Trace-element concentrations in acid mine drainage (AMD) are primarily controlled by the mineralogy at the sediment-water interface. Results are presented for a combined geochemical and mineralogical survey of Dabaoshan Mine, South China. Developed sequential extraction experiments with the analysis of the main mineralogical phases by semi-quantitative XRD, differential X-ray diffraction (DXRD) and scanning electron microscopy (SEM) were conducted to identify the quantitative relationship between iron minerals and heavy metals. Results showed that schwertmannite, jarosite, goethite and ferrihydrite were the dominant Fe-oxyhydroxide minerals which were detected alternately in the surface sediment with the increasing pH from 2.50 to 6.93 along the Hengshi River. Decreasing contents of schwertmannite ranging from 35 wt % to 6.5 wt % were detected along the Hengshi River, which was corresponding to the decreasing metal contents. The easily reducible fractions exert higher affinity of metals while compared with reducible and relatively stable minerals. A qualitative analysis of heavy metals extracted from the sediments indicated that the retention ability varied: Pb > Mn > Zn > As ≈ Cu > Cr > Cd ≈ Ni. Results in this study are avail for understanding the fate and transport of heavy metals associated with iron minerals and establishing the remediation strategies of AMD systems.