Contaminants’ presence in the aquatic environment is relevant for the disturbance of the European stocks of diadromic species. The main goal of this study was to compare the biotransformation and oxidant/antioxidant status of yellow eel (Anguilla anguilla) populations from the estuaries of Minho (reference), Lima and Douro (contaminated) Rivers. Comparatively to the values determined in eels from the reference estuary, low total glutathione and reduced glutathione levels associated with high lipid peroxidation levels and benzo(a)pyrene-type metabolites’ concentrations were found in liver from eels collected in the estuary of Lima river. Eels from Douro estuary showed high liver ethoxyresorufi n-O-deethylase, catalase, glutathione peroxidase, total glutathione, reduced glutathione and oxidized glutathione levels associated with low lipid peroxidation and benzo(a)pyrene-type metabolites relatively to fi sh from the reference estuary. The pollution present in the estuaries of Lima and Douro Rivers is causing alterations on biotransformation and antioxidant stress parameters. In addition, Lima estuary eels are exposed to polycyclic aromatic hydrocarbons as indicated by the high levels of metabolites found. Since polycyclic aromatic hydrocarbons interfere with reproductive parameters and increased cytochrome P450 1A1 activity (as found in eels from the Douro estuary) interfere with reproduction, the exposure of eels to pollution in Lima and Douro estuaries may be decreasing their reproductive potential. In addition, energy to face chemical stress may be allocated from processes such as growth and weight increase that are factors determinant for the success of the long migration to the reproduction area. Therefore, pollution may be decreasing the contribution of these populations to the species evolution.