The continuous record offered by deep-sea sediments has been extensively used to constrain shifting continental and oceanographic conditions. Yet, past fluctuations in deep-sea benthic conditions and bottom-currents are in numerous parts of the globe scarcely documented, one such example being the South Australian margin. Indeed, though variations in surface water masses and continental aeolian dust and river outflow are well documented in the area, little is known about benthic environments and their dynamics during the last interglacial-glacial cycle. We focus here on benthic foraminiferal assemblages sampled from a sediment core recovered at 2420 m depth from a small plateau south of Kangaroo Island within the underwater Murray Canyons Group (South Australian margin). Benthic foraminiferal assemblages show a distinct separation between interglacial and glacial periods over the last 94 ka, and indicate that the benthic environment was well-ventilated and oligotrophic during glacial periods, whilst being rather marked by reduced oxygenation associated to higher food input during the Holocene and Marine Isotope Stage 5a-c. We demonstrate that autochtonous deep-sea benthic foraminiferal communities neither respond to changes in the Murray River's discharges, nor do they follow variations in aeolian dust input from South Australia. Instead, the deep-sea and the terrestrial realm appear decoupled. Moreover, our observations suggest that bottom-water slope currents were stronger during the Holocene and Marine Isotope Stage 5a-c. We propose that this strengthening was triggered by an intensification of the poleward-circulating deep eastern boundary current transporting carbon-rich Indian Deep Water. In contrast, glacial seafloor conditions, especially during the Last Glacial Maximum, may reflect a greater influence and a shoaling of oxygen-rich Antarctic Bottom Water of South Australia. This bottom-water shift would follow the northward displacement of the Subtropical and Subantarctic Fronts and coincide with a withering influence of the Leeuwin Current within surface waters.