Isotopically labeled nitrate ( 15 NO ) was added continuously to the Rowley estuary, Massachusetts, for 22 d to 2 3 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 m 3 ) was achieved for the 3 weeks and allowed us to construct a nitrogen mass balance model for the upper estuary. Mean d 15 NO in the 2 3 estuary ranged from 300‰ to 600‰, and approximately 75%‐80% of the 15 N was exported conservatively as 15 NO to the coastal ocean. Essentially all of the 20%‐25% of the 15 N processed in the estuary occurred in the 2 3 benthos and was evenly split between direct denitrification and autotrophic assimilation. The lack of water-column 15 N uptake was attributed to low phytoplankton stocks and short water residence times (1.2‐1.4 d). Uptake of watercolumn NO by benthic autotrophs (enriched in excess of 100‰) was a function of NO concentration and satisfied 2 2 3 3 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 15 NH . By the end of the study, 15 N storage in sediments and marsh macrophytes accounted for 50%‐70% of the 1 4 15N assimilated in the estuary. These compartments may sequester watershed-derived nitrogen in the estuary for time scales of months to years.