The Makgadikgadi Basin in the Middle Kalahari Desert of Botswana exhibits a complex of salt pans which may partly be filled to shallow water depths during the rainy season. There is good evidence that during the Pleistocene and early Holocene a large lake existed in the Makgadikgadi Basin which, however, became increasingly smaller during the Holocene. For the late Holocene when the regional human population began to grow, no data (except for the last two centuries) about lake levels and thus surface water availability have been published. Age estimates of selected Baobab trees of two size-classes growing on "Kubu Island", a granite outcrop which is located in a "coastal" position at the south-western edge of Sua Pan, are used to infer that at least during the early centuries of the last millennium a maximum lake level of 908 m a.s.l. was reached. During this lake phase Sua Pan and Ntwetwe Pan were interconnected and large wetlands were created. Large numbers of game and livestock could be sustained. These data are in line with palaeoclimate data, but cannot be used to differentiate the "Medieval Warm Period", which was supposedly relatively wet, from the subsequent "Little Ice Age", which likely was comparatively dry.