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 Indonesian archipelago is characterized by strong internal tides, which are trapped in the different semi‐enclosed seas of the archipelago. Using tidal model results a parameterization of the associated 3d tidal mixing is developed. The resulting average vertical diffusivity is 1.5 cm2/s, which independently agrees with the estimates inferred from observations. Introduced in a regional OGCM, the parameterization improves the water mass characteristics in the different Indonesian seas, suggesting that the horizontal and vertical distributions of the mixing are adequately prescribed. In particular, the salinity maximum of the inflow water is reduced along the main route, mainly in the Dewakang sill area. But also it is erased in the Halmahera and Seram seas, the entrance of the eastern route, so that salty waters doesn't penetrate the Banda Sea. As a result the simulated Indonesian Throughflow Water are in good agreement with observations.

International audienceThe hydrological and geochemical properties of the waters constituting the Pacific Equatorial Undercurrent (EUC) determine the properties of the equatorial cold tongue. Understanding and quantifying the various EUC origins is therefore of prime importance. For this purpose, a high-resolution (1/4°) interannual oceanic simulation was analyzed from the western tropical Pacific boundaries to 140°W, using a Lagrangian framework. Waters from the Low-Latitude Western Boundary Currents (LLWBCs) transiting from Vitiaz Strait (the main contributor), from Solomon Strait, and via the Mindanao Current were identified as the principal sources to the EUC. Waters conveyed by the interior ocean off equator are negligible till 180°E. The LLWBCs' waters represent 87% of the EUC transport at 156°E out of which the New Guinea Coastal Undercurrent (NGCU) is as large as 47%. The EUC meridional distribution suggests that the waters originating from Solomon Strait and Mindanao Current mostly remain in the hemisphere from which they originate. Contrastingly, Vitiaz Strait waters are found in both hemispheres. The vertical EUC distribution shows that the lower layer of the EUC is mainly composed of Vitiaz Strait waters. Finally, the source transport distributions were characterized, at their origin and within the EUC, as a function of density. These distributions showed that waters flowing through Vitiaz Strait at densities higher than those of the EUC (down to sigma = 27.2 kg m^-3) undergo a diapycnal mixing and lighten during their journey to join the EUC. This lightening supports the suggestion that the NGCU is a major source for the EUC geochemical enrichment