Gold mining not only introduces mercury (Hg) contamination to soils but also facilitates the mobilization of other toxic substances, including arsenic (As). This study assessed the total content, chemical species, and bioavailable fraction of As in surface soils impacted by mining residues during frequent flooding. Analysis of 207 soil samples across the floodplain region of La Mojana, Colombia, screened to 2 mm with polyethylene mesh, revealed significant correlations (p < 0.05) between inorganic As, the residual phase, sulphur (S), iron (Fe), manganese (Mn), and aluminum (Al), indicating associations with sulfides and oxyhydroxides of Fe and Mn. The origin of toxicity was linked to suspended materials transported by rivers during flooding in areas with intense mining activity. Sites with better oxidizing conditions exhibited a higher presence of phases associated with amorphous and crystalline oxides in non-flooded areas. Although the bioavailable fraction was minimal in flooded sites, reducing conditions facilitated As mobility, resulting in higher concentrations in deeper soil layers, particularly as As(III). The contamination factor (CF) ranged from 1.3 to 11.1, and the geochemical index (Igeo) ranged from −0.2 to 2.9, indicating a moderate to high As contamination level in soils. This poses potential health risks, considering the agricultural use of these soils.
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