A systematic drilling and optical dating programme on Middle Kalahari beach ridge (relict shoreline) sediments has enabled the identification of multiple episodes of lake high stands of an extensive palaeolake system at the terminus of the Okavango Delta, northern Botswana. This paper presents 23 ages from the Mababe Depression and establishes four shoreline construction phases in the late Quaternary coeval with other sub-basin lake high stands (Lake Ngami). These synchronous lake phases result from a coalescence of the sub-basins into a unified palaeolake, Lake Thamalakane, covering an area of ∼ 32,000 km2. Six additional ages are also presented from the Chobe enclave to the north of the basin where shoreline ridges were emplaced at the same time as Lake Thamalakane phases. This suggests that increased flow in the Chobe and Zambezi system significantly contributed to the Middle Kalahari lake phases in both the post-glacial and Holocene periods. The integration of these new data and their compatibility with other regional and tropical palaeo-archives is discussed in the light of understanding Quaternary climate drivers within the Kalahari.