Understanding how large river systems will respond to an invigorated hydrological cycle as simulated under higher global temperatures is a pressing issue. Insights can be gained from studying past wetter-than-present intervals, such as the North African Humid Period during the early Holocene Epoch (~11–6 thousand years ago). Here we present a 1,500-year-long annually laminated (varved) offshore sediment record that tracks the seasonal discharge of the Nile River during the North African Humid Period. The record reveals mobilization of large amounts of sediments during strong summer floods that may have rendered the Nile valley uninhabitable. More frequent and rapid transitions between extremely strong and weak floods between 9.2 and 8.6 thousand years ago indicate highly instable fluvial dynamics. Climate simulations suggest flood variability was paced by El Niño/Southern Oscillation on interannual timescales, while multi-decadal oscillatory modes drove changes in extreme flood events. These pacemakers have also been identified in the Nile flow records from the Common Era, which implies their stationarity under contrasting hydroclimatic conditions.