Abstract: Mostly, conflicting subjects are handled as single subject by several methods in groundwater system management problem. However, these techniques are only capable of finding one solution, which may sometimes contravene decision makers’willingness. On the contrary, multi-objective optimization approaches could provide the decision makers with a set of alternate solutions, being selected for a given site. In this paper, a program named NPGA-GW is developed for groundwater system multiobjective management, based on the niched Pareto genetic algorithm, which is coupled with the groundwater flow simulator MODFLOW and the contaminant transport simulator MT3DMS. NPGA-GW is applied to design pump-and-treat system that solves the multi-objective optimization model for a two-dimensional hypothetical test problem. The results show that a set of Pareto optimal solutions could be found in short term, which spanned trade-off curves wide enough for decision makers. To sum up,NPGA-GW has broad prospects in groundwater system management.