Monitoring heavy metal contaminants in fish is important for the assessment of environmental quality as well as food safety. In this study, European eel samples were collected from Lake Köyceğiz and Lake Võrtsjärv in 2017 and 2018. The concentrations of Mn, Cd, Zn, Pb, and Cu metals were measured by using GF-AAS in four selected tissues of eel, including liver, gill, skin, and muscle in both lakes. The pollution indexes (Pi, MPI) values were calculated for both lakes and the health risk for consumers was assessed for both adults and children in Turkey and Estonia. The estimated weekly intake (EWI), hazard index (HI), and lifetime cancer risk values (CRs) for the metals were calculated for both lakes. According to the results of this study, a significant difference was determined the between the metal concentrations (especially Cu, Cd and Pb) in the tissues of the eel samples taken from the two lakes. These results show that besides the pollution levels in the aquatic environment, physiological needs, and metabolic activities in different habitats have a significant effect on metal accumulation in eels. In addition, HI was found to be < 1 for both adult and child consumers in both lakes, which indicates that consumers would not experience non-carcinogenic health effects. However, the values of CR for Pb and Cd were found negligible in Lake Köyceğiz, while the CR value for Pb was found to be very close to the danger limits in Lake Võrtsjärv.