Manganese is ubiquitous in nature and essential for some metabolic reactions, but also it is present in the environment as a product of anthropogenic activities. Despite evidence linking high concentrations of Mn to several diseases, it is not commonly considered during environmental risk assessment of soils. Changes in chemical forms, oxidation state, and speciation of Mn in impacted agricultural soils by historical mine tailings in central Sonora in northwestern Mexico were studied using X-ray Absorption Near Edge Spectroscopy (XANES), X-ray Diffraction (XRD), and Sequential Extraction Procedures (SEP) techniques. Mn concentrations ranged from 1093 to 2919 mg·kg−1 in these soils, which exceeded the local geochemical background by up to six-fold. According to SEP, the tendency found in agricultural soils was reducible (42–66%) > soluble and exchangeable (16–42%) > residual (5–22%) > oxidizable (4–24%). In contrast, the tendency in sulfide-rich tailings samples was soluble and exchangeable (47–49%) > residual (35–41%) > oxidizable (5–11%) > reducible (5–7%), and in oxide-rich materials was residual (21–79%) > soluble and exchangeable (1–30%) > reducible (1–45%) > oxidizable (2–15%). The considerable percentage of the soluble forms indicated the potential of mobilization and availability to exposed organisms. No Mn-bearing mineral phases were identified with XRD, which suggested that manganese was mostly found in low-crystalline forms. XANES measurements indicated that the oxidation state of Mn in agricultural soil samples varied from Mn2+ through Mn4+. Conversely, the main oxidation state in mine tailings samples was Mn2+. Substantial changes were detected in Mn XANES spectra in the whole sample and residues left from SEP in agricultural soils, which confirmed the presence of all chemical forms (e.g., soluble and exchangeable, reducible, oxidizable, residual). A well-defined structure spectrum was obtained in soils once low crystallinity species and/or organic compounds were removed, which was similar to that acquired for mine tailings, suggesting mobility from tailings deposit to agricultural soils. Substantial contribution of compounds with mineral structures like birnessite (((Na, Ca, K)0.6(Mn4+, Mn3+)2O4·1.5H2O) and minor contributions of hausmannite (Mn3O4), spessartine (Mn3Al2(SiO4)3) and szmikite (MnSO4) were identified by Linear Combination Fitting (LCF) in soils, whereas the significant contribution of structures like hausmannite and spessartine, and minor contributions of rhodochrosite were found in tailings material. An LCF analysis in residues from SEP also suggests that the chemical species involved in the Mn mobilization were scachite and szmikite. In general, the results obtained indicate that leaching processes favored the presence of chemical species of Mn with a considerable potential of mobility and toxicity in agricultural soils interacting with historical mine tailings in central Sonora.