The soils and underlying weathered carbonate rock in karstic regions play an important role in the infiltration, storage and retention of water and nutrients. Because of significant heterogeneity of the karst, the use of individual geophysical techniques is often not sufficient for unambiguous assessment of the irregular distributions of soils and underlying fractures. In this study, ground penetrating radar (GPR) and electrical resistivity tomography (ERT) are jointly used with additional observations to delineate the shallow subsurface structure in two exposed profiles. The results show that ERT is effective for detecting the soil-rock interfaces, even for irregular terrain and fracture structures, such as a funnel-shaped doline, as the soils and rocks show a large resistivity contrast. Although ERT may be able to sense the presence of extensive fracturing it cannot detect individual small aperture fractures. Joint use of different frequencies of the GPR antenna (e.g. 100 MHz and 500 MHz in this study) allowed the detection of most fractures at different depths in the study sites. However, forward modeling of typical weathered rock features illustrates that the GPR data cannot resolve any reflection signals of the vertical fractures, so the features of vertically enlarged fractures filled by soils cannot be seen from the GPR images. Moreover, large uncertainties of resistivity at the interface between soils/fractures and bedrock limit the identification of an irregularly distributed subsurface structure. Despite the limitations of individual techniques, the combination of ERT and GPR enhances the delineation of the soil-bedrock interface and identification of the fracture network, which can allow an enhanced geological interpretation of shallow subsurface features in the karst areas.