Isotopically labeled nitrate (15NO3-) was added continuously to the Rowley estuary, Massachusetts, for 22 d to assess the transport, uptake, and cycling of terrestrially derived nitrogen during a period of high river discharge and low phytoplankton activity. Isotopic enrichment of the 3.5-km tidal prism (150,000 m3) was achieved for the 3 weeks and allowed us to construct a nitrogen mass balance model for the upper estuary. Mean ??15NO3- in the estuary ranged from 300??? to 600???, and approximately 75%-80% of the 15N was exported conservatively as 15NO 3- to the coastal ocean. Essentially all of the 20%-25% of the 15N processed in the estuary occurred in the benthos and was evenly split between direct denitrification and autotrophic assimilation. The lack of water-column 15N uptake was attributed to low phytoplankton stocks and short water residence times (1.2-1.4 d). Uptake of water-column NO3- by benthic autotrophs (enriched in excess of 100???) was a function of NO3- concentration and satisfied up to 15% and 25% of the total nitrogen demand for benthic microalgae and macroalgae, respectively. Approximately 10% of tracer assimilated by benthic autotrophs was mineralized and released back to the water column as 15NH4+. By the end of the study, 15N storage in sediments and marsh macrophytes accounted for 50%-70% of the 15N assimilated in the estuary. These compartments may sequester watershed-derived nitrogen in the estuary for time scales of months to years.