The effects of fish farming activities on the aquatic environment were evaluated by studying the water quality of twelve rivers located in northeast Spain. Two sampling sites were used for each river: the first sampling point was located just upstream from the fish farming facilities and the second one was downstream from fish farm effluent discharge point. In order to avoid any misinterpretation due to watershed location and seasonality, a stratified statistical analysis was performed. The results show significant decreases in pH and dissolved oxygen, in contrast to chemical oxygen demand, ammonia, phosphates and microbiological parameters, which significantly increased downstream from the fish farm discharges. Other significant variations were also found for conductivity and temperature. According to the European and local regulations concerning to support fish populations, our results fell within the allowable limits for salmonid waters. Nevertheless, we suggest that further investigations should be carried out to study the ecological interactions between farmed and wild fish populations.