The importance of intertidal flats as areas of nitrogen filtering has become increasingly apparent in recent times. To understand fully the cycling of this nutrient in these areas of high metabolic activity, it is necessary to elucidate the influence of microphytobenthos (MPB) on stocks of ammonium and nitrate in surface areas. In this study, we aimed to quantify nitrogen uptake and relate it to the in situ concentrations and environmental conditions to which MPB are exposed. In an estuarine system on the Korean Peninsula, we conducted kinetic experiments using 15 N stable isotopes and core sampling over the tidal cycle to determine the temporal evolution of porewater nutrient concentrations and the migration of MPB. The results revealed a range of K s values between 1.5 and 11.8 μmol l -1 for ammonium and 19.2 μmol l -1 for nitrate. Thus MPB communities vary their affinity for dissolved inorganic nitrogen (DIN), which may be related to the substrate conditions to which they are exposed. Uptake of ammonium under experimentally darkened or natural night conditions was, on average, 50% lower than during light periods. The range of porewater DIN concentrations was large and appeared to be primarily determined by tidal influences. This oscillation, coupled to the vertical migration of the MPB in sediments, is likely to have a substantial effect on uptake over the short term (hours). The results indicate that, contrary to our conceptual model, the MPB largely incorporates DIN at the sediment surface during low tide periods when ammonium concentrations are at their highest. As a result, our representation of the MPB in coastal and estuarine models needs to be reassessed.