The importance of temporal changes in the vertical distribution of microphytobenthic algae on the overall functioning of intertidal biofilms were investigated with low‐temperature scanning electron microscopy and high‐resolution single‐cell fluorescence imaging of photosystem II efficiency (estimated by the fluorescence parameter F’q/F’m) in intact cores maintained in tidal mesocosms. Early morning biofilms consisted of smaller naviculoid and nitzschioid taxa or euglenoid species. By midday, Gyrosigma balticum and Pleurosigma angulatum were dominant. Some taxa (e.g., Plagiotropis vitrea) disappeared from surface layers after midday. Species composition continued to change toward the end of the photoperiod, with G. balticum dominating in diatom‐rich biofilms. In Euglena‐rich biofilms, initial dense surface films of euglenids became progressively dominated by smaller diatoms. F’q/F’m (measured at a photosynthetically active photon flux density (PPFD) of 220 µmol m−2 s−1) of individual cells of all taxa declined significantly after midday, but increased toward dusk. There were significant differences in F’q/F’m between species, particularly after midday. F’q/F’m versus irradiance curves and relative electron transport rate (rETRmax) showed higher efficiencies and rETRmax for euglenids, whereas G. balticum, Nitzschia dubia, and small Nitzschia sp. were shade‐adapted with low values of F’q/F’m, rETRmax, and Esat. G. balticum, P. vitrea, and N. dubia showed rapid vertical migration away from the surface with increasing irradiance. Euglenids, P. angulatum, and N. dubia exhibited their highest rETRmax values at midday. Esat for algal cells was between 500 and 600 µmol m−2 s−1, except for N. dubia and small Nitzschia sp., which had an Esat of 300 µmol m−2 s−1. Differences in behavioral and photophysiological traits between microphytobenthic taxa could be a form of niche separation and need to be incorporated into conceptual models of daily patterns of production in intertidal biofilms.