Karst is characteristically complex, hydrogeologically, due to a high degree of heterogeneity, which is often typified by specific features, for example, cavities and sinkholes, embedded in a landscape with significant spatial variability of weathering. Characterization of such heterogeneity is challenging with conventional hydrogeological methods, however, geophysical tools offer the potential to gain insight into key features that control the hydrological function of a karst aquifer. Electrical resistivity tomography (ERT) is recognized as the most effective technique for mapping karstic features. This method is typically carried out along transects to reveal 2D models of resistivity variability. However, karstic systems are rarely 2D in nature. In this study, ERT is employed in valley and hillslope regions of a karst critical zone observatory (Chenqi watershed, Guizhou province, China), using a quasi-3D approach. The results from the extensive geophysical surveys show that there is a strong association between resistivity anomalies and known karstic features. They highlight the significance of a marlstone layer in channeling spring flow in the catchment and confining deeper groundwater flow, evidenced by, for example, localized artesian conditions in observation wells. Our results highlight the need to analyze and interpret geophysical data in a three-dimensional manner in such highly heterogeneous karstic environments, and the value of combining geological and hydrogeological data with geophysical models to help improve our understanding of the hydrological function of a karst system.