Petrographic, XRD, EDS, SEM and SIMS microanalysis demonstrate that Pleistocene Magadi cherts formed primarily from the precipitation of an amorphous siliceous gel and occasionally from hydrous sodium silicates, such as magadiite or kenyaite. Brine simulations and oxygen isotope analysis support the formation of these cherts from highly evaporated brines at modern lake temperatures near surface. Fossils within chert, including, microorganisms, diatoms, gastropods, ostracods, and plant and insect fragments provide valuable paleoenvironmental information, including the presence of alkaliphilic fungal communities found in chert. Identifiable crystal habits in evaporite pseudomorphs of trona and gaylussite suggest saline conditions were present throughout much of the basin history. Labyrinth patterns discovered in Magadi cherts indicate the precipitation of silica gels in the saline-alkaline Lake Magadi system near the surface in conjunction with chert formation. Hele-Shaw cell experiments conducted to replicate Magadi labyrinth patterns, however some of these patterns in nature occurred along non-horizontal planes. The orientations of the Magadi patterns imply invasion of air from above if confined to open cracks or infiltration from all sides if the gels dried and cracked in the vadose zone. Cherts developed from siliceous gel precursors have elevated d18O values, from +41‰ to +47‰ indicating the formation in the presence of brines. Such brines, with total dissolved solids of ~ 220,000 to 300,000 mg/L, exist in the modern Magadi basin during dry periods. Cherts with magadiite and other hydrous sodium silicates precursors form brines with lower salinities than cherts formed from gels. Cementing chalcedony and megaquartz crystals in chert have lower d18O values that require formation from waters at elevated temperatures, which suggests a hydrothermal origin. Finally, siliceous mudstone cherts show relatively wide ranges of d18O, from +37‰ to +46‰, which suggests formation from subsurface brines. Based on this new information, we have further classified the origins of chert in Lake Magadi, Kenya and extended the presence of a high salinity paleoenvironment to ~500 ka before present.