Catchment drainage area is a basic spatial unit in landscape hydrology within which the authorities estimate a water balance and manage water resources. The catchment drainage area is commonly delineated based on the surface topography, which is determined using a digital elevation model. Therefore, only a flow over the surface is implicitly considered. However, a substantial portion of the rainfall water infiltrates and percolates through the soil profile to the groundwater, where geological structures control the drainage area instead of the topography of the soil surface. The discrepancy between the surface topography-based and bedrock-based drainage area can cause large discrepancies in water balance calculation. It this paper we present an investigation of the subsurface media stratification in a headwater catchment in the central part of the Czech Republic using a geophysical survey method - electrical resistivity tomography (ERT). Results indicate that the complexity of the subsurface geological layers cannot be estimated solely from the land surface topography. Although shallow layers copy the shape of the surface, the deeper layers do not. This finding has a strong implication on the water transport regime since it suggests that the deep drainage may follow different pathways and flow in other directions then the water in shallow soil profile or shallow subsurface structures.