Carbonate lithofacies developed along the trunk valley of palaeodrainage channels, as well as those adjacent to gypsite facies in the Lake Napperby drainage basin, in central Australia, show wide ranges of sedimentary characteristics, reflecting significant variation in depositional environments. Sedimentological and geochemical characterization of the calcrete lithofacies in this drainage area indicate that whereas variations in bedrock morphology are important in overall distribution of the phreatic and vadose calcrete varieties, faulting and basin adjustments since the early Quaternary may also have played a significant role in redistribution of the hydrologic zones, and hence, the evolution of these calcretes. Accordingly, phreatic calcretes, which initially precipitated from laterally moving groundwaters along the palaeodrainage channels, undergo systematic mineralogical changes due to direct (evaporative) precipitation and diagenetic displacement/replacement processes (mainly dolomitization and silicification) under present hydro-chemical conditions within the zone of grounwater fluctuations. However, lateral and downward shifts in groundwater flow due to excessive volumetric expansion and reduction in effective permeability of calcrete may ultimately result in isolation of the calcrete, like those observed from the eastern margins of the lake. The evolution of the vadose calcretes is thereafter topographically controlled and relates to mobilization and redistribution of earlier deposited calcretes under present meteorological conditions.