A simulation model based on satellite observations of monthly vegetation cover from the Moderate Resolution Imaging Spectroradiometer (MODIS) was used to estimate monthly carbon fluxes in terrestrial ecosystems of Brazilian Amazon and <i>Cerrado</i> regions over the period 2000–2004. Net ecosystem production (NEP) flux for atmospheric CO₂ in the region for these years was estimated. Consistently high carbon sink fluxes in terrestrial ecosystems on a yearly basis were found in the western portions of the states of Acre and Rondônia and the northern portions of the state of Pará. These areas were not significantly impacted by the 2002–2003 El Niño event in terms of net annual carbon gains. Areas of the region that show periodically high carbon source fluxes from terrestrial ecosystems to the atmosphere on yearly basis were found throughout the state of Maranhão and the southern portions of the state of Amazonas. As demonstrated though tower site comparisons, NEP modeled with monthly MODIS Enhanced Vegetation Index (EVI) inputs closely resembles the measured seasonal carbon fluxes at the LBA Tapajos tower site. Modeling results suggest that the capacity for use of MODIS Enhanced Vegetation Index (EVI) data to predict seasonal uptake rates of CO₂ in Amazon forests and <i>Cerrado</i> woodlands is strong.