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Pump-and-treat technologies are widely used in groundwater remediation and site cleanup. Such technologies involve pumping contaminated groundwater to the surface for treatment. Following treatment, the water is often reinjected back into the aquifer (referred to as pump-treat-inject or PTI) for potential reuse. The treatment system is often designed to remove dissolved-phase contaminants in groundwater such that water meets applicable cleanup standards (herein referred to as "full treatment"). However, in some cases, the treatment system may not effectively reduce the dissolved-phase concentrations (herein referred to as "partial treatment") for some of the contaminants present in groundwater. Modeling PTI under partial treatment conditions is challenging because contaminant concentrations in injected water depend on the pumped water concentrations and the system treatment efficiency. Essentially, the injected water concentration (a transport model input) is unknown prior to transport simulation. This study presents a novel iterative approach to modeling PTI under partial treatment scenarios, where the injected water concentration is linked to the modeled pumped water concentration. The method was developed for a complicated three-dimensional (3D) flow and transport modeling study conducted for a confidential remediation site where PTI with partial treatment was applied. However, due to the complexity of the 3D model and the confidential information of the site, a simple two-dimensional (2D) numerical model is presented to demonstrate the iterative method. The 2D model test runs and the 3D model application in a remediation site showed that the iterative simulation results quickly converged to a viable final solution.