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.

Change in the Indonesian Seas with the circulation and heat and freshwater inventories and associated air-sea fluxes of the regional and global oceans. This white paper puts forward the design of an observational array using multi-platforms combined with high-resolution models aimed at increasing our quantitative understanding of water mass transformation rates and advection within the Indonesian seas and their impacts on the air-sea climate system.

Sea surface temperature (SST) variability at intraseasonal time scales across the Indonesian Seas during January 1998–mid-2012 is examined. The intraseasonal variability is most energetic in the Banda and Timor Seas, with a standard deviation of 0.4°–0.5°C, representing 55%–60% of total nonseasonal SST variance. A slab ocean model demonstrates that intraseasonal air–sea heat flux variability, largely attributed to the Madden–Julian oscillation (MJO), accounts for 69%–78% intraseasonal SST variability in the Banda and Timor Seas. While the slab ocean model accurately reproduces the observed intraseasonal SST variations during the northern winter months, it underestimates the summer variability. The authors posit that this is a consequence of a more vigorous cooling effect induced by ocean processes during the summer. Two strong MJO cycles occurred in late 2007–early 2008, and their imprints were clearly evident in the SST of the Banda and Timor Seas. The passive phase of the MJO [enhanced outgoing longwave radiation (OLR) and weak zonal wind stress) projects on SST as a warming period, while the active phase (suppressed OLR and westerly wind bursts) projects on SST as a cooling phase. SST also displays significant intraseasonal variations in the Sulawesi Sea, but these differ in characteristics from those of the Banda and Timor Seas and are attributed to ocean eddies and atmospheric processes independent from the MJO.