A detailed knowledge on carbon and nitrogen dynamics between under canopy and open canopy in savannas is still lacking, despite their importance and their unique co-existence of trees and grasses. In this study, we used the Kalahari Transect (KT) as a model system to compare with a process-based model the carbon and nitrogen dynamics in soil plots located in grass-dominated and tree/shrub-dominated soil patches.  The KT in southern Africa traverses a dramatic aridity gradient (from ~ 200 mm to more than 1000 mm MAP, through the Republic of South Africa, Botswana, Namibia and Zambia), on relatively homogenous soils (deep Kalahari sands).  Two sites (Tshane and Pandamentago) along the KT were chosen for comparison, with Tshane being at the dry end of the transect (~300 mm MAP) and Pandamentago receiving about 700 mm MAP.  Field data such as soil moisture, soil physical properties, soil organic matter abundance and C:N ratios were determined from samples collected from the 2005 and 2006 wet seasons.  These data were used to parameterize and constrain the model.  The results showed that there were distinct soil moisture, decomposition and nitrogen mineralization dynamics between soil plots located under tree canopies and in open canopy areas. Such differences diminished when moving toward wet end of this transect. These different patterns of soil carbon and nitrogen dynamics existing between open areas and beneath tree canopies have important implications for the tree-grass interactions in savanna ecosystems.