In 2008–2009 the Makassar throughflow profile changed dramatically: the characteristic thermocline velocity maximum increased from 0.7 to 0.9 m/sec and shifted from 140 m to 70 m, amounting to a 47% increase in the transport of warmer water between 50 and 150 m during the boreal summer. HYCOM output indicates that ENSO induced change of the South China Sea (SCS) throughflow into the Indonesian seas is the likely cause. Increased SCS throughflow during El Niño with a commensurate increase in the southward flow of buoyant surface water through the Sulu Sea into the northern Makassar Strait, inhibits tropical Pacific surface water injection into Makassar Strait; during La Niña SCS throughflow is near zero allowing tropical Pacific inflow. The resulting warmer ITF reaches into the Indian Ocean, potentially affecting regional sea surface temperature and climate.