The mineral wealth of the Amazon region is prone to intense exploration with consequent metals mobilization in ecosystems. Besides that, a number of other anthropogenic activities contribute to the imbalance of this important environment. The Pará River is an important water body in the Amazon basin and is under multiple anthropogenic influences, including disorderly urbanization, port activities and processing of minerals such as bauxite and kaolin. In this study, metals concentrations (Al, Cr, Pb, Ba, Ni, and Mn) in water, sediment and organisms (the fish Cheirocerus goeldii and the shrimp Macrobrachium amazonicum) and biochemical biomarkers (total antioxidant capacity, ACAP and lipid peroxidation, LPO) were analyzed along five points in the Para River with different distances to a center of anthropogenic activity, in three seasonal periods (rainy, transition and dry). Metals concentrations were similar among sites in each seasonal period but Aluminium (Al) presented the highest concentrations among all analyzed metals both in sediment and water considering all sampling points and all seasonal periods. In the dissolved fraction, Al had values above those established by the local environmental agency, especially during the rainy season. In the biotic compartment, both fish and shrimps showed higher concentrations of metals (Al and Ba) in the rainy season compared to the other seasons. Shrimp was more responsive to metal accumulation than fish, showing an adaptive response of biomarkers. Fish showed an increase of LPO in gills for individuals from the point of greater anthropogenic interference during the rainy season, but no differences in metal accumulation. We conclude that there is a seasonal pattern of metals concentration in different environmental compartments. Metal concentration in organisms and biomarkers responses, showed the effect of anthropogenic influences, which was not evident in results from chemical analyses alone, due to the intensive hydrodynamics in the region.