Wonderkrater, a Middle Stone Age site in the interior of South Africa, is a spring and peat mound featuring both paleoclimatic and archaeological records. The site preserves three small MSA lithic assemblages with age estimates of 30 ka, >45 ka and 138.01±7.7 ka. Here we present results of the pollen analysis of a core retrieved from the middle of the peat mound, which covers, with hiatuses, the timespan between ca. 70±10 ka and 30 ka. Pollen percentages of terrestrial, local aquatic, and semi-aquatic plants reveal changes in the regional climate and in the water table of the spring. Results identify regional wet conditions at ca. 70±10 ka, followed by a dry and a wet period between 60 ka and 30 ka. Superimposed on these three phases, recurring changes in the size and depth of the water table are observed between >45 ka and 30 ka. Wet conditions at 70 ka and 30 ka are tentatively correlated here with Marine Isotope Stage 4 and Heinrich Stadial 3, respectively. A warm and dry savanna landscape was present during human occupation older than 45 ka, and a wet phase was contemporaneous with the final occupation, dated at ~30 ka.