European eels (Anguilla anguilla L.) were caged for 8 and 48 h in two polluted areas to assess the contamination cleanup process in the Vouga River 2 years after the official closing of a bleached kraft pulp mill effluent (BKPME; experiment 1), and to monitor the effects induced by contaminated offward fishing harbor waters (experiment 2). Plasma cortisol, glucose, and lactate were evaluated as stress responses. In experiment 1, plasma cortisol, glucose, and lactate increased after 8 h of exposure in site 3, which is located farthest from the deactivated sewage outlet. However, A. anguilla seemed to adapt after 48 h of exposure in site 3, because all three parameters returned to control levels. Plasma glucose also significantly increased after 8 h of exposure at sites 1, 2, and 3, returning to control levels after 48 h. Plasma lactate levels increased after 8 h of exposure at site 3 and after 48 h of exposure at site 1. In experiment 2, A. anguilla exposed to contaminated harbor waters increased their plasma lactate after 8 and 48 h of exposure, whereas their cortisol and glucose plasma were elevated only after 48 h of exposure. The results demonstrate that even 2 years after the official closing of the BKPME sewage outlet, the river Vouga water remains contaminated by the sediment associated chemicals. Because the fishing harbor induced in A. anguilla the same type of stress responses, it is also an area of concern. The adopted stress parameters allied to a caging strategy are recommended for future environmental monitoring assessments.