1. The increase in heatwave intensity and duration is challenging microalgal photosynthesis in shallow waters. In particular, the extent of photosynthesis impairment or limitation due to short extreme heat stress events occurring during a heatwave remains unknown.2. In this study, we investigated the importance of microalgal diversity and thermal history in the response of phototrophic biofilms to severe heat stress. We exposed isolated microalgal strains, synthetic communities previously acclimated at three temperatures, and natural phototrophic biofilms sampled at different seasons to several temperature/duration pairs (from 31 to 44 °C for 30, 60, 120 or 180 min). Microalgal photosynthetic activity (FV/FM) was measured after each heat stress and was shown to be a function of thermal dose, defined as the product of time and an exponential function of temperature.3. It appeared that the thermal history plays an important role in tolerance to heat stress, with synthetic communities acclimated at highest temperature being more tolerant. However, the responsiveness (i.e., the strength of the response) to heat stress was driven by the microalgal diversity of the community.4. Synthesis: Our analysis showed that although photosynthetic activity was negatively impacted by heat stress, gross primary productivity was even more strongly and rapidly impacted, highlighting the fact that in situ, even moderate heat stress can significantly impair primary productivity in shallow waters.