The Koora Basin (south Kenya Rift) preserves a continental, tropical, one-million-year record of environmental change driven by global climate, regional tectonism and volcanism. Diatom-based reconstructions from Olorgesailie Drilling Project (ODP) cores indicate lakes that expanded and contracted with conductivities ranging between ∼200 and > 25,000 μS.cm−1 and pH of 7.9–11.2. Benthic and planktonic diatoms document mostly shallow fresh water between 1 Ma and 870 ka with deeper freshwater lakes from 870 to 470 ka. After the Mid-Brunhes Event at about 430 ka, diatoms record many transgression-regression cycles with both freshwater and saline-alkaline lakes present. Palaeosols also indicate episodes of desiccation and lower water tables. Carbonates and zeolites are present in younger sediments, especially after 400 ka. Many high-lake-level stages correlate with low values in ocean benthic δ18O stack data. Most, but not all, low lake levels occurred during higher δ18O MIS intervals, suggesting tectonic and/or volcanic events, in addition to climatic forcing, influenced the drainage, outlet heights and accommodation space.The 870–470 ka period of deeper freshwater lakes at Koora correlates well with the neighbouring Lake Magadi pollen record that suggests generally wetter conditions at this time. Wet-dry cycles after 470 ka at Koora developed when the Magadi record indicates a change towards drier conditions, but with many wetter intervals. High lake level periods at Koora also correlate with phases of diatom-inferred flooding at Magadi. Outcrops north of Koora also document several large lakes during deposition of parts of the Olorgesailie Formation prior to ∼500 ka. The Koora environmental history helps to fill an environmental gap (500–320 ka) encompassing critical changes in hominin lithic technology caused by a hiatus at Olorgesailie. During the first part of this interval (470–390 ka), Koora was occupied by a shallow alkaline lake, suggesting relatively dry conditions. The second part (390–320 ka) was characterised by fluctuating deeper lakes that imply greater variability and wetter conditions. Subsequently, both the Olorgesailie and Koora records indicate variable environments.