Groundwater, the major source of human drinking water, is susceptible to contamination from industrial and agricultural activities. This research develops a web-based simulation system of remote high performance computing model for contaminant transport and retention in soils. A three-dimensional advection-dispersion-reaction MRTM model, based on previous experimental and theoretical studies, is proposed to analyze the transport and retention of chemical contaminants in groundwater flowing through soils. Since three-dimensional experiments are difficult to implement and verify, this simulation system provides scientists an alternative to trace the contaminant movement in soils outside laboratories. The alternating direction implicit (ADI) algorithm is used in this study to reduce the computational complexity. Although the ADI method is very efficient to solve the governing advection-dispersionsorption equations in the three-dimensional MRTM model, achieving higher order accuracy with different boundary conditions remains a difficult research topic. This research develops a new numerical scheme to achieve second-order accuracy with the Neumann-type boundary conditions. Furthermore, parallel computing is used to achieve high performance using powerful multiprocessor computers. A web-based simulation system provides users a friendly interface for remote access to the system through Internet browsers, so as to utilize remote computing resources transparently and efficiently. In the client-side computing one-dimensional MRTM simulation system, the legacy code written in FORTRAN and C are wrapped and reused with Java code, which provides the web-based graphic user interface (GUI). The server-side computing three-dimensional MRTM simulation system integrates the remote high performance computing resources, database management systems, online visualization functionality, and web-based userriendly GUIs. Given access to the Internet, users can execute and manage remote high performance computing jobs anywhere anytime, even through a web browser from a laptop personal computer.