Currently, remediation of Hg(II)-contaminated groundwater is technically challenging and very costly. It is urgently needed to develop effective and cost-effective technology and material to remediate Hg(II)-contaminated groundwater. The efficiency and mechanism of Hg(II) removal from groundwater by two types of iron–based sorbents, natural magnetite and commercial Fe₃O₄, were investigated in this study. Hg(II) sorption and desorption on magnetites were also investigated in simulated groundwater. The results showed that both natural magnetite and commercial Fe₃O₄ removed Hg(II) effectively, and Hg(II) removal efficiency was influenced by initial pH, initial Hg(II) concentration, coexisting ion of Cl^–, and so on. Sorption kinetic data were well fitted to the pseudo-second-order model. The sorption isotherm could be described by the Freundlich model. The sorption of Hg(II) on natural magnetite was mainly due to the complexation between Hg(II) and surface hydroxyl groups and physisorption, while the sorption of Hg(II) on commercial Fe₃O₄ was largely due to the reduction of Hg(II) by Fe(II) in Fe₃O₄ and physisorption. Hg(II) removal from simulated groundwater by natural magnetite and commercial Fe₃O₄ were nearly 90% and 95%, respectively, demonstrating the application potential of both sorbents in remediating Hg(II)-contaminated groundwater.