In this study, heavy metal (Cu, Zn, Cr, Cd, Pb and As) levels in the muscle of economically important fish species (Trachurus mediterraneus, Sparus aurata and Pegusa lascaris) living in different water columns in the North-East Mediterranean Sea were measured. Fish were bought from local fishermen between September 2016-August 2017 in Karatas¸ region (Adana, Turkey). Levels of Cd, Cr, Pb and As were highest in the muscle of T. mediterraneus, S. aurata and P. lascaris in the autumn season, while Cu levels were highest in T. mediterraneus and S. aurata in the spring season. The lowest and highest levels of Cu, Zn, Cr, Cd, Pb and As in the muscle of fish were 0.11–0.37, 0.09–0.57, 0.03–0,28, 0.002–0.03, 0.04–0.11 and 0.09–0.49 (μg/g w.w.), respectively. Metal levels in muscle tissues were within the ranges of acceptable levels according to TFC (Turkish Food Codex), WHO (World Health Organization) and FAO (Food and Agriculture Organization) in terms of human consumption point of view. It was determined that the estimated daily (EDI) and weekly (EWI) metal intake levels were below the tolerable levels, and the Target Hazard Quotient (THQ) and Cancer Risk (CR) (except arsenic for CR) values were below acceptable standards in case of consumption of the examined species. Heavy metal levels in the studied species do not pose any risk to both fish and human health points of view.