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This study aims at investigating heavy metal mobility and bioavailability in sediments from the Mexicana and Jaralito streams, Northern Mexico. A chemical partition analysis (sequential extraction) was performed to determine geochemical phases in which metals are found. Geoaccumulation index (Igeo) and enrichment factor values were obtained from analytical results and geochemical baseline data. Sediments showed high concentrations (mg/kg) of Cd (below detection limit, BDL-3.50), Cr (3–41), Cu (238–1090), Fe (41267–61033), Mn (678–1143), Ni (18–35), Pb (51–124), and Zn (116–356). Metal concentrations in geochemical phases exhibited the following order: residual > interchangeable > Fe/Mn oxide > carbonate >organic matter/sulfide. Both streams presented high degree of enrichment for Cu, Fe, Mn, Ni, Pb, and Zn, indicating anthropic origin of these metals. Metal mobilities in Jaralito and the Mexicana were Fe > Cu > Mn > Pb > Zn > Ni > Cr and Fe > Cu > Mn > Zn > Ni > Pb > Cr > Cd, respectively. Jaralito and the Mexicana sediments exhibit a mostly gravel-sandy texture with higher metal contents than in fine fractions. Sediment Geoaccumulation index values suggest that Jaralito features moderate to strong contamination by Ni, Pb, and Cu, whereas the Mexicana features strong contamination by Cd, Cu, Pb, and moderate contamination by Ni, Pb, and Zn. The quality criteria comparisons (LEL and SEL) indicate these areas are contaminated by metals and represent a substantial environmental risk because of high metal mobility and availability. Future studies on water chemistry and biota are needed to fully assess pollution impact in the Jaralito and Mexicana streams. The probability of adverse biological effects from high metal levels in those streams confirms the urgency of implementing effective environmental management practices.