Faunal baselines are fundamental for understanding and abating biodiversity declines. However, these can be highly reliant on historical records derived from already disturbed ecosystems. In the Murray–Darling Depression bioregion of Australia, European settlement and associated ecosystem changes elicited rapid declines and losses of native species. These losses occurred prior to systematic documentation of the region’s fauna, thus masking their extent. We describe a dated vertebrate fossil assemblage from Light’s Roost, lower Murray Mallee region of South Australia, and combine our findings with other local fossil assemblages and historical records to reconstruct the region's pre-European mammal fauna (excluding bats). Our revised faunal baseline shows that the region’s original mammal fauna was more diverse than formerly known and underwent substantial reduction after Europeans colonised the area. Half of the Murray–Darling Depression’s mammals that were present when Europeans arrived have been lost since this time. Lost species include the mulgara (Dasycercus blythi/cristicauda), placing the taxon within 40 km of the hitherto-disputed type locality for D. cristicauda at Lake Alexandrina. Nearly half of the Murray Mallee fauna is known principally from fossils and over three-quarters of the fauna were represented in the fossil record. Our findings show that baselines for species distributions taken from historical records and modern faunal surveys can be improved by inclusion of fossil remains, particularly for smaller and more cryptic species. Deficiencies in regional records can conceal the scale of mammal declines resulting from European colonisation and associated land-management practices, and thus their vulnerability to anthropogenic disturbance.