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Abstract We describe here an analysis of the H-component of the geomagnetic field recorded in several temporary stations operating simultaneously in the central–eastern region of Brazil during nighttime pulsation events in 1994 and the sudden commencement of the St. Patrick’s Day magnetic storm in 2015. A significant amplification in the amplitude of the geomagnetic variations is consistently observed in one of these stations. Magnetovariational analysis indicates that the amplification factor is period dependent with maximum amplitude around 100 s. Integrated magnetotelluric (MT) and geomagnetic depth soundings (GDS) have shown that this station is positioned just over a huge 1200-km-long crustal conductor (estimated bulk conductivity greater than 1 S/m). We propose that the anomalous signature of the geomagnetic field at this station is due to the high reflection coefficient of the incident electromagnetic wave at the interface with the very good conductor and by skin effects damping the electromagnetic wave in the conducting layers overlying the conductor. There are some indication from the GDS data that the conductor extends southward beneath the sediments of the Pantanal Basin. In this region is being planned the installation of a new geomagnetic observatory, but its preliminary data suggest anomalous geomagnetic variations. We understand that a detailed MT survey must be carried out around the chosen observatory site to evaluate the possible influence of induced currents on the local geomagnetic field. Graphical abstract Crustal conductivity anomaly in central South America