With an urgent need for effective management of petroleum-contaminated sites, a GIS-aided simulation (GISSIM) system is presented in this study. The GISSIM contains two components: an advanced 3D numerical model and a geographical information system (GIS), which are integrated within a general framework. The modeling component undertakes simulation for the fate of contaminants in subsurface unsaturated and saturated zones. The GIS component is used in three areas throughout the system development and implementation process: (i) managing spatial and non-spatial databases; (ii) linking inputs, model, and outputs; and (iii) providing an interface between the GISSIM and its users. The developed system is applied to a North American case study. Concentrations of benzene, toluene, and xylenes in groundwater under a petroleum-contaminated site are dynamically simulated. Reasonable outputs have been obtained and presented graphically. They provide quantitative and scientific bases for further assessment of site-contamination impacts and risks, as well as decisions on practical remediation actions.