Palaeo-environments and past human subsistence patterns are difficult to determine from dual-patterned faunal assemblages where human and non-human predators have accumulated and intensively modified animal bones. This paper examines such records in the Leeuwin–Naturaliste Region of south-western Australia, where a thin belt of coastal limestone contains caves and rock shelters with rich faunal deposits. The Late Pleistocene and Holocene part of this record derives from four archaeological sites: Devil's Lair, Tunnel Cave, Witchcliffe Rock Shelter and Rainbow Cave. Correspondence analysis combined with cluster analysis enables a preliminary assessment of habitat changes using simple species abundances in the faunal assemblages and comparison with indices of past human activity in the sites and the species’ present habitat preferences. These inferred changes, consistent with previous analyses of faunal remains and tree charcoal, suggest that late Holocene sites document Aboriginal occupation in coastal heath, scrub and woodland. Late Pleistocene deposits record hinterland occupation at times of low sea-level when the coast was up to 30 km seawards of its present position and the surrounding vegetation was open-forest or woodland. As rainfall increased and vegetation changed in the Holocene, species foraging in open-woodland declined or became locally extinct, while species requiring closed canopy habitats increased. Rank-order correlations of taxa and archaeological remains from depositional sequences before and after the environmental change indicate that the occupiers of late Holocene sites favoured the same generalist species that occupiers of Late Pleistocene sites had favoured, which were available at all times. Prey habitats, foraging behaviours and historic records of ethnographic hunting and settlement pattern suggest that this local continuity is consistent with maintenance of a “dispersive mode” subsistence pattern in the region.