The study area of the Chobe Enclave (northern Botswana) is defined as mostly covered by Arenosols in available maps. However, recent explorations of the area showed that soils are more diverse than expected. This is because of complex interactions between current alluvial deposition processes, paleo-environmental effects (ancient alluvial deposition, ancient wind-blown sand deposits) and ongoing hydrological effects and colluvial effects on topographic gradients. An in-depth exploration of both soils and vegetation in the area was conducted with the aim (i) to survey the soil diversity at the Chobe Enclave, (ii) to study soil dynamics and identify the key factors of this diversity, and (iii) to create a soil map based on the analysis of the soil-vegetation relationship. For this purpose, thirty-six soil profiles were extensively described according to the World Reference Base for soil resources. In order to better classify these soils, physicochemical parameters, such as pHH2O, exchangeable cations, and particle size distributions, were measured for a specific set of soils (n = 16), representative of their diversity. To assess Soil Organic Matter (SOM) dynamics, samples were studied using Rock Eval pyrolysis. Results show a high soil diversity and heterogeneity with the presence of (i) Arenosols, as expected, but also of (ii) organic-rich soils, such as Chernozems, Phaeozems, and Kastanozems, (iii) salty/sodic soils, such as Solonchaks and Solonetz, and finally (iv) calcium-rich soils, such as Calcisols. Analyses of the different actors driving the soil diversity emphasized the importance of the surficial geology, composed of different sand deposits (red sands/white sands), carbonate and diatomite beds, as well as ancient salt deposits, in which high proportions of exchangeable Na+ were found, associated with high pHH2O (up to 11.3). In addition, as a parameter, the topography creates a complex hydrological system in the Chobe Enclave and therefore, induces a notable soil moisture gradient. Moreover, this study stressed the key role of termites: not only do they modify physicochemical patterns of soils, but they also decay and incorporate large quantities of fresh plant materials into soils. Finally, the analysis of Organic Matter (OM) showed that the Soil Organic Carbon (SOC) is composed essentially by recalcitrant Organic Carbon (OC) substances, such as charcoal, a common carbon type of tropical soils.