© 2015. American Geophysical Union. All Rights Reserved. The impacts of droughts on the Amazon ecosystem have been broadly discussed in recent years, but a comprehensive understanding of the consequences is still missing. In this study, we show evidence of a fragile hydrological equilibrium in the western Amazon. While drainage systems located near the equator and the western Amazon do not show water deficit in years with average climate conditions, this equilibrium can be broken during drought events. More importantly, we show that this effect is persistent, taking years until the normal hydrological patterns are reestablished. We show clear links between persistent changes in forest canopy structure and changes in hydrological patterns, revealing physical evidence of hydrological mechanisms that may lead to permanent changes in parts of the Amazon ecosystem. If prospects of increasing drought frequency are confirmed, a change in the current hydroecological patterns in the western Amazon could take place in less than a decade.