Quagga mussels (Dreissena rostriformis bugensis) are among the most impactful invaders in freshwaters of the Northern Hemisphere. As filter-feeders, they can reduce harmful algal blooms (HABs), but their effects are expected to be dependent on cyanobacteria species and water temperature. However, conclusive studies on these traits and their combination are lacking. Here, we combined laboratory experiments with an analysis of long-term data from a temperate shallow lake 10 years before and after quagga mussel invasion, respectively. We tested the hypotheses that quagga mussel filtration rates in the laboratory would 1) vary among common cyanobacteria species and 2) decrease above a critical temperature. Regarding the field data, we expected that 3) quagga mussels can reduce the summer biovolume of palatable cyanobacteria, but that 4) this effect disappears above a critical temperature. Our results support all four hypotheses. In laboratory experiments, Dolichospermum flos-aquae was classified as palatable to quagga mussels, while Aphanizomenon flos-aquae, Anabaenopsis elenkinii and Microcystis aeruginosa were less-palatable cyanobacteria. Filtration rates decreased above 28.9°C (CI: 27.6–30.2°C) with mussels dying at 32°C. Our long-term lake data show that cyanobacteria biovolumes were lower after quagga mussel invasion, but only below 27.7°C (CI: 26.9–28.4°C), confirming a critical thermal window for quagga mussel filtration. Global warming will therefore facilitate HABs by increasing the growth rates of cyanobacteria and reducing the filtration rates of quagga mussels above critical summer water temperatures, which are increasingly being reached in invaded lakes. This critical thermal window must be considered when making HAB predictions.