Here, we show that alpine lake ecosystems are responsive to interannual variation in climate, based on long-term limnological and meteorological data from the Canadian Rockies. In the 2000s, in years with colder winter temperatures, higher winter snowfall, later snowmelt, shorter ice-free seasons, and dryer summers, relative to the 1990s, alpine lakes became clearer, warmer, and mixed to deeper depths. Further, lakes became more dilute and nutrient-poor, the latter leading to significant declines in total phytoplankton biomass. However, increased concentrations of dissolved organic carbon in lake water stimulated the appearance of small mixotrophic algal species, partially offsetting the decline in autotrophic phytoplankton biomass and increasing algal species richness. The climate regime in the 2000s altered the physical, chemical, and biological character and the function of high-elevation aquatic ecosystems. Forecasts of increased climatic variability in the future pose serious ramifications for both the biodiversity and ecosystem function of high-elevation lakes.