Estuarine ecosystems are increasingly being affected by pollution caused by anthropogenic activities. In this study, Crassostrea gasar oysters were transplanted and maintained for seven days at three sites (S1, S2, and S3) in the Laguna Estuarine System (LES)-situated in southern Brazil-that has been exposed to multiple anthropic stresses. On the basis of the concentrations of metal and organic pollutants in oysters, we identified marked spatial variations in pollutant levels, with S3 showing the highest concentration of Ag, Fe, Ni, Zn, and total polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and linear alkylbenzenes (LABs), followed by S2 and S1. Along with the concentrations of pollutants, a set of biomarkers was analyzed. Oysters maintained at S3 showed enhanced protective defenses in gills, as observed by the increased levels of superoxide dismutase (SOD-like) and heat shock protein 90 (HSP90-like) transcripts and catalase (CAT) activity, concomitant with reduced lipid peroxidation (MDA) levels. Decreased antioxidant activities together with increased MDA levels are indicative of the digestive gland being more susceptible to pollutant-induced oxidative damage. Oysters transplanted into LES showed lower levels of cytochrome P450 transcripts (CYP356A1-like and CYP2AU1), and decreased glutathione S-transferase (GST) enzyme activity, suggesting lower biotransformation capacity. By integrating information regarding the concentration of metal and organic pollutants with that of molecular as well as biochemical biomarkers, our study provides novel insights into pollutant exposure and the potential biological impacts of such exposure on estuarine organisms in southern Brazil.