Draining through industrial areas of the Minas Gerais mining state (Brazil), some tributaries of the São Francisco River constitute a potential environmental hazard for this great river and threaten the quality of the regional soils for agriculture and other activities. Extensive geochemistry and mineralogy of sediments, soils and alluvial plains from six selected areas within the Consciência drainage basin close to an important Zn-extraction plant, have been carried out. In this report, detailed mineralogy of those samples and supporting geochemical data are discussed, taking into account their specific climactic and environmental context. Petrographic and electron microprobe characterization of the sand-grained fraction of these materials was complemented by XRD on their finer fraction: the main contaminant minerals are willemite (one of the Zn ores used in the industrial plant) and jarosite, though their contents are quite variable in the studied areas and also with depth; minor amounts of Zn-, Pb-, Cd-, and Mn-bearing mineral phases are also frequent, usually as inclusions in willemite or in polycrystalline clasts, or adsorbed on the finer materials, such as clay minerals and associated Fe-hydroxides. Mineralogical contamination is responsible for high metal contents in the soils and sediments of the areas closer to the plant (e.g. Zn ≫ 2000 mg kg−1 and Cd ≫ 20 mg kg−1, which are the Intervention Values for Industrial Areas) and the greatest contamination risks are related to the more labile phases that circulate throughout the alluvial plains, the shallow sediments and the stream bed. Monitoring the mineral/chemical contamination and its extent also constitutes a useful basis for future proposals to remediate and recover this industrial area in order to decrease medium- and long-term negative impacts of metal contamination on the local and downstream environments.