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.

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 are −1.98 ± 0.23 Sv (1 Sv = 10⁶ m³/s), −209.68 ± 15.19 TW (1 TW = 10¹² W), −99.87 ± 15.11 mSv (1 mSv = 10^‐3 Sv) in boreal winter, and 0.47 ± 0.20 Sv, 61.06 ± 15.46 TW, 31.67 ± 8.76 mSv in boreal summer, respectively (negative transport defined from SCS to Java Sea). The annual mean volume, heat and freshwater transports are −0.78 ± 0.12 Sv, −77.31 ± 4.99 TW, and −30.87 ± 6.15 mSv, respectively. The freshwater transport through Karimata Strait is as large as 42% of rainfall input to the entire Indonesian seas in boreal winter, thereby modulating the Indonesian Throughflow (ITF) through the “freshwater plug” effect in the Makassar Strait. The interannual variability of the transports is not significantly correlated to the Indian Ocean Dipole and El Niño‐Southern Oscillation. There is a significant decreasing trend of volume and heat transports from the SCS to Java Sea over the period of 1997–2015, with a reduction of 0.26 Sv and 15 TW, respectively. The freshwater transport decreases 12.29 mSv by 2016 compared with that in 2009, equivalent to 33.2%–49.72% of the annual mean freshwater transport during 2009–2016. This decreasing trend would play contradictory roles in the decadal trend of ITF transport by building a “freshwater plug” in the southern Makassar Strait and a ‘buoyant plume’ in the Indo‐Australian Basin, respectively.

The southern coast of Java is known as one of the most productive fishing grounds for tuna, feeding by nutrient-rich water along the coast caused by the subsurface water upwelling. This primary productivity can be evidenced by the high sea surface chlorophyll-a concentration (SSC). Based on satellite remote sensing products, we investigate the multi-scale variability in SSC along the Sumatra-Java coast. The results show that seasonal variability of SSCs is primarily due to monsoon-driven upwelling and rainfall in the Indian Ocean and Indonesian seas sides of the Sumatra and Java Islands, respectively. Local Ekman pumping plays a secondary role, while rainfall input to the ocean has little effect. Coastally trapped Kelvin waves and mesoscale eddies are responsible for the intraseasonal SSC anomalies in regions along the south coast of Java and off the Sunda and Lombok Straits, respectively. The interannual variability in SSC is caused by the anomalous upwelling related to the Indian Ocean Dipole. There was a weak increasing trend of ~0.1–0.2 mg/m³ per decade, above the global averaged trend, which may be related to enhanced local Ekman pumping. These analyses provide an overall description of SSC variations based on satellite observations; however, further investigations based on in situ observations are needed to achieve better quantification.

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.