Mineral prospection zones are known for their ability to alter environmental quality. The most recent cases of degradation of water resources in the cities of Brumadinho (MG), Mariana (MG) Santo Antônio do Grama (MG) and Barcarena (PA) show that this is a difficult theme to approach. The presence of potentially deleterious chemical species in mining tailings may negatively impact aquatic environments, making it impossible to use the contaminated water for consumption and leading to the extinction of local life. In this sense, environmental assessments in the mining, water and sediment tailings of water systems close to the mining areas present themselves as a tool to identify changes in the river basins that support them. Although studies point to the influence of mining activities on the quality of sediments of water systems, there are few contributions on the risks associated with the environmental quality of sediments in zones of mineral extraction of semiprecious rocks. Thus, this study characterized the influence of mineral extraction activities (amethyst, quartz, agate, calcite and gypsum) on the potential risk associated with the sediment quality of Rio de Várzea, southern Brazil, the world's largest region of ametetic rock extraction. Physical and chemical parameters (OD, pH, EH, CE, NTU, STD and T) of the water column were quantified in situ. Daily and monthly precipitations were also evaluated in the year of collection and the historical series (1976-2017) at the station 2753015, the fluviometry of the monthly and daily flows, and the historical flow series (2008-2017) at station 74270000, data from the National System Information on Water Resources. Sediment grading classes were investigated for coarse fractions (from 2000 to 75 μm) and for fine fractions (< 75 μm), their moisture content (gravimetric methods) was determined. Chemical species concentrations were quantified by Wavelength Scattering Spectrometry (WDXRF), Dispersive Energy X-ray Emission Spectrometry (EDXRF); Optical Emission Spectrometry by Coupled Inductive Plasma (ICP OES). It was demonstrated, through Background strategies and Environmental Quality Indexes, the moderate contamination of the sediments of Rio de Várzea-RS. It was established, by distinct geochemical strategies, the construction of the baseline (Background) of the Várzea River Watershed-RS, through the use of local soils of environmental preservation areas and, finally, the negative implication of the non use of local references in the evaluation of sediment quality.