Cave sediments pose dating challenges due to complex depositional and post-depositional processes that operate during their transport and accumulation. Here, we confront these challenges and investigate the stratified sedimentary sequence from Wonderwerk Cave, which is a key site for the Earlier Stone Age (ESA) in Southern Africa. The precise ages of the Wonderwerk sediments are crucial for our understanding of the timing of critical events in hominin biological and cultural evolution in the region, and its correlation with the global paleontological and archaeological records. We report new constraints for the Wonderwerk ESA chronology based on magnetostratigraphy, with 178 samples passing our rigorous selection criteria, and fourteen cosmogenic burial ages. We identify a previously unrecognized reversal within the Acheulean sequence attributed to the base of the Jaramillo (1.07 Ma) or Cobb Mtn. subchrons (1.22 Ma). This reversal sets an early age constraint for the onset of the Acheulean, and supports the assignment of the basal stratum to the Olduvai subchron (1.77–1.93 Ma). This temporal framework offers strong evidence for the early establishment of the Oldowan and associated hominins in Southern Africa. Notably, we found that cosmogenic burial ages of sediments older than 1 Ma are underestimated due to changes in the inherited 26Al/10Be ratio of the quartz particles entering the cave. Back calculation of the inherited 26Al/10Be ratios using magnetostratigraphic constraints reveals a decrease in the 26Al/10Be ratio of the Kalahari sands with time. These results imply rapid aeolian transport in the Kalahari during the early Pleistocene which slowed during the Middle Pleistocene and enabled prolonged and deeper burial of sand while transported across the Kalahari Basin.