ABSTRACTThe role that the Indonesian Throughflow plays on climate is investigated in an alternative scenario, expected during glacial ages. The equatorwards shift of the Southern Hemisphere westerlies found in glacial ages acts to decrease the Agulhas Leakage (AL) and the thermohaline circulation (THC) in the Atlantic. Recent results suggest that these changes are followed by an increased THC in the Pacific, through an inter‐basin seesaw mechanism. The enhanced circulation in the Pacific demands thermocline water to cross the equator towards northern latitudes, which shifts the water source of the throughflow from the low‐salinity North Pacific to the relative saltier South Pacific. It is shown that in this equilibrium, the salinity anomalies of the throughflow impact the inter‐basin seesaw towards the restoration of the modern climate, enhancing the North Atlantic Deep Water (NADW) formation and decreasing the THC in the Pacific. These results are consistent with paleo‐observations and provide new insights to interpreting the climate changes in glacial periods.