Xenobiotics may affect fish endocrine system, making endocrine responses relevant in pollution monitoring. Five critical sites in Ria de Aveiro (Portugal), having different contamination profiles, were assessed in comparison to a reference site (Torreira), focusing on Liza aurata stress (plasma cortisol, glucose and lactate) and thyroidal (plasma thyroid stimulating hormone—TSH, thyroxine—T4 and triiodothyronine—T3) responses. L. aurata at Vagos (PAHs contaminated) and Laranjo (mercury contaminated), respectively, displayed, low cortisol and high glucose as well as lactate levels. Considering thyroidal responses, high TSH levels were found at Laranjo; low T4 levels were found at Barra (subject to naval traffic) and low T3 levels were found at Rio Novo do Principe (near a former bleached kraft pulp mill effluent), Laranjo and Vagos. The integrated biomarker index ranked impacted sites as: Laranjo>Vagos>Gafanha>Rio Novo do Principe>Barra>Torreira. Endocrine responses reflected xenobiotics exposure suggesting environmental risk to fish at Ria de Aveiro. However no clear relation was found between stress and thyroidal responses.