The effects of marine aquaculture on the environment were evaluated by studying the water quality of San Pedro river, a canal located within the Bay of Cadiz (SW of Spain). Marine aquaculture, both extensive and intensive, is one of the most important activities carried out in this area. Several facilities are located on this river, the most important being devoted to the intensive culture of Gilthead Seabream (Sparus aurata). The characterization of the water consisted of the evaluation of the variation of several parameters along the river and during different seasons. These parameters were pH, temperature, salinity, dissolved oxygen, suspended solids and nutrients (ammonium, nitrite, nitrate and phosphate). With a water quality criteria based on local laws, a significant but not dangerous pollution was observed in the area, with ammonium and suspended solids being the most significant pollutants.