A computer infrastructure which integrates the geographic information system (GIS), hydrodynamic model, visualization and network applications was developed and applied in Tamshui River, Taiwan. A digital terrain model (DTM) of the study area was first generated. We used it as a basis to construct the computation grids, conduct the flow simulations, and visualize the predicted flow scenarios in the virtual world. The three-dimensional hydrodynamic and water quality model system WQMAP was employed to simulate flows under the tidal forcing, upstream river inflows and seawater–freshwater interactions of Tamshui River. Model predictions were generally in good agreement with other simulations. Computed results were visualized in both the innovative virtual reality (VR) environment and Internet-based collaborative visualization environment (CVE). The VR environment enabled us to observe firsthand the complicated flow phenomena in the virtual world. Internet-based CVE supports distributed visualization and collaboration. The GIS-based system exhibits great potential in data visualization capabilities and the improvement of water management. We anticipate that these computer technologies will popularly be applied to hydroinformatics and other related domains in the foreseeable future.