Anthropogenic-induced changes in nutrient ratios have increased the susceptibility of large temperate lakes to several effects of rising air temperatures and the resulting heating of water bodies1. First, warming leads to stronger thermal stratification, thus impeding natural complete water turnover (holomixis), which compensates for oxygen deficits in the deep zones, Second, increased water temperatures and nutrient concentrations can directly favour the growth of harmful algae. Thus, lake-restoration programmes have focused on reducing nutrients to limit toxic algal blooms. Here we present evidence that the ubiquitous harmful cyanobacterium Planktothrix rubescens has become the dominant species in a large lake during the past four decades, although the phosphorus content of the ecosystem decreased fivefold. However, the nitrogen input was not diminished concomitantly, favouring this non-N2-fixing cyanobacterium owing to increased N:P ratios. P. rubescens contains gas vesicles that allow for buoyancy to accumulate within the depth of optimal irradiance. As the toxic cyanobacterium has low consumption by predators, water turnover represents the main mechanism of seasonal population control. Thus, unidirectional lake-restoration measures in parallel with recurrent absence of holomixis owing to lake warming may lead to similar undesired effects that have formerly emerged from fertilization.