Kenya's Baringo-Tugen Hills-Barsemoi drill site is one of six localities across Kenya and Ethiopia from which the Hominin Sites and Paleolakes Drilling Project has obtained sediment cores in an effort to investigate the role of environmental forcing in shaping human evolution. The Baringo Basin site features extensive exposures of the Chemeron Formation, which contains >100 fossil vertebrate localities including five hominin sites. The 228-m drill core, dating from ~3.29 to 2.56 Ma, is characterized by fluvio-lacustrine sediments, including multiple diatomites, with evidence of variable degrees of later pedogenic modification. In the lower part of the core (~3.29–3.04 Ma), diatoms were preserved only in very low abundance, consistent with predominantly fluvial or lake marginal environments. In contrast, five diatomites and two additional diatom-rich intervals were deposited after ~3.04 Ma, reflecting a major shift in the basin hydrology. Planktonic freshwater species dominated these diatom-rich intervals, whereas periphytic taxa were present in proportions less than 2%, suggesting that these intervals represent open-water deposition during lake highstands. Littoral or saline assemblages are largely absent throughout the core. Instead, we observed a pattern of increasing diatom frustule dissolution at the tops and bottoms of diatomite units, indicating increased alkalinity during the transgressive/regressive phases. A Na-bearing zeolite (analcime) indicative of saline waters precipitated in clastic-dominated intervals between diatomites, suggesting extreme environmental variability between lake highstands and lowstands. Diatom assemblages were consistently dominated by a few species belonging to the genera Aulacoseira and Stephanodiscus, which were at times co-dominant. We infer that assemblages dominated by Aulacoseira represent a well-mixed lake with abundant supply of silica. When Stephanodiscus was dominant, which occurred more frequently in the later freshwater phases, we infer incomplete mixing and reduced silica flux to the epilimnion (upper water layer).