The western Tropical Atlantic Ocean is a biogeochemically complex region due to the structure of the surface current system and the large freshwater input from the Amazon River coupled with the dynamics of precipitation. Such features make it difficult to understand the dynamics of the carbon cycle, leading to contrasting estimates in sea-air CO2 exchanges in this region. Here, we demonstrate that these contrasting estimates occur because the western Tropical Atlantic Ocean can be split into three distinct sub-regions in terms of the sea-air CO2 exchanges. The sub-region under the North Brazil Current domain acts as a weak annual CO2 source to the atmosphere, with low interannual variability. The sub-region under the North Equatorial Current influence acts as an annual CO2 sink, with great temporal variability. The third sub-region under the Amazon River plume influence shows greater interannual variability of CO2 exchanges, but it always acts as a net oceanic sink for CO2. Despite this large spatial variability, the entire region acts as a net annual CO2 sink of −1.6 ± 1.0 mmol m−2 day−1. Importantly, the Amazon River plume waters drive 87% of the CO2 uptake in the western Tropical Atlantic Ocean. In addition, we found a significant increasing trend in sea surface CO2 partial pressure in the North Brazil Current and North Equatorial Current waters. Such trends are more pronounced than the increase in atmospheric CO2 partial pressure, revealing the sensitivity of carbon dynamics in these sub-regions to global climate change.