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Sedimentological and microbiological studies have been undertaken of the cherts of the Magadi basin in the deepest part of the Kenya Rift. The results of field studies, supported by microscopic and SEM analyses, have produced new ideas on the genesis of the cherts. Formation of the cherts has previously been explained abiotically by the alteration of Na silicates. However, high concentrations of coccoid and filamentous cyanobacteria and other organisms were found in the cherts and the precursor sediments (calcified Pleurocapsa in colonies, blooms, mats, and bacterial stromatolites; Microcoleus; Microcystis).

Two main chert horizons with different precursor sediments have been distinguished: (1) a lower chert horizon of Pleistocene age that contains amorphous silica, minor Na-silicates, erionite, and calcite (Green Beds), and (2) a thinner upper chert horizon with preserved magadiite laminae (High Magadi Beds). The precursor sediments of both cherts were deposited on trachyric pyroclastic detritus in a muddy faulted depression. The pyroclastic deposits were decomposed by alkaline groundwater, which discharged from silica-enriched springs along fault lines and formed colloidal silica sols. The precipitation of silica phases, Na-silicates, and caicite was controlled by the production of biogenic CO2 and its resulting effects on the pH.

The precursor sediments had an unusual viscous, putty-like consistency. The sediments acquired thixotropic properties when mixed with silica-erionite suspensions and became liquefied during earthquake activity. Numerous synsedimentary dike swarms and diapirs of pillow-shaped chert were formed during rift faulting. The precursor sediments lithified by the crystallization of quartzine spherules when they came in contact with hypersaline brines. The strong microbial metabolism was a catalyst for intense chemical sedimentation, which resulted in voluminous chert formation in the Magadi Basin.

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