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Climate variability may affect the functioning of Amazon moist tropical forests, and recent modeling analyses suggest that the carbon dynamics of the region vary interannually in response to precipitation and temperature anomalies. However, due to persistent orbital and atmospheric artifacts in the satellite record, remote sensing observations have not provided quantitative evidence that climate variation affects Amazon forest phenology or productivity. We developed a method to minimize and quantify non-biological artifacts in NOAA AVHRR satellite data, providing a record of estimated forest phenological variation from 1982–1993. The seasonal NDVI amplitude (a proxy for phenology) increased throughout much of the basin during El Niño periods when rainfall was anomalously low. Wetter La Niña episodes brought consistently smaller NDVI amplitudes. Using radiative transfer and terrestrial biogeochemical models driven by these satellite data, we estimate that canopy energy absorption and net primary production of Amazon forests varied interannually by as much as 21% and 18%, respectively. These results provide large-scale observational evidence for interannual sensitivity to El Niño of plant phenology and carbon flux in Amazon forests.