In 2023, an unprecedented drought and heat wave severely affected Amazon waters, leading to high mortality of fishes and river dolphins. Five of 10 lakes monitored had exceptionally high daytime water temperatures (over 37°C), with one large lake reaching up to 41°C in the entire approximately 2-meter-deep water column and up to 13°C of diel variation. Modeling showed that high solar radiation, reduced water depth and wind speed, and turbid waters were the main drivers of the high temperatures. This extreme heating of Amazon waters follows a long-term increase of 0.6°C/decade revealed by satellite estimates across the region’s lakes between 1990 and 2023. With ongoing climate change, temperatures that approach or exceed thermal tolerances for aquatic life are likely to become more common in tropical aquatic systems.