A three-dimensional groundwater flow management model for making decisions on the design of hydrodynamic control of a groundwater flow system using a combination of extraction and/or injection wells is developed. The model takes into account constraints imposed on the system to stop the horizontal spread of contaminants and to ensure a net upward flow in areas where downward vertical gradients exist. The mathematical formulation of the groundwater remediation problem as a mixed-integer model and the strategy for solving the model are presented. Numerical results are presented for the Toms River Plant site, which is modeled as a five-layer aquifer system with interconnecting aquitards. A sensitivity analysis on the relative magnitude of the continuous operating costs and the fixed-charge costs is also presented.