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The objective of this research is to assess of heavy metal pollution and its fractionation in sediments of the Sonora and Bacanuchi rivers located in arid and semi‐arid climates. Sediment quality guidelines (U.S. EPA; SQGs), enrichment factor (EF) and geoaccumulation index (Igeo) were used to evaluate the extent of heavy metal pollution. Total heavy metals concentrations for both rivers were as follows (mg/kg): Cd (< BDL), Cu (2 ‐ 103), Cr (5 ‐ 27), Fe (9156 ‐ 34343), Mn (114 ‐ 573), Ni (22 ‐ 38), Pb (12 ‐ 59), and Zn (27 ‐ 111). According to sediment quality guidelines Cr, Ni, Pb, and Zn were classified as moderately polluted, while Cu and Fe were strongly polluted. Metals predominated in geochemical fractions in the following order: Residual> Fe/Mn oxides> interchangeable> organic matter. A significant proportion of heavy metals (Cu, Mn, Ni, Pb, Zn) was associated to the nonresidual fraction, proving that those metals have greater mobility and may be bioavailable to living beings. EF values indicated that Cu, Cr, Mn, Ni, Pb, and Zn come from enriched sources due to anthropogenic activities. In both rivers, Igeo values indicated non contaminated or moderately contaminated levels in the sediments. The present study confirms an anthropogenic source of heavy metals, which could be a danger for biota in the surrounding areas, due to its mobility and bioavailability. Therefore, it is recommended to monitor water and sediment quality periodically.