The present work aims to evaluate the chemical quality and establish the geochemical baseline values of elements in the surface waters of the Parauapebas River basin (PRB), which is one of the major subbasins in the Itacaiúnas River watershed (IRW) located in the Brazilian Amazon. A total of 327 surface water samples were collected during the rainy and dry seasons in 2017. Results indicate that waters are slightly acidic to alkaline (pH 6 to 8), and there was a strong influence of the seasonal variation on water quality, with higher values of turbidity, Fe, Al, Mn, TDS, etc. in the rainy season. Two geochemical baseline types for the PRB were defined, i.e., ‘conservative baseline’ (CB), represented by the cumulative frequency curve, and the ‘environmental baseline’ (EB), comprising the sum of natural and diffuse anthropogenic contributions, represented by the 98th percentile. Except Fe, Mn and Al, the CB and EB values of various trace elements (Ba, Co, Cr, Cu, Ni, Rb, Sn, Sr, Ti, V and Zn) were lower than the recommended limits of CONAMA 357/05—class 2. The principal component analysis (PCA) identified the major geochemical association (Al-Ti-Cu-Cr-Ni-V), which is an imprint of the local geological setting. Ni and Cr showed enrichment at sites where mafic and ultramafic rocks are concentrated, while Cu concentration is mainly associated with the north and south mineralization belts. High concentrations of Fe and Mn are characteristic of the waters of this region and this is mostly influenced by specific land use activities and intense weathering/erosion of catchment materials. At the upper Parauapebas, anthropogenic contributions associated with soil use and occupation were also important along with the geogenic effects. The obtained results regarding sources of contaminants in some microbasins can be taken as a starting point for future studies on the environmental quality of the region’s water resources.