Wetlands are highly effective systems mitigating the negative effects of N excess, but at the same time they contribute to global warming through greenhouse gas emissions. The present study aimed to ascertain the role of Phragmites australis in N transformations in eutrophic semiarid salt marshes, under low (NO3 − = 20 mg L−1 ) and high (NO3 − = 200 mg L−1 ) nutrient level and alternating flooding-drying phases. Methacrylate mesocosms were filled with a saline soil, with and without the presence of Phragmites stands, and subjected to alternating flooding-drying conditions. For 44 weeks the soil Eh was regularly monitored at two depths and the N-NO3 − and N-NH4 + concentration in pore water and drainage and the potential soil N-N2O emissions to the atmosphere measured. In the surface soil layers, more than the 80% of N-NO3 − was removed regardless of the presence of plants, the nutrient level and the season of the year. Denitrification seemed to be the main responsible of this. In the subsurface soil layers N-NO3 − decreased an average of ~83% in presence of Phragmites and ~32% without plants during the warmer period (soil temp. ~15 to ~30 °C), but the effectiveness was reduced to b10% during the colder period (soil temp. ~10 to ~15 °C). The N-NH4 + increased during the flooding phases (reaching 2– 6 mg L−1 ), and the results indicated that it was nitrified during the following drying phases. A tendency to lower potential soil N-N2O emissions was observed in treatments with Phragmites during drying phases, pointing that the plants absorbed this newly formed N-NO3 −. Hence, we propose harvesting Phragmites stands at the beginning of the summer, but after a lag time to permit N-NO3 − absorption by plants before the complete drying of the watercourses.