knowledge of the physical processes that contribute to variability in the coupled air-31 sea climate system within the Indonesian seas, which in turn also affects the marine 32 ecosystem at the heart of the ecologically important Coral Triangle. 33The tropical Indonesian seas play a central role in the climate system. They lie at 34 the climatological center of the atmospheric deep convection associated with the 35 ascending branch of the Walker Circulation. They also provide an oceanic pathway for 36 the Pacific and Indian inter-ocean exchange, known as the Indonesian Throughflow 37 (ITF), conveying the only link in the global thermohaline circulation at tropical latitudes 1 . 38As such, the volume of heat and freshwater carried by the ITF are known to impact the 39 state of the Pacific and Indian Oceans as well as the air-sea exchange 2-6 , modulating 40 climate variability on a variety of time scales. Sea surface temperature (SST) anomalies 41 3 over the Indonesian seas are associated with both the Pacific El Niño-Southern 42 Oscillation (ENSO) and the Indian Ocean Dipole (IOD), causing changes in the regional 43 surface winds that alter precipitation and ocean circulation patterns within the entire 44 Indo-Pacific region 7,8 . Indeed, proper representation of the coupled dynamics between the 45 SST and wind over the Indonesian seas is required for a more realistic simulation of 46The ITF had originally been thought of as occurring within the warm, near surface 48 layer with a strong annual signal driven by seasonally reversing monsoons 10 . However 49 recent observations reveal the inter-ocean exchange primarily occurs as a strong velocity 50 core at depth within the thermocline and exhibits large variability over a range of time 51 scales 11,12 . Ongoing in situ measurements indicate that the vertical profile of the flow has 52 changed significantly over the past decade. In particular there has been a prolonged 53 shoaling and strengthening of the ITF subsurface core within the Makassar Strait inflow 54 channel occurring in concert with the more regular and stronger swings of ENSO phases 55 since the mid-2000s 13 . On longer time scales, coupled models reveal that reduced Pacific 56 trade winds will correspondingly reduce the strength and change the profile of the ITF. 57These changes have important implications to the air-sea coupled system, since it is the 58 vertical profile of the ITF that is critical to the climatically relevant inter-basin heat 59 transport 12 . 60In this article we discuss recent observational evidence supported by models that 61show how recent changes in the wind and buoyancy forcing affect the vertical profile and 62properties of the flow through the Indonesian seas. Intense vertical mixing through 63 vigorous tides and strong air-sea interaction set the vertical stratification of the ITF 64 4 flow 14 , and is found to impact both ENSO and the IOD variability through thermocline 65 and wind coupling 9,15 . We highlight how these changes have direct consequences for the 66 ocean...

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.

[1] Time series observations during [2004][2005][2006] reveal the presence of 60-90 days intraseasonal events that impact the transport and mixing environment within Makassar Strait. The observed velocity and temperature fluctuations within the pycnocline reveal the presence of Kelvin waves including vertical energy propagation, energy equipartition, and nondispersive relationship. Two current meters at 750 and 1500 m provide further evidence that the vertical structure of the downwelling Kelvin wave resembles that of the second baroclinic wave mode. The Kelvin waves derive their energy from the equatorial Indian Ocean winds, including those associated with the Madden-Julian oscillations, and propagate from Lombok Strait to Makassar Strait along the 100-m isobath. The northward propagating Kelvin waves within the pycnocline reduce the southward Makassar Strait throughflow by up to 2 Sv and induce a marked increase of vertical diffusivity.

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.

The Indonesian Throughflow (ITF) transport in the upper layer of Makassar Strait was reduced by an unprecedented 25–40% during June to September 2016, the weakest northern summer ITF transport measured through 2004 to mid‐2017. A negative Indian Ocean Dipole (IOD) event occurring through boreal summer and fall 2016 was the main driver for the reduced ITF transport. Elevated sea surface temperature and height off the southern coast of Sumatra and Java islands, attributed to the IOD event, suppressed the Pacific to Indian pressure gradient, resulting in a reduction in the ITF transport. Intensified Wyrtki jets, energetic westerly winds, and downwelling Kelvin waves associated with the strong IOD event contributed to the suppressed interocean pressure gradient. The influence from the 2016 La Niña event on the other hand was secondary. This study showcases the role of coupled ocean‐atmosphere interactions in Indian Ocean in regulating an extreme interannual variation of the ITF in 2016, which is a unique event in the observational record.

The role of turbulent mixing in regulating the ocean’s response to the Madden–Julian oscillation (MJO) is assessed from measurements of surface forcing, acoustic, and microstructure profiles during October–early December 2011 at 0°, 80.5°E in the Indian Ocean. During the active phase of the MJO, the surface mixed layer was cooled from above by air–sea fluxes and from below by turbulent mixing, in roughly equal proportions. During the suppressed and disturbed phases, the mixed layer temperature increased, primarily because of the vertical divergence between net surface warming and turbulent cooling. Despite heavy precipitation during the active phase, subsurface mixing was sufficient to increase the mixed layer salinity by entraining salty Arabian Sea Water from the pycnocline. The turbulent salt flux across the mixed layer base was, on average, 2 times as large as the surface salt flux. Wind stress accelerated the Yoshida–Wyrtki jet, while the turbulent stress was primarily responsible for decelerating the jet through the active phase, during which the mean turbulent stress was roughly 65% of the mean surface wind stress. These turbulent processes may account for systematic errors in numerical models of MJO evolution.

Dynamical understanding of the Madden–Julian Oscillation (MJO) has been elusive, and predictive capabilities therefore limited. New measurements of the ocean's response to the intense surface winds and cooling by two successive MJO pulses, separated by several weeks, show persistent ocean currents and subsurface mixing after pulse passage, thereby reducing ocean heat energy available for later pulses by an amount significantly greater than via atmospheric surface cooling alone. This suggests that thermal mixing in the upper ocean from a particular pulse might affect the amplitude of the following pulse. Here we test this hypothesis by comparing 18 pulse pairs, each separated by <55 days, measured over a 33-year period. We find a significant tendency for weak (strong) pulses, associated with low (high) cooling rates, to be followed by stronger (weaker) pulses. We therefore propose that the ocean introduces a memory effect into the MJO, whereby each event is governed in part by the previous event.