Rocky desertification is a significant threat in the karst regions of southwest China. Studies of soil distribution can contribute to protecting and recovering the fragile karst ecosystem that is prevalent in this region. With an underlying aim of being able to assess soil stocks in karstic environments, this study evaluates the use of electrical resistivity tomography (ERT) for delineating the soil–rock interface. Using a synthetic model (that recognizes the three-dimensional nature of the subsurface), experiments are performed to assess the impact of measurement errors and measurement configuration on recovery of the interface. The inverted results show that the accuracy of the delineation of the soil–rock interface decreases with the increase of measurement error and dipole spacing. The results also show the importance of reliable estimation of measurement errors. Field-based applications of ERT at five exposed profiles in southwest China are also reported. For the field data, three-dimensional modelling was necessary to account for the exposed face. The field experiments show that ERT can be effective at delineating the interface between soil and bedrock, but resolution can be limited due to the scale of features or lack of contrast between soil and bedrock. The method shows great promise as a means of assessing, in a non-invasive manner, the soil–bedrock interface, and, perhaps, more significantly, quantifying estimates of total soil stocks, as we seek to quantify the vulnerability or resilience of this important landscape to anthropogenic and natural stresses.