Biochemical and physiological parameters in the croaker Micropogonias furnieri were evaluated as biomarkers of chemical contaminants in estuaries. Juvenile croakers (10-20?cm total body length) were collected in summer and winter (2011 and 2012), in two sites at the Lagoa dos Patos estuary (southern Brazil). Fish were also collected in summer (2011 and 2012) in one site at the Barra do Chui estuary (southern Brazil). Tissue (gills, muscle or liver) samples were dissected and analyzed for contaminants [metals, polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs)] and selected biochemical and physiological parameters [metallothionein-like proteins (MTLP), acetylcholinesterase (AChE) activity, ethoxyresorufin-O-deethylase (EROD) activity, and lipid peroxidation (LPO)]. Additionally, water samples were collected for water chemical analyses (salinity, pH, temperature, dissolved oxygen, total alkalinity, and sulfate concentration). Data obtained were integrated and analyzed, using Principal Component Analysis (PCA) and Generalized Additive Model (GAM) approaches. Results showed that changes in concentrations of chemical contaminants and responses of biochemical and physiological parameters did not show any pattern according to the site, season and year of fish collection. However, they were influenced by fish body length and water temperature and salinity. Liver LPO and EROD activity were not responsive to PAHs. However, liver LPO was responsive to HCB, p,p-DDD, p,p-DDT and endosulfan sulfate. In turn, gill MTLP concentration, muscle AChE activity and liver EROD activity were responsive to non-essential metals (Pb, Cd and Ag). Considering that the ecotoxicological modeling approach adopted (GAM) accounted for biological, spatial and temporal variability of data associated with fish body size and site, season and year of fish collection, gill MTLP concentration, muscle AChE activity, as well as liver LPO and EROD activity can be considered as reliable biomarkers of fish exposure to chemical contaminants in estuaries.