The near juxtaposition of the Makgadikgadi Basin (Botswana), the world’s largest saltpan complex, with the Okavango Delta, one of the planet’s largest inland deltas (technically an alluvial megafan), has intrigued explorers and scientists since the middle of the 19th century. It was clear from early observations that the Makgadikgadi Basin once contained a huge lake, paleo–Lake Makgadikgadi. Several authors have since speculated that this lake also covered wide regions to the north and west of the Makgadikgadi Basin. Our interpretation of unusually high-quality helicopter time-domain electromagnetic (HTEM) data indicates that paleo–Lake Makgadikgadi extended northwestward at least into the region presently occupied by the Okavango Delta. The total area of paleo–Lake Makgadikgadi exceeded 90,000 km2, larger than Earth’s most extensive freshwater body today, Lake Superior (North America). Our HTEM data, constrained by ground-based geophysical and borehole information, also provide evidence for a paleo-megafan underlying paleo–Lake Makgadikgadi sediments.