Most ecosystems are threatened by multiple biotic and abiotic stressors simultaneously. Projections estimate an increase in the frequency, intensity, and duration, of extreme weather events (e.g. heatwaves) in coming years. Yet, whether species extinctions compound the impacts of extreme events on ecosystems is largely unknown. Moreover, studies aiming to experimentally mimic the effects of climate change mostly over- or underestimate temperature changes in the relevant region. Here, I use 48 aquatic mesocosms to investigate the combined effect of predator extinctions and heatwaves—current and projected future heatwaves—on aquatic community dynamics in a subarctic stream in Hokkaido, Japan. I show that predator extinctions increase the vulnerability of macroalgal composition to aquatic heatwaves, as mediated through trophic cascades—increased abundance of macroinvertebrate consumers. Algal biomass was less affected than composition, indicating that predatory fish stabilise algal communities but not their productivity in response to extreme events. However, predator effects on algal biomass established later in the experiment, highlighting differences in the speed with which predator extinctions alter algal biomass and composition. Critically, my heatwaves were informed by downscaling regional climate projections, allowing unprecedented insight into the likely future consequences of climate change and aquatic heatwaves on subarctic freshwater communities in Japan.