Pollen, spores, and microscopic charcoal from a sediment core from Lake Ngami, in the Middle Kalahari, reflect paleovegetation and paleoclimatic conditions over the last 16,600 cal years BP. The location of Lake Ngami allows for the receipt of moisture sourced from the Indian and/or Atlantic oceans, which may have influenced local rainfall or long distance water transport via the Okavango system. We interpret results of statistical analyses of the pollen data as showing a complex, dynamic system wherein variability in tropical convective systems and local forcing mechanisms influence hydrological changes. Our reconstructions show three primary phases in the regional precipitation regime: 1) an early period of high but fluctuating summer rainfall under relatively cool conditions from ~16,600e12,500 cal BP, with reduced tree to herb and shrub ratio; 2) an episode of significantly reduced rainfall centered around c. 11,400 cal BP, characterized by an increase in xeric Asteraceae pollen, but persistent aquatic elements, suggesting less rainfall but cool conditions and lower evaporation that maintained water in the basin; and 3) a longer phase of high, but fluctuating rainfall from ~9000 cal BP to present with more woody savanna vegetation (Vachellia (Acacia) and Combretaceae). We propose a model to relate these changes to increased Indian Ocean-sourced moisture in the late Pleistocene due to a southerly position of the African rain belt, a northerly contraction of tropical systems that immediately followed the Younger Dryas, and a subsequent dominance of local insolation forcing, modulated by changes in the SE Atlantic basin.