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Research on the carbonate system in the tropical regime of the Indonesian Seas is limited and required to understand carbonate dynamics due to the Indonesian throughflow (ITF). Here, we present marine carbonate system along the main routes of the ITF spanned Mindanao-Sulawesi, Sulawesi Sea, Makassar Strait and Lombok Strait during strong 2015 El Niño and transition seasons of October 2017. Along the main routes, dissolved inorganic carbon (DIC) and total alkalinity (TAlk) were shown lower compared to the main outflow passage of the Lombok Strait. Physical and biogeochemical processes in the upper thermocline is dominated by photosynthesis and carbon dioxide (CO2) release to the atmosphere induced by vertical mixing. DIC vs. TAlk relationship shown mixing process occurred in the upper thermocline following the stratified North Pacific waters. In the upper 150 m, freshwater contribution changed the ITF water structures particularly after the Labbani channel to the Lombok Strait. Strong seasonal and spatial variabilities of sea-air exchange along the main routes. The difference between sea and air partial CO2 (ΔpCO2) in the Mindanao-Sulawesi to eastern Sulawesi Sea showed the main inflow act as sink with a slightly source of atmospheric CO2 ranged from -7 to 23 μatm (-0.19-0.72 mmol C m-2 d-1), while the Makassar strait (3.4-128 μatm) and along southern Makassar Strait to the Lombok Strait (51-76 μatm) were act a source within CO2 degassing of 0.09-8.3 and 2.2-6.9 mmol C m-2 d-1, respectively. Estimating potential carbon flux to support the Indian Ocean primary productivity from the Makassar Strait was ~9972 Tg C y-1 whereas 2090 Tg C y-1 exports to the Indian Ocean via the Lombok Strait, while the remained carbon of 7881 Tg C y-1 were transported to the Banda Sea.