Our results show that the late Pleistocene Nile in northern Sudan was shifting position and actively aggrading at 145 ± 20 kyr, 83 ± 24 kyr, 32 ± 8 kyr and 20.7 ± 0.2 kyr and indicate, for the first time, a phase of high-energy flow in the White Nile at 27.8 ± 3.2 kyr, with still high but somewhat reduced flow in that river at 13.3 kyr, 10 kyr and 4.8-4.0 kyr. Beach ridges associated with a 386 m strandline of the White Nile have OSL ages of 27.5 ± 2.7 kyr and 14.5 ± 1.6 kyr. The Holocene terraces and former channels of the main Nile have ages of 11 kyr, 6.5-5.0 kyr and 4.8-4.0 kyr, after which there was a general decline in flood discharge. The now arid main Nile valley in northern Sudan was significantly wetter during the early to middle Holocene, with a lake up to 450 km2 in area, fed by an overflow channel from the early Holocene Nile between 9.5 kyr and 7.5 kyr. Previously stable late Pleistocene dunes were reactivated at intervals during the Holocene, with five samples from the White Nile valley indicating brief phases of Holocene dune activity at 9.9 ± 2.0 kyr, 9.0 ± 2.8 kyr, 6.6 ± 0.9 kyr, 4.8 ± 0.9 kyr and 2.9 ± 0.5 kyr, the earliest of which occurred within periods of generally wetter climate and higher Nile flow. The youngest freshwater shells on the Khor Abu Habl alluvial fan west of the White Nile correspond to a time of regionally wetter climate between 1.7 and 1.0 kyr. Our results suggest that millennial scale climatic instability may have been characteristic of Holocene climates in this region.