We constructed an empirical mass balance model of nutrient fluxes in the Ogeechee River estuary (Georgia, USA) from eight surveys of seasonal estuarine nutrient concentrations during 2015 and 2016. The model results indicated a net removal of dissolved phosphorus and a net production of dissolved nitrogen (N) within the estuary over an annual cycle. During summer and autumn low flow periods, much of the dissolved N discharged to the ocean seems to be recycled into the estuary in the form of phytoplankton biomass. As a result, the outwelled N is not new nitrogen fueling coastal production but is nitrogen trapped within a recycling loop across the ocean–estuarine boundary. Higher flows in the fall and winter lead to direct discharge of nutrients with minimal recycling. A balanced N budget for the Ogeechee River estuary requires that estuarine N-fixation must exceed burial and denitrification losses within the estuary.