The formation of the East African Rift System has decisively influenced the distribution and evolution of tropical Africa’s biota by altering climate conditions, by creating basins for large long-lived lakes, and by affecting the catchment and drainage directions of river systems. However, it remains unclear how rifting affected the biogeographical patterns of freshwater biota through time on a continental scale, which is further complicated by the scarcity of molecular data from the largest African river system, the Congo.

The Makgadikgadi–Okavango–Zambezi basin (MOZB) is a structural depression in the south-western branch of the East African Rift System of the northern and middle Kalahari, central southern Africa. In the present day, the mainly dry subbasins of the MOZB are part of a long-lived lacustrine system that has likely existed since Early Pleistocene and from which an extant freshwater fish radiation emerged seeding all major river systems of southern Africa. During hydrologically favourable periods the subbasins were connected as a single mega-lake termed Lake Palaeo-Makgadikgadi. Previous geomorphological studies and OSL dates have provided evidence for repeated mega-lake periods since approximately 300 ka. The environmental and climatic implications of such large scale late Quaternary lake-level fluctuations are controversial, with the duration of mega-lake phases poorly constrained. Here, we present the first evidence for a Marine Isotope Stage (MIS) 5 mega-lake period (about 935–940 m a.s.l.) reconstructed from a diatom-rich, 30-cm-thick lacustrine sediment section, exposed close to a palaeo-shoreline of the Makgadikgadi Basin. Based upon the environmental setting and in comparison with sedimentation rates of other similar lake environments, we tentatively estimated that the highstand lasted approximately 1 ka during MIS 5d–b. The 30-cm section was sampled in 0.5-cm steps. Diatom species diversity ranges from 19 to 30 through the section. The dominant species are Pseudostaurosira brevistriata, Rhopalodia gibberula, Cyclotella meneghiniana and Epithemia sorex. The total of 60 sediment samples provide us with a record at decadal to bi-decadal resolution. Based on diatom assemblages and their oxygen isotope composition (δ¹⁸O) we infer an alkaline and mostly oligohaline lake with shallow water conditions prevailing in MIS 5, and is potentially analogous to a Heinrich event. The climate over southern Africa during MIS 5 has been considered very arid but the hydromorphological context of our sediment section indicates that we captured a mega-lake period providing evidence that short-term excursions to significantly higher humidity existed. A hydrologically more favourable environment during MIS 5 than formerly presumed is in line with the early human occupation of the Kalahari.