This work aims at developing a flexible, extensible and interoperable parallel-computing infrastructure for groundwater flow simulation. The infrastructure takes a hierarchical layered model to provide a set of services, enabling the transparent use of high performance simulator for end users and user-defined customization for advanced users. The iterative solver for the groundwater flow equation was developed and illustrated in detail. The efficiency and robustness of the solver was demonstrated by simulating the simplified model of Erdos area in China. The numerical results show that it has achieved desirable speedup and scalability.