The nitrogen cycle in the lagoon of Venice, which is the largest Italian lagoon, was investigated by means of a 3D fully coupled transport – water quality model, which had been validated against a substantial amount of real-world data. Nitrogen fluxes among different ecosystem compartments were computed for each month of a reference year, and for each one of the three sub-basins into which the lagoon is conventionally subdivided. The computation included the loads of nitrogen discharged by the tributaries, the direct inputs from the industrial area and the city of Venice, the atmospheric loads, the fluxes at the three lagoon inlets and the internal fluxes between sediment and water compartments and among the three sub-basins. The results of the analysis show that the lagoon, as a whole, exports nitrogen towards the sea. Approximately 4000 tN/year are recycled by the system, while 4640 tN/year is the net input from the drainage basin and the other sources, thus leading to about 8640 tN/year of dissolved inorganic nitrogen that enter the water compartment. Around half of the this amount is used by primary producers, one fourth is exported towards the sea, and one fourth is transferred into the sediment compartment, or lost to atmosphere. These findings suggest that the exchanges through the inlets play an important role in keeping nitrogen concentration at an acceptable level. A more detailed analysis of the model results shows that the non-homogeneous spatial distribution of tributary discharges and point sources is the main cause of the differences in the ecosystem response and water quality among the three sub-basins. Nutrient poorer sub-basins fix a ration of available inorganic nutrient higher than nutrient rich ones. However, they are more efficient in transferring the biomass to the highest trophic levels. Results also include estimates of fluxes that were not quantified so far (such as grazing and recycling), and a validated model, which could have a practical use, for example for assessing implications of reduction of nutrient loads.