Fe(Ⅱ) derived from mining activities is precipitated as various Fe(Ⅲ)-oxyhydroxides when exposed to an oxidizing environment including mine drainage. Ferrihydrite, one of the representative precipitated Fe(Ⅲ) minerals, is easy to adsorb heavy metals and other pollutants because of the large specific surface area caused by very low crystallinity. Most ferrihydrite is transformed to goethite in the natural environment due to its unstability. Hence, information on the transformation of ferrihydrite to goethite and the related mobility of heavy metals in the acid mine drainage is important. The behaviors of heavy metals during the transformation of ferrihydrite to goethite are investigated for core samples from an AMD treatment system by using X-ray diffraction (XRD), Scanning Electron Microscopy (SEM), chemical analysis, statistical analysis and sequential extraction. XRD and SEM showed that ferrihydrite had gradually transformed to goethite from the top to the bottom of the core samples. The mineral transformation affected the concentration of heavy metals showing that concentration ratio of As, Co and Zn to Fe decreased with increasing depth for core samples and that of Cr increased. Correlation analysis indicated that As can be easily removed from mine drainage during iron mineral precipitation due to its high affinity to Fe. Sequential extraction results showed that Cd and Cr were weakly bonded to the mineral surface regardless of the mineral transformation. The mobilities of As, Pb and Zn decreased by decreasing their exchangeable fraction during the mineral transformation. In contrast, Co and Ni increased the contents of exchangeable fractions indicating that the transformation of ferrihydrite to goethite made these metals easy to be released into the environment.