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The transfer of Pacific water into the Indian Ocean through the Indonesian seas affects the heat and freshwater budgets of both oceans. The observed transport in the Makassar Strait, the primary Indonesian throughflow pathway, from January 2004 through November 2006 is 11.6 ± 3.3 Sv (Sv = 106 m3/s). This transport is 27% larger than observed during 1997 when a strong El Niño suppressed the flow. The 2004‐06 Makassar transport displays clear seasonal behavior, with associated heat and freshwater variability, in contrast to the El Niño dominated 1997 transport. The 2004‐06 transport reached maximum values towards the end of the northwest and southeast monsoons, with minimum transport are in October‐December. A sustained high transport is observed in early 2006, perhaps in response to an La Niña condition. The maximum throughflow occurs within the thermocline, as in 1997, though the longer 2004‐06 measurements also reveal a shallowing of transport as speeds increase. The transport‐weighted temperature is 15.6°C in 2004‐06, nearly 1°C warmer than that observed in 1997, presumably a consequence of El Niño.

River outgassing has proven to be an integral part of the carbon cycle. In Southeast Asia, river outgassing quantities are uncertain due to lack of measured data. Here we investigate six rivers in Indonesia and Malaysia, during five expeditions. CO2 fluxes from Southeast Asian rivers amount to 66.9±15.7 Tg C per year, of which Indonesia releases 53.9±12.4 Tg C per year. Malaysian rivers emit 6.2±1.6 Tg C per year. These moderate values show that Southeast Asia is not the river outgassing hotspot as would be expected from the carbon-enriched peat soils. This is due to the relatively short residence time of dissolved organic carbon (DOC) in the river, as the peatlands, being the primary source of DOC, are located near the coast. Limitation of bacterial production, due to low pH, oxygen depletion or the refractory nature of DOC, potentially also contributes to moderate CO2 fluxes as this decelerates decomposition.

In Indonesia, land use change (LUC) in the form of peatland degradation induces carbon loss through direct CO2 emissions, but also via soil leaching of which circa 50% is decomposed and emitted as CO2 from the rivers. However, the fate of the remaining exported leached carbon is uncertain. Here, we show that the majority of this carbon is respired in the estuaries and emitted to the atmosphere. However, a portion is adsorbed into the marine carbon pool where it favors CaCO3 dissolution and can therefore be seen as the invisible carbon footprint. We conclude that the effects of LUC stretch beyond the terrestrial realm and are not limited to CO2 emissions, but also affect marine ecosystems. Considering the ecological and economical importance of these ecosystems, it is important that this so far invisible carbon footprint, as well as the aquatic and marine CO2 emissions, are included in climate mitigation strategies.

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