Fluxes of nutrients (NH4+, NO3-, PO43- and Si(OH)4) were studied on an intertidal mudflat in Marennes-Oléron Bay, France, at two different seasons and at different times of the emersion period. Fluxes through the sediment-water interface were both calculated from vertical profiles of nutrient concentration in pore-water (diffusive fluxes, JD) and measured in light and dark benthic mini-chambers (measured fluxes, J0). Results indicate that ammonia was mainly released in summer while nitrate was mainly taken up in late winter. This uptake from the overlying water was probably due to the coupling of nitrification-denitrification within the sediment. The J0/JD ratio further indicates that bioturbation likely enhanced ammonia release in summer. Concerning phosphate, the comparison of diffusive and measured fluxes suggests that PO43- could be assimilated by the biofilm in winter while it was released in summer at a high rate due to both bioturbation and desorption because of the relative anoxic conditions in summer. Silica was always released by the sediment, but at a higher rate in summer. Statistically significant differences in measured fluxes were detected in dark chambers at different times of low tide, thus suggesting a short-term variability of fluxes. Microphytobenthos preferred ammonia to nitrate, but assimilated nitrate when ammonia was not available. It also turned out that benthic cells could be limited in nitrogen during low tide in late winter. In summer, ammonia was not limiting and microphytobenthic activity significantly decreased the measured flux of NH4+ in the middle of low tide when its photosynthetic capacity was highest.