The Amazon basin is the largest watershed on Earth. Although the variability of the Amazon hydrological cycle has been increasing since the late 1990s, its underlying causes have remained elusive. We use water levels in the Amazon River to quantify changes in extreme events and then analyze their cause. Despite continuing research emphasis on droughts, the largest change over recent decades is a marked increase in very severe floods. Increased flooding is linked to a strengthening of the Walker circulation, resulting from strong tropical Atlantic warming and tropical Pacific cooling. Atlantic warming due to combined anthropogenic and natural factors has contributed to enhance the change in atmospheric circulation. Whether this anomalous increase in flooding will last depends on the evolution of the tropical inter-ocean temperature difference.