The Lake Kivu catchment in the East African Rift is subject to various geologic hazards, including frequent volcanic eruptions, earthquakes, and potential limnic overturns and degassing events. Integration of high-resolution seismic reflection data, 14C dated sediment cores, and lake-floor bathymetry reveals large axial and transverse turbidite systems in the eastern basin of the lake. The turbidites were sourced by hyperpycnal river flows during exceptional floods, and the temporal occurrence of the turbidites was climatically controlled. The turbidite record over the past ∼12 k.y. is correlated with the regional paleohydrologic records from tropical East Africa. Our study suggests that flood-introduced turbidites preserved in deep lakes are indicators of hydrological changes, and that extreme floods in Lake Kivu’s recent history may have triggered deep mixing events. This study also has implications for the current degassing efforts in Lake Kivu; potential geologic hazards may be triggered by extraordinary turbidity currents, and need to be considered in the design and deployment of gas extraction facilities.