As an additional opportunistic component to the southern African magnetotelluric experiment, natural-source audio-magnetotelluric (AMT) data were acquired during phase IV to investigate the local-scale electric conductivity subsurface structure in the Otjiwarongo and Katima Mulilo regions (Namibia) as an aid in locating the installation points for high-voltage direct current earth electrodes. The study showed that the shallow subsurface of areas containing one measurement site in the Otjiwarongo region and three sites in the Katima Mulilo region have appropriate high conductivities for the optimal placement of the earth electrodes. Both of the AMT surveys are situated close to the edge of the orogenic Neo-Proterozoic Damara mobile belt (DMB). Previous studies all suggest the existence of a highly conductive midcrustal zone, which correlates well with the spatial location of the DMB. Two-dimensional inverse modeling of the Otjiwarongo AMT data confirms the existence of the high-conductive zone at midcrustal depths (10–15 km). The high conductivity of the DMB is explained by the presence of interconnected graphite in the marble units present. The Katima Mulilo inversion results are characterized by a conductive upper crustal layer that does not form part of the DMB conductive belt. It was deduced that at the uppermost subsurface (maximum ), Kalahari sediments are responsible for the high conductivity observed, whereas at greater depth (up to 6 km), its cause remains enigmatic, albeit the hypothesis of ironstone or graphite being present and causing the observed conductive upper crust.