Past heat waves are considered harbingers of future climate change. In this study, we have evaluated the effects of two recent Central European summer heat waves (2003 and 2006) on cyanobacterial blooms in a eutrophic, shallow lake. While a bloom of cyanobacteria developed in 2006, consistent with our expectations, cyanobacterial biomass surprisingly remained at a record-low during the entire summer of 2003. Critical thresholds of abiotic drivers extracted from the long-term (1993-2007) data set of the studied lake using classification tree analysis (CTA) proved suitable to explain these observations. We found that cyanobacterial blooms were especially favoured in 2006 because thermal stratification was critically intense (Schmidt stability >44 g cm cm(-2)) and long-lasting (>3 weeks). Our results also suggest that some cyanobacterial species (Anabaena sp.) benefitted directly from the stable water column, whereas other species (Planktothrix sp.) took advantage of stratification-induced internal nutrient loading. In 2003, conditions were less favourable for cyanobacteria due to a spell of lower temperatures and stronger winds in mid-summer; as a result, the identified thresholds of thermal stratification were hardly ever reached. Overall, our study shows that extracting critical thresholds of environmental drivers from long-term records is a promising avenue for predicting ecosystem responses to future climate warming. Specifically, our results emphasize that not average temperature increase but changes in short-term meteorological variability will determine whether cyanobacteria will bloom more often in a warmer world.