Understanding how large river systems will respond to an invigorated hydrological cycle as simulated under higher global temperatures is a pressing issue. We present here a 1500 yr-long annually-laminated (varved) record that tracks the seasonal discharge of the Nile River during the wetter- and warmer-than-present Early Holocene. This unique record depicts the mobilization of large amounts of sediments during strong summer floods that probably rendered the Nile valley inhabitable. More frequent and rapid switching between extreme (strong and weak) floods between 9.2 and 8.5 ka BP indicate highly instable fluvial dynamics. On interannual timescales, flood variability is paced by El Niño-Southern Oscillation while multi-decadal oscillatory modes drive the changes in extreme flood events. These pacemakers are also identified in Nile flow records from the Common Era, which demonstrates their stationarity under different climatic conditions.