We performed a simulation of a complex contaminant capture system at one of the largest groundwater pump-and-treat remediation operations in Michigan. The hierarchical modeling system was calibrated to water level measurements collected from 208 monitoring wells located both on-site and in its immediate proximity and flux measurements from 6 trenches on-site. Systematic hierarchical simulations, including forward and reverse particle tracking as well as integrated water budget analyses, were performed to study the on-going remediation. The hierarchical modeling results show that some contamination leaked off-site because of small-scale inefficiencies in the design of the remediation system.