The sediments in two stacked megafans in the Owambo Basin of northern Namibia and southern Angola were made accessible by a c. 400 m long, continuously cored borehole. Previous studies have indicated that the lower buried Paleocene– Eocene Olukonda Megafan was deposited by a palaeo-Kunene River transporting material from the NW (i.e. from the Kunene Intrusive Complex and the adjacent Angola Shield). The morphology of the overlying Eocene–Pliocene Cubango Megafan suggests the input of sediments from the north via the Cubango River. Mineralogical and geochemical data from the upper fan indicate felsic metamorphic and granitoid sources. Previous studies, however, did not provide a unique provenance identifier. Combining detrital zircon U–Pb data from both megafans with previously published and newly obtained mineralogical and geochemical data confirms two distinct provenances. The Olukonda Megafan can now be uniquely attributed by means of its detrital zircon ages to the Kunene Intrusive Complex and the surrounding Epupa Metamorphic Complex. In good agreement with the geochronologically more varied geology of the source region in the north, the Cubango Megafan detrital zircon record shows a wide distribution of Paleoproterozoic to Archean ages, but also a younger age range, probably related to a later Damaran/Pan-African source, which is absent in the Olukonda detrital zircon record.