Plio-Pleistocene speleothems from australopithecine-bearing caves of South Africa have the potential to yield paleoenvironmental and geochronological information using isotope geochemistry. Prior to such studies it is important to assess the preservation of geochemical signals within the calcitic and aragonitic speleothems, given the tendency of aragonitic speleothems to recrystallize to calcite. This study documents the geochemical suitability of speleothems from the principal hominin-bearing deposits of South Africa. We use petrography, together with stable isotope and trace element analysis, to identify the occurrence of primary aragonite, primary calcite, and secondary calcite. This study highlights the presence of diagenetic alteration at many of the sites, often observed as interbedded primary and secondary fabrics. Trace element and stable isotopic values distinguish primary calcite from secondary calcite and offer insights into geochemical aspects of the past cave environment. δ13C values of the primary and secondary calcites range from +6 to −9‰ and δ18O values range from −4 to −6‰. The data are thus typical of meteoric calcites with highly variable δ13C and relatively invariant δ18O. High carbon isotope values in these deposits are associated with the effects of recrystallization and rapid outgassing of CO2 during precipitation. Mg/Ca and Sr/Ca ratios differ between primary and secondary calcite speleothems, aiding their identification. Carbon and oxygen isotope values in primary calcite reflect the proportion of C3 and C4 vegetation in the local environment and the oxygen isotope composition of rainfall. Primary calcite speleothems preserve the pristine geochemical signals vital for ongoing paleoenvironmental and geochronological research.