Bafa Lake is one of the largest Turkish Lagoon lakes in Aegean Region covering a surface area of 50km(2). Because of its water capacity and myriad benefits in aquaculture facility, agricultural activities and tourism. The lake is considered as an important wetland within Buyuk Menderes basin. This study investigate the aquaculture facilities and anthropogenic sources of pollutions and how they affect the water quality of Bafa Lake. The major factors that control the quality-of Bafa Lake water are agricultural activities in the basin, domestic and industrial wastes that come from Buyuk Menderes River and its surrounding lake, fisheries and aquaculture facilities. Contaminants located in the Lake are continuously having a negative impact on its water quality during the last three decades. The effect of sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax) cultivation facilities on surface water quality in the Lake were determined. Water samples were taken from five stations between April 2013 and March 2014 from Bafa Lake. Sample were analyzed for water temperature, pH, dissolved oxygen, electrical conductivity, amonium nitrogen, nitrite nitrogen, nitrate nitrogen, and orthophosphate. From result surface water quality was assessed based on the comparison of samples collected near aquaculture stations. For reference, a sample was taken outside the cultivation area and compared with the Water Pollution Registration Act (WPRA) standards. According to the WPRA, surface water quality of the Lake was classified as level II. At the end of analyses, it was revealed that the area where aquaculture activities were intense showed high rate of polution than the other 3 stations as well as the reference station. The results show that, aquaculture activities on sea bream and sea bass have a negative impact in the entire Bafa Lake.