One of the key challenges in developing a calibrated three-dimensional (3D) groundwater flow and transport model is the integration of the data in the hydrogeologic conceptual model into Visual MODFLOW. This requires the incorporation of all geologic and hydrogeologic data in a geographic information system (GIS), which is then used to assign model property values and boundary conditions. Equally important is the presentation of model results in a GIS environment to allow hydrogeologists with limited understanding of groundwater modeling processes or the Visual MODFLOW interface to make interpretations with relative ease. To facilitate this transfer a GIS package has been specifically designed to assist both in conceptual model development and in the interpretation of the hydrogeologic environment within which the modeling occurs. HydroGeo Analyst (HGA) was used to assemble site conceptualization data for contaminated sites, for the purpose of developing a flow and transport model to predict future plume conditions. The database was set up to make it relatively simple to develop input parameter distributions, boundary conditions and model calibration data. Visual MODFLOW was used to develop a calibrated groundwater model of the site, and to export predictions of solute movement within the groundwater flow system. HGA was then used to present these results in 3D to compare model results with existing monitored conditions.