The Haasgat fossil-bearing karstic system is situated within the Skurweberg Mountain range in the northeastern portion of the Fossil Hominids of South Africa UNESCO World Heritage Site in South Africa. As is the case for the nearby Gondolin hominin locality, Haasgat occurs in an area of substantial modern topographic relief that contrasts with the low-relief landscape of the southwestern extent of the World Heritage Site surrounding the Blauubank Stream Valley sites (e.g., Sterkfontein, Swartkrans, Kromdraai, Bolt's Farm). This suggests differential landscape formation processes during the Neogene and potentially novel palaeoecosystems and taphonomic processes governing karstic fossil assemblage composition across even a small geographic region. This is particularly critical given the overall paucity of taphonomic data from the region, the substantial cercopithecoid primate assemblage that is uniquely dominated by the basal baboon species Papio angusticeps, and the recent announcement of the first hominin specimen from Haasgat.Here we provide the first comprehensive taphonomic analysis of the Haasgat HGD faunal assemblage that was developed from ex situ calcified sediment blocks in the 1990s. There is direct evidence for biotic activity (e.g., large-bodied carnivores and porcupines) mediating the formation of parts of the HGD faunal assemblage, including at least part of the primate craniodental and postcranial sample. There is minimal evidence for pre-depositional element UV exposure and weathering or winnowing of the assemblage, but there is abiotic distortion and crushing of elements. Our analysis has equally found that taphonomic data from the HGD assemblage is compromised by a modern ‘overprint’ of damage through mechanical preparation and a lack of documentation generated during sampling, processing, and initial curation. Nearly half the cortical surfaces and many dental specimens in the assemblage exhibit evidence of substantial preparation damage rendering many purported biotic modifications ambiguous or suspect. Element proportions may be artificially skewed towards craniodental specimens and more reflective of block selection and/or selective processing rather than original deposition composition. As a result, the Haasgat HGD sample provides only limited data on the depositional processes mediating karstic assemblage formation in the region, and ultimately serves as a cautionary tale of the impacts of palaeontological sampling strategies on subsequent analysis and research.