The Amazon river basin has been recently affected by extreme climatic events, such as the exceptional drought of 2005, with significant impacts on human activities and ecosystems. In spite of the importance of monitoring freshwater stored and moving in such large river basins, only scarce measurements of river stages and discharges are available and the signatures of extreme drought conditions on surface freshwater dynamics at the basin scale are still poorly known. Here we use continuous multisatellite observations of inundation extent and water levels between 2003 and 2007 to monitor monthly variations of surface water storage at the basin scale. During the 2005 drought, the amount of water stored in the river and floodplains of the Amazon basin was ∼130 km 3 (∼70%) below its 2003–7 average. This represents almost a half of the anomaly of minimum terrestrial water stored in the basin as estimated using the Gravity Recovery and Climate Experiment (GRACE) data.