The São Francisco River (one of the most important South American rivers) has many contamination sources, but just a few environmental assessments have been conducted. A weight-of-evidence approach identified the pollution sources (industrial activities, mineral processing, fisheries, and tourism) in the river and the city of Três Marias based on two different lines of evidence: the structure of the benthic community (biological monitoring working party score system, abundance of taxa, number of individuals, Margalef species richness, Pielou evenness, and Shannon–Wiener diversity) and the physicochemical determination of sediments (%fines, TOC, nitrate, ammonium, ammonia, ammoniacal nitrogen, metalloids, and SEM/AVSs). The results show that the wastewater treatment plant was the most important source of pollution. A factory was also detected as a source of contamination, with related adverse effects having been measured downstream. Other sources of contamination and stress were detected in the studied area. The macro-benthic identification study identified three different sentinel species (Tanytarsus sp., Crytochironomus sp., and Polypedilum sp.) for future monitoring assessments of the sediment quality in riverine areas. Thus, an improvement in the management of river effluents and more measures focused on cutting contaminant emissions from the waste treatment plant are recommended.
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