The Okavango Delta is a vast wetland wilderness in the middle of the Kalahari Desert of Botswana. It is a largely closed hydrological system with most water leaving the delta by evapotranspiration. In spite of this, the channels and swamps of the delta remain surprisingly low in salinity. To help understand the hydrological processes at work, we reanalyzed a previous inversion of data collected from a helicopter transient electromagnetic (HTEM) survey of the entire delta and performed an inversion of a high resolution dataset recorded during the same survey. Our results show widespread infiltration of fresh water to as much as ∼200 m depth into the regional saline aquifer. Beneath the western delta, freshwater infiltration extends to only about 80 m depth. Hydrological modeling with SEAWAT confirms that this may be due to rebound of the regional saltwater–freshwater interface following the cessation of surface flooding over this part of the delta in the 1880s. Our resistivity models also provide evidence for active and inactive saltwater fingers to as much as ∼100 m beneath islands. These results demonstrate the great extent of freshwater infiltration across the delta and also show that all vegetated areas along the delta's channels and swamps are potential locations for transferring solutes from surface water to an aquifer at depth.