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This paper identifies spatial associations between surface nutrients, biological soil crusts and vegetation in the Kalahari. Four locations, with different land use and substrate characteristics were used to determine the extent of biological crust cover and the factors affecting the spatial heterogeneity in soil nutrients and ecology. Despite the sandy texture of Kalahari soils and regular surface disturbances, there is a significant biological soil crust cover (19-40%) at all locations. This is due to a combination of resistance to trampling, sub-canopy niches protected from disturbance and the prevalence of Microcoleus vaginatus cyanobacteria, which are able to rapidly reform crusts. Crust cover and diversity is enhanced on ironstone and calcrete soils. The spatial variability of soil nutrients is low but is increased by grazing-induced bush encroachment. The preferential development of nitrogen-fixing biological soil crusts under bushes could enhance the competitive advantage of Acacia mellifera favouring further bush encroachment. Whether this constitutes land degradation is dependent upon the extent to which sub-bush canopy niches retain palatable grass species. Copyright (C) 2004 John Wiley Sons, Ltd.