Detailed, well-dated palaeoclimate and archaeological records are critical for understanding the impact of environmental change on human evolution. Ga-Mohana Hill, in the southern Kalahari, South Africa, preserves a Pleistocene archaeological sequence. Relict tufas at the site are evidence of past flowing streams, waterfalls, and shallow pools. Here, we use laser ablation screening to target material suitable for uranium-thorium dating. We obtained 33 ages covering the last 110 thousand years (ka) and identify five tufa formation episodes at 114-100 ka, 73-48 ka, 44-32 ka, 15-6 ka, and ∼3 ka. Three tufa episodes are coincident with the archaeological units at Ga-Mohana Hill dating to ∼105 ka, ∼31 ka, and ∼15 ka. Based on our data and the coincidence of dated layers from other local records, we argue that in the southern Kalahari, from ∼240 ka to ∼71 ka wet phases and human occupation are coupled, but by ∼20 ka during the Last Glacial Maximum (LGM), they are decoupled.