The present short-term in situ study was carried out in a freshwater–wetland – Pateira de Fermentelos – considered an enlargement of Cértima River, in the centre of Portugal. This ecosystem is an important fishing and recreation place, receiving effluents from different origins namely, electroplating industrial effluents containing heavy metals, domestic wastes, as well as pesticides and fertilizers resulting from agriculture activities. The aim of the present research work was to monitor the effects induced by the contaminants present in Pateira de Fermentelos water, using Anguilla anguilla L. (European eel) as a bioindicator. The eels were caged for 48 h at four Pateira de Fermentelos sites, differing in their distances to the main known pollution source (Cértima River): A (close to the lagoon entrance), B, C and D (the farthest from the Cértima River). A reference site was selected near the Cértima river spring. The following parameters were measured: liver ethoxyresorufin-O-deethylase (EROD) and alanine transaminase (ALT) activities, plasma levels of cortisol, 17β-estradiol (E2), thyroid-stimulating-hormone (TSH), free thyroxine (T4), free triiodothyronine (T3), as well as glucose and lactate. The erythrocytic nuclear abnormalities (ENA) frequency was also scored as a genotoxicity indicator. The results revealed increased plasma cortisol and glucose concentrations at all exposure sites, displaying a similar response pattern. Plasma T3 showed a significant decrease only at site A when compared to reference site, whereas plasma E2 increased at sites B and D when compared to all the other sites, including reference site. The present results indicate the Pateira de Fermentelos water contamination, demonstrating the usefulness of the adopted strategy.