This study presents a new multi-objective optimization method, the niched Pareto tabu search (NPTS), for optimal design of groundwater remediation systems. The proposed NPTS is then coupled with the commonly used flow and transport code, MODFLOW and MT3DMS, to search for the near Pareto-optimal tradeoffs of groundwater remediation strategies. The difference between the proposed NPTS and the existing multiple objective tabu search (MOTS) lies in the use of the niche selection strategy and fitness archiving to maintain the diversity of the optimal solutions along the Pareto front and avoid repetitive calculations of the objective functions associated with the flow and transport model. Sensitivity analysis of the NPTS parameters is evaluated through a synthetic pump-and-treat remediation application involving two conflicting objectives, minimizations of both remediation cost and contaminant mass remaining in the aquifer. Moreover, the proposed NPTS is applied to a large-scale pump-and-treat groundwater remediation system of the field site at the Massachusetts Military Reservation (MMR) in Cape Cod, Massachusetts, involving minimizations of both total pumping rates and contaminant mass remaining in the aquifer. Additional comparison of the results based on the NPTS with those obtained from other two methods, namely the single objective tabu search (SOTS) and the nondominated sorting genetic algorithm II (NSGA-II), further indicates that the proposed NPTS has desirable computation efficiency, stability, and robustness and is a promising tool for optimizing the multi-objective design of groundwater remediation systems.