Capping is typically used to control contaminant release from the underlying sediments. While conventional capping doesn’t necessarily provide the removal of contaminants, incorporating a ‘‘funnel and gate’’ reactive barrier with capping has the potential to treat contaminants or limit contaminant migration. The purpose of this study was to develop a model of funnel and gate systems for remediation of contaminated sediment. Numerical modeling of vertical two dimensional water flow and solute transport was built in COMSOL MULTIPHYSICS 3.4. The model was employed to evaluate the performance of the funnel and gate system, i.e. residence time, removal efficiency, and breakthrough curve. Two types of gates, reactive and adsorptive gates, were evaluated for the remediation of phenanthrene contaminated sediment. The simulated results showed that the performance of the reactive gate depended on Damkohler number at the gate, and the adsorptive gate could effectively slow contaminate migration into water body, and decrease the maximum concentration at the gate. This model could potentially serve as a design tool of funnel and gate systems for a range of typical sediment capping conditions.