The Quaternary Period is characterized by dramatic global climatic changes. Quaternary fossil deposits, which can offer excellent stratigraphic resolution, provide a unique opportunity to understand how fauna respond to past environmental change. Here, we test if the herpetofauna of McEachern’s Deathtrap Cave, a late Pleistocene to Holocene pitfall trap deposit from Victoria, Australia, shows climate-related shifts in taxonomic relative abundance through time. During the last 14,000 years, southeastern Australia experienced pronounced periods of aridity, while temperatures remained relatively stable. We show that the stratigraphic layers of this deposit are characterized by different relative abundances of reptile subfamilies, and that changes in subfamily abundance between layers correlate with known shifts to aridity, based on the percentage of C4 grasses present in the region. We further identify 13 lizard morphotypes from the fossil deposit and compare this diversity with the present-day lizard fauna. Our analyses indicate that gradual changes in community structure, which are typically observed in southeastern Australian vertebrate communities during the Pleistocene–Holocene transition, can partly be explained by changing aridity. These findings represent an important contribution to understanding Quaternary community change in Australia, particularly because evidence of faunal succession of reptile and amphibian communities in Victoria is lacking. Our results further demonstrate the utility of the Australian herpetofaunal fossil record for detecting community responses to past climate change on relatively shallow timescales and at higher levels of taxonomic identification.