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Climate change in the Andes has already affected phenology, glaciology, and other ecosystem attributes, and now threatens to alter long-standing fundamental limnological properties. In the equatorial Andes, most lakes have traditionally been described as having waters that circulate continuously (polymictic), with only rare episodes of stratification. This characterization, albeit based on relatively few studies, is widely accepted, despite accelerated regional warming over the past 30 years.Here, we show that protracted periods of thermal stratification are presently the norm, not the exception, in equatorial mountain lakes. Annual circulation and stratification patterns recorded in four lakes from Ecuador’s southern Sierra show extended periods of stratification, which are stable and do not break down with nocturnal cooling. These data contrast with earlier research from this region, which reported full water column mixing and only infrequent stratification, but are not surprising in light of recent trends toward rising temperatures and declining wind velocities. Paleolimnological studies show that changes to the thermal regimes of these lakes likely began several decades ago and have resulted in ecosystem-scale changes including regime shifts in phytoplankton and declines in aquatic production.