Here we provide a multiproxy record of climate change and human occupation at Wonderkrater, a spring and peat mound site situated in the interior of southern Africa. Recently extracted sediment cores yielded a number of Middle Stone Age (MSA) artefacts, prompting exploratory excavation of the sediments to understand better the geomorphology of the site, age of the sediments, cultural lithic sequence, vegetation and faunal remains, and to try to establish whether human use of the site was to some extent climatically driven. Excavations yielded late Pleistocene mammal fauna and flora, and three small MSA lithic assemblages with age estimates of 30 ka, >45 ka and 138.01 ± 7.7 ka. The upper layers comprise peat that preserves macrobotanical and faunal remains, implying local fen conditions in Acacia savanna woodland at 12 ka. Below the upper peat layers, a 1 m-thick layer of white sand yielded two MSA lithic assemblages in association with faunal remains dated to between 30.8 ± 0.7 ka and >45 ka. Clay underlying the sand has an OSL age of 63.1 ± 5.8 ka, and sandy peat below it has an Infrared Stimulated Luminescence (IRSL) age of 70 ± 10 ka. Faunal remains in the lower sand levels, and dental stable carbon isotope analysis of herbivores, indicate a substantial grassland component in the landscape during late MIS 3 (>45 ka). Charcoal, phytolith and pollen data show a change from moderately warm and dry grassy savanna woodland in the lower sand levels, to cooler and wetter grassland with woody shrubs in the uppermost levels by 30 ka. The conditions that resulted in the deposition of the sand also attracted people to the site, but whether it served as an oasis in an arid landscape, or was occupied during wet phases, is unclear. The composition of the lithic assemblages, which include many tools suitable for cutting, suggest that the peat mound may have been used as a place to harvest reeds, process plant materials and butcher animals that were either deliberately or accidentally trapped in mud or peat.