Estimations of the global carbon budget include a quantitative understanding of the evolving processes that occur along river-to-ocean gradients. However, high spatiotemporal resolution observations of these processes are limited. Here we present in situ measurements of the partial pressure of CO2 (pCO2) made through the Amazon River plume (ARP) during different discharge seasons, from 2010 to 2012. We evaluated the spatiotemporal distribution of pCO2 using Soil Moisture and Ocean Salinity (SMOS) satellite observations for each hydrologic period in the ARP. Regression models were used to estimate pCO2 at the ARP for the period of 2010–2014. From these distributions we calculated sea-air gas exchange of CO2 between the plume waters and the atmosphere (FCO2). Intra-annual variability of FCO2 was related to discharge at the river mouth and ocean currents as well as trade winds in the plume. Climatic events during the study period had a significant impact on the FCO2. Including the plume area closer to the river mouth makes the ARP a net source of CO2 with an annual net sea-air flux of 8.6 ± 7.1 Tg C y−1 from 2011 to 2014.