Air temperatures in the tropical Andes have risen at an accelerated rate relative to the global average over recent decades. However, the effects of climate change on Andean lakes, which are vital to sustaining regional biodiversity and serve as an important water resource to local populations, remain largely unknown. Here, we show that recent climate changes have forced alpine lakes of the equatorial Andes towards new ecological and physical states, in close synchrony to the rapid shrinkage of glaciers regionally.