Archaeological deposits from Waterfall Bluff Rock Shelter (Eastern Cape) span from Marine Isotope Stage 3 (~39–29 ka) to the mid-Holocene (~8 ka), showing persistent human occupations. The site’s consistent proximity to the shoreline and stable coastline over millennia makes it key for exploring human settlement patterns. This study reports on preliminary results of identifiable fauna from Marine Isotope Stage 3 to the Early Holocene layers at Waterfall Bluff. The identified species may suggest a mosaic environment, although caution is warranted given the small sample size. Furthermore, leopard seal remains were recovered in layers dating to the Last Glacial Maximum. This is the first direct evidence of a leopard seal recovered from Pleistocene and Holocene archaeo-faunal assemblages along the South African coast.