With the development of remote sensing and large-scale environmental modelling, large amount of environmental data are continuously becoming available. An intuitive and comprehensive visualization of these data could facilitate data exploration, communication and collaboration between the stakeholders for informed decisions making. In Poyang lake basin regions, we demonstrate how to develop a software platform that can visualize three-dimensionally environmental data layers including terrain, weather, river net, water level, land use changes and interrelations between these data layers for environmental system monitoring and decision supporting. The tool is built by combining several prevailing projects including Unity, Paraview, and hydrological models, etc. We develop an open standardized framework for the software tool to host environmental data layers permitting the application of the tool, which could be employed for the intuitive and comprehensive data visualization in other regions facing environmental challenges.