In this paper, a new hybrid multi-objective evolutionary algorithm (MOEA), the niched Pareto tabu search combined with a genetic algorithm (NPTSGA), is proposed for the management of groundwater resources under variable density conditions. Relatively few MOEAs can possess global search ability contenting with intensified search in a local area. Moreover, the overall searching ability of tabu search (TS) based MOEAs is very sensitive to the neighborhood step size. The NPTSGA is developed on the thought of integrating the genetic algorithm (GA) with a TS based MOEA, the niched Pareto tabu search (NPTS), which helps to alleviate both of the above difficulties. Here, the global search ability of the NPTS is improved by the diversification of candidate solutions arising from the evolving genetic algorithm population. Furthermore, the proposed methodology coupled with a density-dependent groundwater flow and solute transport simulator, SEAWAT, is developed and its performance is evaluated through a synthetic seawater intrusion management problem. Optimization results indicate that the NPTSGA offers a tradeoff between the two conflicting objectives. A key conclusion of this study is that the NPTSGA keeps the balance between the intensification of nondomination and the diversification of near Pareto-optimal solutions along the tradeoff curves and is a stable and robust method for implementing the multi-objective design of variable-density groundwater resources.