Operation of recession and inundation in Three Gorges Reservoir (TGR) revealed a potential contribution to the migration of heavy metals in soil and fluvial systems, thus led to negative ecological impacts. The work herein investigated the concentration and speciation of three typical heavy metals (Cd, Cr and Cu) in a water-level-fluctuation zone of TGR, as well as simulated the adsorption and desorption behavior of heavy metals on soils, which aimed at elucidating the fate of heavy metals in this special area. Field investigation revealed that water level fluctuation greatly enabled the migration of heavy metals to inner or upper soil layers. Laboratory experiments showed that adsorption of Cd(II) was a chemical process and dissolved organic matters (DOM) in soils strengthened the combination of Cd(II) to soil surface which inhibited the desorption process. Cr(VI) was physically adsorbed and readily to be desorbed. DOM enabled deposition of Cr(VI) in soils. Cation exchange was dominate mechanism in Cu(II) adsorption process, whereas DOM presented positive effects on desorption of Cu(II). The results presented in this study would provide basic theory for scientific research in TGR.