Climate extremes are rare events that usually have devastating effects on society and the environment. Any changes in their frequency or intensity are thus of major importance. Here we quantify changes in extreme floods and droughts in the largest river on Earth – the Amazon. Our results reveal that despite the repeated emphasis on droughts in Amazonia, the largest change in extremes over the past 113 years is a recent intensification and five-fold increase in the frequency of floods, which is linked to the intensification of the global atmospheric Walker circulation since the mid-1990s. By quantifying and attributing these changes, this study completes our understanding of the ultimate causes of the observed intensification of the hydrological cycle in the Amazon basin.