Abstract Amidst the global extinction crisis, climate change will additionally expose ecosystems to more frequent and intense extreme climatic events, such as heatwaves. Yet, whether predator species loss—a prevailing characteristic of the extinction crisis—will exacerbate the ecological consequences of extreme climatic events remains largely unknown. Here, we show that predator species loss can interact with heatwaves to affect the compositional stability of ecosystems. By exposing multitrophic stream communities to realistic current and future heatwaves—locally informed by weather station data and downscaled regional climate projections—in the presence and absence of an apex fish predator, we found that heatwaves destabilised algal communities by homogenising them in space. However, this only happened when predators were absent. Additional heatwave impacts on multiple aspects of stream communities—including changes to the structure of algal and macroinvertebrate communities, total algal biomass, and the temporal variability of algal biomass—were not apparent during heatwaves and emerged only after the heatwaves had passed. Taken together, our results suggest that, though the ecological consequences of heatwaves can amplify over time as their impacts propagate through biological interaction networks, those impacts can be mitigated by the presence of predators. These findings underscore the importance of conserving trophic structure and the integrity of biological communities, and highlight the considerable potential for species extinctions to amplify the effects of climate change and extreme events. Methods The dataset contains the Chlorophyll a concentrations of mesocosms measured during a multifactorial experiment from terracotta tiles with a Benthotorch fluorometer, as well as data on leaf dry mass decomposition, and macroinvertebrate community composition, richness, and abundance. We conducted an experiment looking at the combined effects of predator loss and heatwaves on multiple aspects of aquatic communities in semi-open mesocosms with immigration and emigration from the adjacent Horonai stream, in Tomakomai experimental forest, Hokkaido, Japan. Our focal predator was Cottus nozawae, a freshwater sculpin. We exposed 2/3 of our 48 mesocosms to heatwaves based on either observed current or projected future heatwaves and tested for interactions between predator presence/absence and heatwaves. Our dataset also contains algal time series for different functional groups (based on fluoroprobe chlorophyll a data) across our experiment, including dates that were not the focus of our analyses. See Methods section in the associated manuscript for details on data processing and the measurement of different experimental variables. Usage notes See readme file for further details and 'data descriptions.csv' file for descriptions of data structure.