Archaeological and paleoecological studies of cave and rock shelter deposits have been essential in understanding human and biotic responses to Late Quaternary environmental changes. While numerous studies have focused on identifying accumulation agents responsible for site assemblages, there has been less emphasis on exploring the biases they impose or their potential to skew ecological interpretations. This study reports new findings from a paleontological investigation of a cave deposit on Kangaroo Island, South Australia, where mammalian species richness and relative abundances were used to infer changes in regional paleoecology over the past 20,000 years. These data were then compared to faunal species richness and relative abundance derived from archaeological excavations within the same ecotone on Kangaroo Island to better understand how accumulator biases affect species representation. This study shows that the archaeological assemblages underrepresent local diversity and do not record significant changes revealed by the paleontological record. Although species richness decreased during the early Holocene, most species survived isolation of the island 9000 years ago and persisted until Europeans arrived in the 19th century. Our work highlights the importance of not only identifying accumulation agents but understanding how they bias assemblages differently if we are to successfully assess late Quaternary anthropogenic impacts versus climatic change.