A conceptual framework is developed using atmospheric measurements from aircraft to determine fluxes of CO2 from a continental land area. The concepts are applied to measurements of CO2, O3, and CO concentrations from the Amazon Boundary Layer Experiment (ABLE-2B, April–May 1987) to estimate fluxes of CO2 for central and eastern Amazonia late in the wet season of 1987. We observed that column amounts of CO2 from 0 to 3 km decreased during the day over Amazonia at the average rate of −6.3 ± 1 μmol m−2 s−1, corresponding to an uptake flux modestly smaller than the daytime uptake (−10.2 μmol m−2 s−1) at a flux tower in the study area. The estimated net flux of CO2, integrated over 24 hours, was −0.03 ± 0.2 μmol m−2 s−1, indicating that the carbon budget of a substantial area of central Amazonia was close to balance in April 1987. We argue that net CO2 fluxes on the continental scale of Amazonia, with its heterogeneous landscape and large areas of inundation, are strongly modified by the influence of seasonal hydrological factors that enhance respiration and decomposition in forests and wetlands, offsetting growth of forest trees in the wet season.