Lake Magadi is an internally drained, saline and alkaline terminal sump in the southern Kenya Rift. Geochemistry of samples from an ~200 m core representing the past ~1 m.y. of the lake's history shows some of the highest concentrations of transition metals and metalloids ever reported from lacustrine sediment, including redox-sensitive elements molybdenum, arsenic, and vanadium. Elevated concentrations of these elements represent times when the lake's hypolimnion was euxinic—that is, anoxic, saline, and sulfide-rich. Euxinia was common after ca. 700 ka, and after that tended to occur during intervals of high orbital eccentricity. These were likely times when high-frequency hydrologic changes favored repeated episodes of euxinia and sulfide precipitation. High-amplitude environmental fluctuations at peak eccentricity likely impacted water balance in terrestrial habitats and resource availability for early hominins. These are associated with important events in human evolution, including the first appearance of Middle Stone Age technology between ca. 500 and 320 ka in the southern Kenya Rift.