The most prominent responses of Lake Zurich to climate warming include the increase of surface water temperatures, a reduced depth of spring mixing, and the persistent thriving of the harmful cyanobacterium Planktothrix rubescens, a low-light adapted species concentrating in the metalimnion during summer. To study changes of its habitat, we assessed the spatio-temporal metalimnetic boundaries by applying low-pass filtering and binary thresholding to temperature profiles of long-term data (1978–2013, weekly measurements). Due to increasing temperatures over the last 3.5 decades, the onset and duration of metalimnion formation changed significantly (stratification increased by 33 days). Moreover, the upper metalimnetic boundary has undergone a significant drawdown of 2.3 m, accounting for an overall decrease in metalimnion thickness. Being the most abundant species in this zone, P. rubescens was not negatively affected by altered temporal or spatial stratification patterns during its phase of net growth (July–September), as the zone of its optimal light-dependent buoyancy was still located within the metalimnion. The biomass of P. rubescens in August was even significantly related to increasing temperatures. Nevertheless, a further depression of the metalimnetic top boundary may eventually restrict P. rubescens by forcing it into layers of unfavourable light conditions or into the turbulent epilimnetic zone.