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The clay fraction of the deposits of the Otjomongwa Pan, southwestern Kalahari, is dominated by Mg-smectite. This mineral formed as an authigenic precipitate in a groundwater-fed lake, without involving the transformation of a precursor mineral. During the earliest recorded period, Mg-smectite formed together with sepiolite and dolomite in a shallow lake. This period was ended by a change in environmental conditions that led to an increase in the depth of the lake and a decrease in salinity and Mg content of the water. This resulted in a transition to a mineral association without sepiolite and including calcite, together with Mg-smectite and dolomite. The depth of the lake gradually decreased after this event, while the lake water progressively became depleted in Mg.