The Nata Sanctuary is situated at the mouth of the Nata River delta, about 15 kilometers (9.3 mi) from the Nata village at the northeastern border of the Sua Pan (salt pan) within the larger Makgadikgadi The Makgadikgadi Pans Landscape, located in the Central Kalahari Game Reserve to the southeast of the Okavango Delta, is the most important of natural habitats. It covers wildlife conservation parks such as the Makgadikgadi National Park and the Nxai Pan National Park, apart from the Nata Bird Sanctuary, which is “one of the largest breeding sites of Lesser and Greater flamingo in the world

The Nata Sanctuary is situated 170km northwest of Francistown, on the northeastern tip of the great Makgadikgadi Salt Pans. It covers approximately 230 square kilometers, 45% of which is fully panned surface area. The Makgadikgadi was once the site of the largest inland lake in southern Africa, which dried up between 10,000 and 20,000 years ago. Today remnants of this great lake exist in the form of two large salt pans, Ntwetwe Pan in the west and Sua Pan in the east, that flood only temporarily in the wet season.