Climate change is threatening aquatic ecosystems worldwide, notably through the increase in heatwave intensity and frequency. Photosynthesis is one of the most heat-sensitive cellular processes, it is therefore necessary to better understand the heat stress effects on photosynthetic activity and corresponding primary productivity. Currently, these effects are not well documented due to the lack of a modeling approach able to integrate both temperature intensity and heat duration experienced during short extreme heat stress events. This is especially the case for phototrophic biofilms, for which the probability to face heat stress increases, in both fresh and marine ecosystems. For this purpose, we implemented a laboratory controlled experimental set up (30 to 45°C, up to 3 h, using in vivo chlorophyll fluorescence as a proxy of photosynthetic activity) to expose to short-term heat stress benthic diatoms from shallow freshwaters or intertidal mudflats. The concept of "thermal dose" was then used to compute a dose of heat, defined as the product of time and an exponential function of temperature. This approach allowed us to compare the tolerance and responsiveness to heat stress across a various set of experiments involving isolated algal strains, simplified synthetic communities or natural biofilms. We also showed that this modeling approach can be applied to in situ temperature data, for predicting the effects of heat stress events in situ. Our results show that even moderate heat stress can significantly impair primary productivity. While obtained on benthic diatoms, this approach offers promising research avenue for other (photosynthetic) organisms.