Soils, through their control over resources in drylands play a fundamental role in determining the structure, function and diversity of these terrestrial ecosystems. In semi-arid ecosystems soil moisture controls plant growth, both directly and through its control over soil processes such as microbial activity and biogeochemical cycling. Soils present a measurement challenge, in that they are difficult to easily observe and determine their properties without disturbance. There is a strong need for quantitative spatial soils data on hydrological and biogeochemical properties in the root zone, that can be linked to above ground measures of ecosystem structure. Geophysical methods combined with soil sensors can provide us with new ways of quantifying soil properties in small watersheds with minimal invasiveness. We demonstrate how geophysical methods can be used to obtain spatially exhaustive data, on soil properties, in small watersheds, and how this information can be used to investigate mixed woodland-grassland community structure. The information obtained, and the insight gained, helps us to understand how subsurface processes contribute to ecosystem structure in drylands.