Because of technical difficulties in measuring soil properties at a large scale, little is known about the effect of soil properties on the spatial distribution of trees in grasslands. We were interested in the associations of soil properties with the phenomenon of tree encroachment, where trees increase in density at the expense of grasses. The spatial variation of soil properties and especially soil texture may modify the properties of hydraulic conductivity, and the availability of soil water and mineral nutrients, which in turn may affect the spatial distribution of encroaching trees. Through the development of a geophysical method (Slingram) using an electromagnetic device EM38 and Bayesian inversion, we were able to accurately map soil electrical conductivity (EC) of a Luvisol in a grassland of South Africa. EC measured at the 0·8 to 2 m depth on a 1·5 ha area is a proxy for clay content and was correlated with the spatial distribution of four size classes of the encroaching Acacia sieberiana. Tree location (all sizes considered) was significantly correlated with EC. Tall acacias (>3m height) were totally absent from patches with EC >24 mS m−1. For all other size classes from medium trees to seedlings, tree density decreased with increasing EC. This suggests that high clay contents at depth associated with high EC values may prevent the establishment and/or survival of trees and influence the spatial distribution of A. sieberiana. This result also shows that geophysical tools may be useful for demonstrating important ecological processes. Copyright © 2014 John Wiley & Sons, Ltd.