Electrical resistivity models derived from exceptionally high-quality helicopter transient electromagnetic data recorded across the Okavango Delta in Botswana, one of the world’s great inland deltas or megafans, include three principal layers: (1) an upper heterogeneous layer of dry and water-saturated sand, (2) an intermediate electrically conductive layer that likely comprises saline-water-saturated sand and clay, and (3) a lower fan-shaped electrically resistive layer of freshwater-saturated sand/gravel and/or crystalline basement. If part of the lower layer comprises a freshwater aquifer, it would be evidence for a recently proposed Paleo Okavango Megafan and a major new source of freshwater. In an attempt to constrain the interpretation of the lower layer, we acquired two high-resolution seismic refraction and reflection data sets at each of two investigation sites: one near the center of the delta and one along its western edge. The interface between unconsolidated sediments and basement near the center of the delta is well defined by an ∼1800 to ∼4500  m/s increase in P-wave velocities, a change in seismic reflection facies, and a strong continuous reflection. This interface is about 45 m deeper than the top of the lower resistive layer, thus providing support for the Paleo Okavango Megafan hypothesis. Subhorizontal seismic reflectors are additional evidence for a sedimentary origin of the upper part of the lower resistive layer. In contrast to the observations at the delta’s center, the interface between unconsolidated sediments and basement along its western edge, which is also defined by a ∼1800 to ∼4500  m/s increase in P-wave velocities and a continuous reflection, coincides with the top of the resistive layer.

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