Dissolved nitrogen fluxes and denitrification were studied during 1 yr in intertidal sediments of the Tagus estuary (Portugal). This study focused on the factors regulating both nitrogen fluxes across the sediment-water interface and denitrification, and on the effect of microphytobenthos activity in controlling nitrogen cycling in these areas. Sampling was performed monthly at 2 stations located in inner and outer intertidal areas. Fluxes of O 2 , NO 3 - , NO 2 - , NH 4 + and N 2 O, and denitrification (determined by the nitrogen-isotope pairing technique) were measured simultaneously in closed chambers incubated in the laboratory under simulated in situ temperature and light conditions, as well as in the dark. At the sediment-water interface, higher DIN fluxes and lower denitrification rates were registered at higher temperatures and lower NO 3 - concentration in the water column. Oxygen uptake by the sediment was generally higher than release, particularly in summer. Primary productivity displayed a seasonal cycle, positively influenced by temperature. Denitrification rates were closely related to NO 3 - river-input, Temperature, NO 3 - concentration in the water column, microphytobenthos, infauna and tidal height were the key parameters involved in controlling nitrogen cycling at the sediment-water interface in the Tagus estuary. A comparison of annual nitrogen fluxes and denitrification rates between sites was made, taking into account tidal immersion periods. Hence, N-removal by denitrification accounted for 156 mmol m -2 yr -1 in the inner station and 482 mmol m -2 yr -1 in the outer station. These rates represent respectively ca 3 and 9% of total DIN available in the estuarine water column at those 2 stations, respectively. N 2 O production was comparatively very low (0.3 to 0.6 mmol m -2 yr -1 ). The estimated nitrogen assimilation rates by microphytobenthos were 707 mmol m -2 yr -1 in the inner station and 333 mmol m -2 yr -1 in the outer station, indicating that a considerable amount of nitrogen was retained within benthic microalgae. The assimilation/denitrification ratio, with a mean value of 2, shows the relative importance of the denitrification role as a N-sink. Apart from denitrification, it is suggested that other processes must be involved in the removal of nitrogen from the estuary.