How rain and wind regulate the seasonal heartbeat of the Indonesian Throughflow

The Indonesian throughflow (ITF), the only tropical connection of the global ocean circulation system, is important to oceanic physical and biogeochemical processes as well as climate. Remote winds from the Pacific and Indian Ocean are known to drive much of the ITF variability on intra-seasonal and interannual time scales associated with various climate modes (e.g., MJO, ENSO, IOD). On seasonal time scales, semi-annual winds over the equatorial Indian Ocean affect the thermocline and deeper flows of the ITF, resulting in a semi-annual signal in the total ITF transport. In the upper 50-100 m, however, ITF transport shows a dominant annual cycle with much weaker flow during boreal winter. This had been attributed to the effect of a “freshwater plug”, with the South China Sea being the source of that freshwater. Here, based on a comprehensive analysis of a suite of ocean-atmosphere-land satellite observations and reanalysis products, we show that the main sources of the freshwater plug are monsoonal rain over the Java Sea and runoff from southern Borneo. The freshening is sufficient to explain the anomalous upstream sea-level gradient along the Makassar Strait during boreal winter, exemplifying a “back pressure” that weakens the upper-layer ITF. Moreover, local winds along the Makassar Strait cannot explain the annual cycle of the along-strait sea-level gradient. Therefore, monsoonal water cycle in the Indonesian Seas plays an important role in regulating the seasonal heartbeat of the ITF, influencing its vertical profiles and the depth-integrated transports of oceanic properties (e.g., heat). The results have implications to longer-term changes of the water cycle and the ITF.