The Leeuwin Current flowing southward along West Australia is an important conduit for the poleward heat transport and interocean water exchange between the tropical and the subantarctic ocean areas. Its past development, and its relationship to Southern Ocean change and to Australian ecosystem response, however is largely unknown. We here reconstruct sea surface and thermocline temperatures and salinities from foraminiferal-based Mg/Ca and stable oxygen isotopes from offshore southwest and southeast Australia reflecting the Leeuwin Current dynamics over the last 60 kyrs. Its variability resembles the biomass burning development in Australasia from ~60–20 ka BP implying that climate-modulated changes related to the Leeuwin Current most likely affected Australian vegetational and fire regimes. In particular during ~60–43 ka BP, warmest thermocline temperatures point to a strongly developed Leeuwin Current during Antarctic cool periods when the Antarctic Circumpolar Current weakened. The pronounced centennial-scale variations in Leeuwin Current strength appear in line with the migrations of the Southern Hemisphere frontal system and are captured by prominent changes in the Australian megafauna biomass. We argue that the concerted action of a rapidly changing Leeuwin Current, the ecosystem response in Australia, and human interference since ~50 BP enhanced the ecological stress on the Australian megafauna until a tipping point was reached at ~43 ka BP, after which faunal recuperation no longer took place. While being weakest during the last glacial maximum, the deglacial Leeuwin Current intensified at times of poleward migrations of the Subtropical Front. During the Holocene, the thermocline off South Australia was considerably shallower compared to the short-term glacial and deglacial periods of Leeuwin Current intensification.