The western margin of Australia is unique in being the only eastern boundary region undergoing no upwelling as the poleward flowing Leeuwin Current (LC) nullifies the equatorward-driven wind-induced circulation. The principal forcing mechanism of the Leeuwin Current is the alongshore pressure gradients and associated zonal geostrophic flows along the West Australian margin. Based on planktic foraminiferal census counts and stable isotopic analysis of a surface-dwelling planktic foraminifera, Globigerinoides sacculifer, we show that during the Quaternary there have been five intervals when this eastern boundary region behaved in an opposite manner and the margin experienced extensive upwelling due to weakening of the LC and dominance of equatorward wind-driven circulation, causing offshore Ekman transport. These events occurred at 2.22, 1.83, 0.68, 0.45 and 0.04 Ma and have been named here as PL-1 to PL-5 in ascending stratigraphic order. We demonstrate here that the previous two events, PL-1 and PL-2, occurred due to ENSO-induced changes in the Western Pacific Warm Pool, while the last three events, PL-3, PL-4, and PL-5, occurred due to reduced Indonesian throughflow as a result of lowered sea level caused by ice volume expansion. We envisage here that these periods must be those of reduced net heat input to the Indian Ocean from the Pacific via Indonesian Seaway and thus should have an effect on sea surface temperature of the Indian Ocean and Indian monsoon.