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Long-term heavy metals accumulation caused by acid mine drainage (AMD) irrigation in paddy soils poses a severe threat to environmental health. However, the soil adsorption mechanisms under AMD flooding remain unclear. This study provides key insights into the fate of heavy metals in soil, particularly the retention and mobility mechanisms of Cu (copper) and Cd (cadmium) after AMD flooding. The migration and fate of Cu and Cd in uncontaminated paddy soils treated by AMD in Dabaoshan Mining area was investigated via column leaching experiments in the laboratory. The maximum adsorption capacities of Cu (658.04 mg kg−1) and Cd (335.20 mg kg−1) cations were predicted and the breakthrough curves were fitted using the Thomas and Yoon-Nelson models. Our findings demonstrated that Cd was more mobile than Cu. Furthermore, the soil had a greater adsorption capacity for Cu than Cd. Tessier's five-step extraction method was used to determine Cu and Cd fractions in leached soils at different depths and times. After AMD leaching, the relative and absolute concentrations of the easily mobile forms were all increased at different soil depths, thus increasing the potential risk to the groundwater system. Mineralogical characterization of the soil indicated that AMD flooding leads to the formation of mackinawite. This study provides insights into the distribution and transportation processes of soil Cu and Cd and their ecological effects under AMD flooding, as well as a theoretical basis for the establishment of corresponding geochemical evolution models and environmental governance in mining areas. • Long-term acid mine drainage (AMD) promotes secondary iron mineral formation. • Cu was preferentially adsorbed and retained in paddy soils compared to Cd. • The exchangeable and carbonate-bound Cd remarkably increased during AMD flooding. • Cu was mainly in Fe/Mn oxides-bound and organic matter-bound under AMD. [ABSTRACT FROM AUTHOR]