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Abstract Aquatic heatwaves are increasing in frequency, intensity, and duration worldwide. While increases in mean water temperatures are linked to enhanced phytoplankton biomass, it is unclear how heatwaves alter phytoplankton dynamics in lakes at an ecosystem scale. We investigated changes in surface chlorophyll during 29 summer heatwaves between 2008 and 2019 in 3 north temperate lakes. These lakes vary in staining and were either references or manipulated with nutrients and top predator additions. The manipulations provided a variety of nutrient, grazing, and light conditions during heatwave and non‐heatwave conditions. Surface chlorophyll concentrations increased during 24 out of 29 heatwaves. In the low‐nutrient reference lake the mean increase in chlorophyll was 57% while in the two experimental lakes the mean increases were 127% and 183%. Overall, the effects of the whole‐lake experiments were variable but still provided context for possible patterns amid a diverse set of food web and nutrient conditions.