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We hypothesised that (i) a summer heat wave would increase the thermal stability of lakes and (ii) the size and trophic state differences would modify the lakes’ responses to heating. Within 2 years, 2008 and 2009, we studied the thermal and optical regimes of two adjacent stratified lakes in northern Italy, the oligo-mesotrophic Lake Monate (2.5 km2, max. depth 34 m) and the eutrophic Lake Varese (14.8 km2, 26 m). After the cold winter 2008–2009, a heat wave starting in May turned the whole year 2009 the second hottest after 2003. The particular sequence of meteorological events resulted in extreme vertical temperature gradients and unusually high thermal stability of both lakes. All calculated thermal parameters showed the highest values in 2009 while also the values for 2008 exceeded considerably those published for these lakes in the past. Due to the large wind exposed surface, wind mixing was supposedly the dominating mechanism of heat transfer in the shallower eutrophic Lake Varese where, due to low water transparency, large amount of solar energy trapped in the upper layers markedly increased the thermal stability. In the deeper and more transparent Lake Monate, the deeper penetrating solar irradiance contributed to better energy dissipation within the water column and smaller interannual differences in thermal stability.