Climate models consistently project a substantial decrease in the Indonesian Throughflow (ITF) in response to enhanced greenhouse warming. On interannual timescales ITF changes are largely related to tropical Pacific wind variability. However, on the multidecadal timescales investigated here we demonstrate that regional winds and associated changes in the upper ocean circulation cannot explain the projected ITF decrease. Instead, the decrease is related to a weakening in the northward flow of deep waters entering the Pacific basin at ~40°S and an associated reduction in the net basin-wide upwelling to the north of the southern tip of Australia. This can be traced back to consistent changes in the Antarctic Circumpolar Current and Southern Ocean overturning, although questions still remain as to the ultimate drivers. In contrast to the ITF decrease, substantial projected changes to the upper ocean circulation of the Pacific basin are well explained by robust changes in the surface winds.