Heavy metal (Cu and Zn) concentrations in liver, gills, and muscle of leaping grey mullet, Liza saliens, from the Portuguese Esmoriz–Paramos coastal lagoon were measured to evaluate their bioaccumulation as a function of sediment contamination. The highest metal concentrations were observed in the liver (254 mg Cu kg −1) and gills (114 mg Zn kg −1). Bioaccumulation factors (BAFs) were found to follow the order: Cu-liver>Cu-gills>Cu-muscle and Zn-gills>Zn-liver>Zn-muscle. The highest BAFs were observed in the organs mainly implicated in metal metabolism and a significant positive relationship was found between BAFs and fish age. These results suggest the loss of homeostatic capacity of L. saliens under chronic metal exposure leading to bioaccumulation. Furthermore, Cu-liver and Zn-gills accumulation can be good environmental indicators of metal stress in L. saliens.