The lower Paleozoic Elk Creek carbonatite is a 6–8-km-diameter intrusive complex buried under 200 m of sedimentary rocks in southeastern Nebraska. It hosts the largest known niobium deposit in the U.S. and a rare earth element (REE) deposit. The carbonatite is composed of several lithologies, the relations of which are poorly understood. Niobium mineralization is most enriched within a magnetite beforsite (MB) unit, and REE oxides are most concentrated in a barite beforsite unit. The carbonatite intrudes Proterozoic country rocks. Efforts to explore the carbonatite have used geophysical data and drilling. A high-resolution airborne gravity gradient and magnetic survey was flown over the carbonatite in 2012. The carbonatite is associated with a roughly annular vertical gravity gradient high and a subdued central low and a central magnetic high surrounded by magnetic field values lower than those over the country rocks. Geophysical, borehole, and physical property data are combined for an interpretation of these signatures. The carbonatite is denser than the country rocks, explaining the gravity gradient high. Most carbonatite lithologies have weaker magnetic susceptibilities than those of the country rocks, explaining why the carbonatite does not produce a magnetic high at its margin. The primary source of the central magnetic high is interpreted to be mafic rocks that are strongly magnetized and are present in large volumes. MB is very dense (mean density 3200  kg/m³) and strongly magnetized (median 0.073 magnetic susceptibility), producing a gravity gradient high and contributing to the aeromagnetic high. Barite beforsite has physical properties similar to most of the carbonatite volume, making it a poor geophysical target. Geophysical anomalies indicate the presence of dense and strongly magnetized rocks at depths below existing boreholes, either a large volume of MB or another unknown lithology.