The Makassar Strait throughflow of ~12–13 Sv, representing ~77% of the total Indonesian Throughflow, displays fluctuations over a broad range of time scales, from intraseasonal to seasonal (monsoonal) and interannual scales. We now have 13.3 years of Makassar throughflow observations: November 1996 to early July 1998; January 2004 to August 2011; and August 2013 to August 2017. Strong southward transport is evident during boreal summer, modulated by an ENSO interannual signal, with weaker southward flow and a deeper subsurface velocity maximum during El Niño; stronger southward flow with a shallower velocity maximum during La Niña. Accordingly, the southward heat flux, a product of the along‐channel current and temperature profiles, is significantly larger in summer and slightly larger during La Niña. The southward flow relaxed in 2014 and more so in 2015/2016, similar though not as extreme as during the strong El Niño event of 1997. In 2017, the throughflow increased to ~20 Sv. Since 2016, the deep layer, 300‐ to 760‐m southward transport increases, almost doubling to ~7.5 Sv. From mid‐2016 into early 2017, the transports above 300 m and below 300 m are about equal, whereas previously, the ratio was about 2.7:1. Near zero or northward flow occurs in the upper 100 m during boreal winter, albeit with interannual variability. Particularly strong winter reversals were observed in 2014/2015 and 2016/2017, the latter being the strongest winter reversal revealed in the entire Makassar time series.

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Volume, heat and freshwater transports from the South China Sea (SCS) to the Java Sea through the Karimata Strait are estimated based on direct measurements of current, temperature, salinity, and satellite observations. Subject to strong seasonal variability, the volume, heat, freshwater transports

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We present a unique water column data set of dissolved inorganic carbon (DIC) and total alkalinity (TAlk) from a cruise to the western Indonesian Seas during the southeast monsoon, covering the Karimata Strait, western Java Sea, and Sunda Strait. Salinity-normalized TAlk (NTAlk) in the surface water ranged 2,297-2,348 μmol kg −1 , very close to typical values observed in the tropical ocean. In the Karimata Strait, the Kapuas River plume was observed, featuring low salinity, DIC, and TAlk. In the western Java Sea, where waters were well mixed, we observed relatively homogeneous distributions of salinity, DIC, and TAlk. In the Sunda Strait, waters intruding from the Java Sea occupied the upper layer, and below was the Indian Ocean water with lower values of salinity, DIC, and TAlk. In its deep portion, depth profiles of normalized DIC and NTAlk were very similar to those observed in the Indian Ocean. Physical processes and air-sea gas exchange exerted predominant controls on the carbonate system in the Karimata Strait and western Java Sea. While both processes play large roles in the Sunda Strait, a net DIC removal of 31 ± 23 μmol kg −1 in the surface mixed layer were revealed. The drawdown of DIC is consistent with an overall supersaturation of dissolved oxygen (102-107%), suggesting significant organic carbon production. In the subsurface-intermediate waters of the Sunda Strait mainly influenced by the advection of Indian Ocean water, a net DIC consumption of 54 ± 45 μmol kg −1 was distinct, likely stimulated by the nutrients supplied from the Indian Ocean. Plain Language SummaryResearch on the carbonate system in the tropical regime of the Indonesian Seas is minimal, which hampers our understanding to its essential role in interbasin exchanges of material and energy via the Indonesian throughflow. Here we present a unique data set to examine the dynamics of the carbonate system in the western Indonesian Seas. Based on DIC and TAlk relationships, we show that water mass mixing in the western Indonesian Seas during the southeast monsoon is dominated by zonal wind-mixed waters from the plume of the Kapuas River, the Java Sea and South China Sea mixed water, and the subsurface Indian Ocean water. These processes resulted in homogenous distributions of physical properties and carbonate system parameters. However, biologically mediated DIC consumption occurred in the surface mixed layer of the Sunda Strait, which led to an increase in dissolved oxygen saturation, the saturation state of aragonite (Ω arag ), and pH. Overall, our region was a source of atmospheric CO 2 as previously reported, although the controlling processes may vary with respect to time at both seasonal and interannual timescales.