The presence of intensive fish farms in the Orbetello Lagoon (Italian West Coast) has produced a heavy impact on the environment and has led to a large-scale cyclic development of opportunistic macroalgae. The farms are equipped with phytotreatment basins to treat the effluent. Although it is possible to find reports in the literature of phytotreatment techniques suitable for fish-farming effluents, they refer solely to pilot scale. The flooded areas used for phytotreatment permit the growth of huge quantities of macroalgae, which remove nitrogen (N) and phosphorus (P) from the effluent. These ponds are unmanaged, and N and P are released when this vegetation dies during the Summer. Between June 1999 and May 2000 research was carried out on an intensive fish-farming facility that produces about 100 tonnes per year of European sea bass ( Dicentrarchus labrax L.) and gilt head sea bream ( Sparus aurata L.), occupying a volume of 9000 m 3. The wastewater from the plant is discharged to four phytotreatment ponds, arranged in series, and, ultimately, released into the nearby sea-lagoon canal. The research aims were: (a) to quantify the N and P in the effluent from an intensive fish farm facility which are retained by the macroalgae and sediments as the effluent passes through the phytotreatment system; (b) to detect any seasonal variations in nutrient distribution; (c) to determine spatial distribution of the nutrients between input and output of the phytotreatment system. During the test period the physico-chemical parameters of the water were recorded; sediment total organic carbon (STOC), sediment total nitrogen (STN), sediment total phosphorus (STP), macroalgal total carbon (MTC), macroalgal total nitrogen (MTN) and macroalgal total phosphorus (MTP) were determined. Also the micro- and macroalgal biomasses were determined and a floristic list was made. The data collected over the test period were subjected to discriminant type multivariate analysis. The results indicate that: (1) the system size and water residence time are not sufficient to produce adequate abatement; (2) the quantity of nutrients involved in this system is too high for the system itself to be controlled by macroalgal growth alone; (3) the Ulva rigida biomass develops over too short a period of the year (February–June) and is accompanied by rapid decomposition that produces extreme environmental conditions.