Alpine temperatures have risen at twice the rate compared to the northern-hemispheric average during the past century. This can be expected to affect Alpine lake ecosystems via, for example, intensified thermal stratification, shorter ice cover periods, and altered catchment processes. Our study assesses changes in some main constituents of the planktic and benthic communities of five mid-Alpine lakes in the Niedere Tauern region in Austria in relation to climatic warming, by comparing community and environmental data from 1998–1999 to data from 2010–2011. Although lake chemistry remained relatively stable between the study periods, we observed an increase in lake water temperatures and a decrease in ice cover durations. Several of the dominant diatom species and chrysophyte cyst types show relatively clear changes; the responses of the whole communities, however, are less evident. Yet, in particular, diatoms show distinct assemblage changes along the climatic gradients in the two lakes with the largest decrease in ice-cover duration. Chironomid communities appear to be less sensitive compared to diatoms and chrysophyte cysts, which are known for reacting quickly to changes in their environment. Finally, Alpine lakes, which are moderately nutrient-enriched because of human activities in the catchment area, are likely to experience increases in their productivity with climate warming.