Apalachicola Bay, a bar-built, sub-tropical estuary in the northeastern Gulf of Mexico (GOM), USA, receives freshwater from the Apalachicola River and exchanges water with the GOM at 4 sltes. The output from a 3-dimensional circulation model and nitrogen measurements in the river and the estuary over a 2 yr period were used to determine nitrogen input to the estuary and exchange with the GOM. The Apalachicola River was the major nitrogen source to the estuary and accounted for 92 and 73% of the total dissolved Inorganic and organic mtrogen (DIN and DON) input, respectively Nitrogen input from the GOM provided the remainder. DIN compnsed 61 % of total dissolved nitrogen (TDN) input to the estuary from the river and 26% of TDN input from the GOM. Maxima in TDN input to the estuary occurred during the high river-flow period (October to February). In contrast, TDN input minima occurred d u r~n g the summer (May to September), when river flow was low. Benthic ammonium flux to the water column was maxinlum durlng the summer. However, it was not large enough to satisfy phytoplankton nitrogen demand during that period. The fractlon of DIN input that was exported to the GOM increased linearly as estuarine water residence time decreased from 2 wk during summer to less than 3 d during winter. Seasonal nitrogen budgets indicated that DIN export to the GOM was maximum during winter (87 + 5.4 mg N m-' d-') and minimum during summer (9 + 1.4 mg N d-'). In contrast to the large decrease in DIN export to the GOM between these 2 periods, DON export to the GOM decreased from 81 * 5.8 mg N m-2 d-' during winter to only 45 i 3.2 mg N m-2 d-' during summer. Estimated denitrification rates indicated that 9% of the annual total nitrogen input to the estuary was removed by that mechanism. The f ratio in Apalachlcola Bay varied from 0.1 1 during the summer to 0.74 during the winter and averaged 0.19 for a 2 yr period. On an annual basis, DON ~n p u t to the estuary and export to the GOM were in balance, while 66% of DIN input to the estuary was exported to the GOM. The nitrogen budget for Apalachicola Bay was balanced to within 6 % of total nitrogen input.