The effects of the recent warming trend in many northern temperate lakes on the species composition of spring phytoplankton remain poorly understood, especially because a recent change in nutrients has complicated efforts, and previous studies have defined spring according to the calendar. We analysed data from 1979 to 2004 from Lake Müggelsee (Berlin, Germany), using physical and biological parameters to define the spring period. We show that a change in timing of spring plankton events in warm years led to the paradox of lower mean water temperatures during the growth period, favouring cold-adapted diatoms over cyanobacteria, and within the diatoms, some cold-adapted centric forms over pennate forms. Under high P : Si ratios, the increased time between phytoplankton and cladoceran peaks opened a loophole for filamentous cyanobacteria (Oscillatoriales) in warm years to establish dominance after the diatoms, which are silicate limited. Therefore, the warming trend promotes filamentous cyanobacteria, a well-known nuisance in eutrophic lakes, and surprisingly, cold-adapted diatoms.