Afforested riparian zone can provide important services beyond forestry, such as the removal of nitrogen from diffuse pollution. Within the Venice Lagoon watershed, a pilot experimental scale system was designed to manage and monitor the hydrological fluxes and quantify N removal processes. The main objectives of this research, carried out from 2008 to 2010, were (i) to analyze “in situ” and potential denitrification rates and their limiting factors, (ii) to compare present rates, in a maturation stage of the riparian forest, with those measured in 2002. To achieve these objectives, we quantified: (i) the “in situ” denitrification process, (ii) the soil potential denitrification activity, and (iii) the nitrogen removal rates. The highest rates of “in situ” denitrification were recorded in the medium soil layer, but we observed a rate decrease compared to the initial phase (2002). Denitrification potential was significantly higher in the top soil layer. In the medium layer, the availability of organic carbon was limiting, although there was a slight increase of organic carbon near the irrigation ditch. Denitrification, carbon availability and bacterial activities remained low in the deeper soil layer.