This research uses analyses from Nile catchment rivers, wadis, dunes and bedrocks to constrain the geological history of NE Africa and document influences on the composition of sediment reaching the Nile delta. Our data show evolution of the North African crust, highlighting phases in the development of the Arabian-Nubian Shield and amalgamation of Gondwana in Neoproterozoic times. The Saharan Metacraton and Congo Craton in Uganda have a common history of crustal growth, with new crust formation at 3.0-3.5 Ga, and crustal melting at c. 2.7 Ga. The Hammamat Formation of the Arabian-Nubian Shield is locally derived and has a maximum depositional age of 635 Ma. By contrast, Phanerozoic sedimentary rocks are derived from more distant sources. The fine-grained (mud) bulk signature of the modern Nile is dominated by input from the Ethiopian Highlands, transported by the Blue Nile and Atbara rivers. Detrital zircons in the Nile trunk are predominantly derived from Phanerozoic cover rocks. Most detritus from the upstream White Nile is trapped in the Sudd marshes and contributes little to the Nile trunk. Therefore, the White Nile downstream is dominated by locally derived Phanerozoic cover. The White Nile proximal to the Gezira Fan is influenced by the fan’s Blue Nile signature.