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We combined a mass balance approach with measurements of air–water and sediment–water nitrogen (N) exchange to better understand the mechanisms attenuating N throughputs in a eutrophic coastal lagoon. We were particularly interested in how seasonal shifts in external versus internal N fluxes and the transition from diatom- to cyanobacteria- dominated phytoplankton communities influence N storage and loss to the atmosphere. We found that on an annual basis almost all of the N removed by the lagoon was due to sediment storage following the spring diatom bloom. This period was characterized by high riverine inputs of dissolved inorganic nitrogen, high rates of assimilatory conversion to particulate nitrogen (PN), and net accrual of N in sediments. By contrast, the larger summer bloom was associated with low sediment N storage, which we attribute in part to the presence of positively-buoyant …