The aim of the study is to determine the relationship between the water quality properties which can vary depending on pollution sources and biogenic amine concentrations in the muscle tissues of farmed Oncorhynchus mykiss (Walbaum, 1792) in concrete pond farms located in Candır River (Station I), Karacaören I Reservoir (Station II) and Çatak Reservoir (Station III) in Isparta, Turkey. The O. mykiss muscle tissue and water samples were obtained in three stations, on February 2016, simultaneously. In three stations, fourteen physicochemical parameters were measured in water samples and water quality levels determined by YSKYY (Surface Water Quality Management Regulation). Muscle tissue tryptamine, 2-phenylethylamine, putrescine, cadaverine, tyramine concentrations were determined with high-performance liquid chromatography (HPLC) method, and histamine were determined with ELISA in O mykiss flesh from three fish farms. The water’s physical and chemical parameters show that the water quality in all stations are categorised as class II, according to the Turkish YSKYY. However, based upon its nitrite and total nitrogen values, Station II was found to be less polluted than the other stations, followed by a moderate degree of pollution for Station III, and significantly higher levels or pollution for Station I. The putrescine and histamin levels were higher in muscle of the O. mykiss from the station I, compared to station II and III (p<0.001). We concluded that microbial contamination due to environmental pollutant accumulation and exposure are an important source of biogenic amines generation within the fish tissues. Contamination of water bodies causes biogenic amines accumulation in fish tissues and consequently negatively contributing to quality of fish as food as well as fish welfare.