Temperate deep freshwater lakes are important resources of drinking water and fishing, and regional key recreation areas. Their deep water often hosts highly specialised fauna surviving since glacial times. Theoretical and observational studies suggest a vulnerability of these hydro-ecosystems to reduced mixing and ventilation within the ongoing climatic change. Here we use a numerical thermal lake model, verified over the 20th century, to quantify the transient thermal behaviour of two European lakes in response to the observed 20th-century and predicted 21th-century climate changes. In contrast to Lac d'Annecy (France) which, after adaptation, maintains its modern mixing behaviour, Ammersee (Germany) is expected to undergo a dramatic and persistent lack of mixing starting from ~2020, when European air temperatures should be ~1¿C warmer. The resulting lack of oxygenation will irreversibly destroy the deepwater fauna prevailing since 15 kyrs.