We use magnetic susceptibility and remanent magnetization measurements of the Eyreville and Cape Charles cores in combination with new and previously collected magnetic field data in order to constrain structural features within the inner basin of the Chesapeake Bay impact structure. The Eyreville core shows the first evidence of several-hundred-meter-thick basement-derived megablocks that have been transported possibly kilometers from their pre-impact location. The magnetic anomaly map of the structure exhibits numerous short-wavelength (<2 km) variations that indicate the presence of magnetic sources within the crater fill. With core magnetic properties and seismic reflection and refraction results as constraints, forward models of the magnetic field show that these sources may represent basement-derived megablocks that are a few hundred meters thick or melt bodies that are a few dozen meters thick. Larger-scale magnetic field properties suggest that these bodies overlie deeper, pre-impact basement contacts between materials with different magnetic properties such as gneiss and schist or gneiss and granite. The distribution of the short-wavelength magnetic anomalies in combination with observations of small-scale (1–2 mGal) gravity field variations suggest that basement-derived megablocks are preferentially distributed on the eastern side of the inner crater, not far from the Eyreville core, at depths of around 1–2 km. A scenario where additional basement-derived blocks between 2 and 3 km depth are distributed throughout the inner basin—and are composed of more magnetic materials, such as granite and schist, toward the east over a large-scale magnetic anomaly high and less magnetic materials, such as gneiss, toward the west where the magnetic anomaly is lower—provides a good model fit to the observed magnetic anomalies in a manner that is consistent with both gravity and seismic-refraction data.