New evidence was sought for sub-pan silcrete formation along the southern margin of Ntwetwe Pan in the Botswana Makgadikgadi basin. This was achieved by integrating drillhole and surface sample descriptions with element and isocon analysis. The silcrete deposit which lies ~1.0 m below the pan surface, comprises Ntane sandstone fragments and detrital infill, cemented by amorphous silica. The deposit probably evolved during sequential periods of palaeo-lake infilling and drying since at least the Mid-Pleistocene. Changes in basin water pH brought about during fresher water infill interspersed with brine evapo-concentration and later evaporative pumping, induced the mobilisation and precipitation of the silica cement immediately below the pan floor.