In shallow coastal areas the amplitude and range of benthic silicic acid fluxes can have a significant influence on benthic–pelagic coupling and the functioning of the pelagic system. To explore the oscillation in fluxes over the diurnal cycle and in particular the influence of microphytobenthos (MPB), an experiment was carried out in a shallow subtidal site in the Bay of Brest (France). Benthic chambers were employed over a 48 h period to measure the variability in silicic acid and oxygen fluxes; MPB migration was investigated using a diving Pulse Amplitude Modulated (PAM) fluorometer and uptake rhythms of silicic acid by natural MPB populations were measured using the 32Si isotope. It was discovered that silicic acid fluxes fluctuated greatly throughout the diurnal period resulting in an oscillation in the availability of this nutrient for phytoplankton communities. The uptake of silicic acid by the MPB was quantified for the first time and highlighted a 2-fold increase in the demand from night to afternoon periods. The combined silicic acid uptake and the concentration of cells at the sediment–water interface, forming a dense biofilm of MPB, were postulated to be the main processes reducing effluxes at midday. Our work highlighted the many processes which influence silicic acid effluxes in shallow coastal areas and the possible interaction between uptake and dissolution processes. The variations in benthic fluxes over the diurnal period were comparable to observations reported at the seasonal scale. Therefore, up-scaling hourly flux observations to daily and annual estimates should be undertaken with caution. Further we suggest that the main processes influencing flux oscillations over the diurnal period should be considered when planning sampling strategies and extrapolating to larger time scales.