was the single collective end point of three drainage systems feeding southwards off the central Angolan highlands, the Cubango and Kunene Megafans and the Cuvelai Drainage System. The lake beds consist of 50 m of saline, olive green clay, the Etosha Pan Clay Member, containing authigenic analcime, monoclinic K-feldspar and glauconite. Fossil suites in two local sandstones near or at the top of the clay, the Oshigambo and Ekuma Delta Sandstone Members, include various antelope, pig, zebra, quagga, rhinoceros, elephant, lion, spring hare, ostrich, flamingo, crocodile, hippopotamus, freshwater turtles, catfish, bivalves and trees, which have respective ages of 6 ± 1 Ma and 4 ± 1 Ma. An oolitic, pan-margin limestone of limited lateral extent, the Poacher’s Point Carbonate Member, was the last unit deposited in the palaeolake. Flooding and complete desiccation were common occurrences in Palaeolake Etosha before it dried up completely at about 4 Ma under conditions of progressively increasing aridity. Over the ensuing 2 Ma, a huge groundwater calcrete, the Etosha Calcrete Formation, advanced northwards over the dry lake deposits and the surface Kalahari sands were reworked to produce the regional Kalahari dune fields.
Resumption of periodic flow in the Cuvelai system resulted in cycles of flooding and desiccation in an ephemeral Cuvelai endpoint lake atop the Etosha Calcrete Formation in the Etosha area. Fragmentation of the calcrete by salt enabled strong easterly winds to remove the calcrete fines from the Etosha depression. This initiated the ‘excavation’ of the present Etosha Pan by wind ablation. Lunette dunes on the western side of Etosha Pan contain an inverted pan stratigraphy. Flooding of the present pan occurs occasionally and has been as deep as 10 m in the past. White magadi-type chert nodules have formed locally on the pan floor in animal footprints.