The concentrations of 14 potentially toxic elements in freshwater and marine sardines from the Western Balkan Peninsula were determined. In Prespa Lake, a natural lake, the concentrations of toxic Pb and Cd were above the maximum permissible concentrations in freshwater sardines. The As concentrations were elevated in sardines from Boka Kotorska Bay. The Target Hazard Quotient (THQ) and Hazard index (HI) were above their defined limits in Boka Kotorska Bay and Skadar Lake, indicating a health risk for Montenegrin consumers. The results of this study set apart Zavoj, Vlasina and Međuvršje artificial reservoirs as potential ecosystems for developing commercial fishing and for the safe use of freshwater sardines for human consumption. Constant monitoring of Ohrid, Prespa and Dojran natural lakes, as well as Boka Kotorska Bay, may be implemented in the interest of public health.