Sediments of two stacked megafans in the Owambo Basin of northern Namibia and southern Angola were made accessible by a ca. 400 m long, continuously cored borehole. Previous studies indicate that the lower, buried Palaeocene–Eocene Olukonda Megafan was deposited by a palaeo-Kunene River transporting material from the northwest, i.e. the Kunene Intrusive Complex and the adjacent Angola Shield. The morphology of the upper, Eocene–Pliocene Cubango Megafan suggests a northern sediment input by 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 already 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 accordance with the geochronologically more varied geology of the source region in the north, the Cubango Megafan detrital zircon record shows a wide distribution of Palaeoproterozoic to Archaean 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.