This paper is part of the special publication No.165, Geoarchaeology: exploration, environments, resources. (eds A.M. Pollard) Remains of Australopithecus africanus from the Limeworks Cave, Makapansgat, South Africa, are believed to belong mainly to a metre-thick, bone-rich, speleothem layer. The flowstone is one stratum among a sequence of speleothems, muds, silts, sands and fine and coarse breccias, the study of which has evoked some disagreement. The limeworkers' excavations revealed some stratigraphic relationships but they have obscured others. Partly because of this controversy surrounds the supposition about whether there are separated depositional basins within the overall site and, if so, whether strata can be securely correlated. This is important because a reconstruction of an overall stratigraphic sequence was used as a basis for a magnetostratigraphic reversal record and by which the site has been tentatively dated. There is qualification and disagreement about the origin of the various flowstones and the actual depositional environment of the muds and silts. Evidence is presented which rules out some previous interpretations. From the point of view of the Australopithecine fossils themselves, it can be said that the calcite matrix in which they were provenanced was a low-energy environment and that the dense bone accumulation of this layer almost certainly did not arise by the action of floods, as previously supposed. The most likely main cause of the dense accumulation was hyena denning activity. It is clear that further work is needed to see how a reliable overall sequence can be established and that closer sampling is required for magnetostratigraphy.