Ideally, scientists should be able to format, explore, analyze, and visualize GIS-based data in a simple, powerful, and fast application that would seamlessly integrate georeferenced data from a variety of data sources into a powerful intuitive visualization. Virtual reality has made visualization easily accessible to many users using desktop tools but has limitations in scope and analysis. In this project we used a combination of Java/Java3D and the recently introduced ESRI ArcGIS Engine product to create a prototype of a tool to calculate a number of parameters for an oceanographic module to be included in a scientific GIS. We combined the spatial tools exposed through ArcGIS Engine with the analytical capabilities of algorithms written in Java and the complex visualization capabilities of Java3D. Modules from each of these technologies could be combined to create innovative tools to allow users to import data, perform spatial and scientific analyses and output the results as visualizations for further examination.