Two distinct CO2 sink/source characteristics are found in the tropical Indonesian seas from the compilation of observed data for the period 1984-2013. The western region persistently emits CO2 to the atmosphere, whereas the eastern region is dynamic and acts either as a small source or sink of CO2 to the atmosphere, depending on sites. The segregation is proximal to the Makassar Strait, which is located over the continental shelf and is one of the main routes of the Indonesian Throughflow (ITF). Lower salinity and higher silicate were found in the western region, suggesting a terrestrial influence in this area. Temperature has a limited influence in controlling different CO2 sink/source characteristics in the west and east. However, an SST change of -2.0°C during La Niña events effectively reduces the pCO2 difference between the atmosphere and surface seawater by 50% compared to normal year conditions. During La Niña events, higher wind speeds double the CO2 flux from the ocean to the atmosphere compared to that of a normal year. In the continental shelf area where the CO2 sink area was found, data of over 29 years show that the seawater pCO2 increased by 0.6-3.8 μatm yr−1. Overall, the seawater pCO2 of the Indonesian Seas is supersaturated relative to the atmosphere by 15.9 ± 8.6 μatm and thus acts as a source of CO2 to the atmosphere. This article is protected by copyright. All rights reserved.