The mud surface temperature (MST) of an intertidal mudflat in Marennes-Oléron Bay (France) and the biomass-specific photosynthetic capacity (PBmax) of benthic microalgae were modelled to investigate their spatio-temporal dynamics. Simulations were performed over 2 different periods during and after the microphytobenthos spring bloom (April and June, respectively) and under 2 different tidal conditions (spring and neap tides). The deterministic MST model is based on thermodynamic processes. Comparison at different periods between measured data series and simulations clearly establishes the reliability of the model, thus allowing extrapolations over time and space. The spatio-temporal dynamics of MST is primarily controlled by the immersion-emersion alternation combined with the solar cycle, with a strong influence of the phase difference in their respective oscillations: the highest MSTs are achieved in summer in the highest parts of the mudflat, when spring low tide occurs at midday. Three relevant time scales characterize the MST dynamics: long-term (seasonal cycle), medium-term (lunar cycle) and short-term (solar and tidal cycles). Within that framework, the response of PBmax to changes in MST depends upon Topt, the optimum temperature for photosynthesis (Topt = 25°C all year round). In April, when the MST values are below Topt, PBmax varies exponentially with MST at short time scales. Conversely, in June, when the range of MST partially exceeds Topt, PBmax is inhibited on most of the mudflat surface area (up to 75%). This thermo-inhibition is highest in summer, when low tide occurs at midday.