Microphytobenthos (MPB) regulate nitrogen fluxes across the sediment-water interface in shallow coastal and estuarine environments, where the water-phase concentrations exhibit pronounced variations in time and space. The impact of MPB and N-availability on anaerobic ammonium oxidation (anammox) and denitrification was studied in experimental microcosms using a combination of N-15 isotope and microsensor techniques (NO3- + NO2- and O-2). The presence of MPB at low water-column NO3- concentrations led to an 85 % reduction in the capacity of the sediments for performing the anammox reaction within a 3 wk period, but did not affect the denitrification potential. The presence of MPB also had a significant impact on both O-2 and NO3- + NO2- (NOx-) concentrations in the sediment. At low NO3- concentrations, NOx- was almost depleted in the alga-colonized sediments within 2 wk of incubation, due to assimilation and inhibition of nitrification. The depth distribution Of O-2 displayed significant variations during the light-dark cycles, leading to periodical O-2 exposure of sediment strata that may harbor the anammox process. A sustained high anammox potential in sediments where MPB was allowed to colonize in the presence of 600 mu M NO3- in the overlying water indicated that a steady supply of NOx- and not protection from O-2 exposure was the vital factor for maintenance of anammox capacity. In this case, NOx- penetrated approximately 9 mm into the sediment. We therefore suggest that a continuous supply of NOx- to the anoxic sediment layers is the key factor for the presence of anammox in marine sediments. On the basis of these results, we suggest that anammox is of very limited significance in environments that periodically experience N-limitation and that occurrence of high rates of anammox in coastal sediments is limited to estuaries with permanently high concentrations of NOx- in the water column.