Magnetic variation data recorded at 143 sites in the period range of 1000−6000 seconds were used to model the conductance distribution in the eastern part of the Bohemian Massif (BM) and the West Carpathians (WCP). The region represents a contact zone of the Palaeozoic Hercynian and Tertiary Carpathian orogenic systems. Two anomalies in the distribution of the electrical conductivity were found. One with a simple two-dimensional feature is located approximately near the boundary of the Inner and Outer West Carpathians, but the other of a complicated three-dimensional character is at the eastern margin of the BM. We inverted the observed geomagnetic data for the conductance in a unimodal thin sheet embedded at a specific depth. The inversion algorithm minimises the parametric functional that sums the squared norm of the misfit and the stabilising functional, and employs conjugate gradient optimisation. To express the sharp tectonic boundaries, we employed a minimum gradient support functional, which is applied in areas with strong variations of the model parameters. The inversion results confirmed a quasi-linear character of the regional anomaly distinguishing the Carpathian plate and led to new insight into the anomaly over the eastern margin of the BM. According to the results of the modelling the anomaly is formed by several conductive belts intersecting the anomalous zone. These belts follow important faults, dividing the transition zone between the BM and the WCP into individual blocks.