Marine heatwaves are increasing worldwide, with several negative impacts on biological communities and ecosystems. This 24-day study tested heatwaves' effect with distinct duration and recovery periods on benthic estuarine communities' diversity and contribution to ecosystem functioning experimentally. The communities were obtained from a temperate estuary, usually subjected to high daily thermal amplitudes. Our goal was to understand the communities' response to the thermal change, including the community descriptors and behavioural changes expected during heat extremes. We measured community composition and structural changes and the bioturbation process and nutrient release as ecosystem functioning measurements. Overall, our findings highlight the potential tolerance of studied estuarine species to the temperature ranges tested in the study, as community composition and structure were similar, independently of the warming effect. We detected a slight trend for bioturbation and nutrient release increase in the communities under warming, yet these responses were not consistent with the heatwaves exposure duration. Overall, we conclude on the complexity of estuarine communities’ contribution to functioning under warming, and the importance of scalable experiments with benthic organisms' responses to climate variability, accommodating longer time scales and replication. Such an approach would set more efficient expectations towards climate change mitigation or adaptation in temperate estuarine ecosystems.