The aim of this study was to quantify the N removal efficiency of an Ulva-based phytotreatment system receiving wastewaters from a land-based fish farm (Orbetello, Italy), to identify the main biogeochemical pathways involved and to provide basic guidelines for treatment implementation and management. Fluxes of O2 and nutrients in bare and in Ulva colonised sediments were assessed by light/dark core incubations; denitrification by the isotope pairing technique and Ulva growth by in situ incubation of macroalgal disks in cages. O2 and nutrient budgets were estimated as sum of individual processes and further verified by 24-h investigations of overall inlet and outlet loads. Ulva uptake (up to 7.8 mmol Nm(-2) h(-1)) represented a net sink for water column and regenerated NH4+ whilst N removal via denitrification (10-170 micromol Nm(-2) h(-1)) accounted for a small percentage of inorganic nitrogen load (<5%). Laboratory experiments demonstrated a high potential for denitrification (over 800 microM Nm(-2) h(-1)) indicating that N loss could be enhanced. The control of Ulva standing stocks by optimised harvesting of surplus biomass may represent an effective strategy to maximise DIN removal and could result in the assimilation of approximately 50% of produced inorganic nitrogen.