This article brings forward a design and realization scheme of Web GIS in the Yellow River basin for the management of groundwater resources. The main goals are to manage and share data of massive-scale, to support the research of groundwater resources in the Yellow River basin. In this paper we point out the necessity and feasibility of building the distributed Web GIS for geographical research objects on a large scale.We put forward some solutions for the construction of this kind of system including a holistic deployment strategy in the Internet, a scheme of distributed data storage and management, a design of application structure based on three tires architecture by each province and how they collaborate with each other. It also illuminates how the application server works, and sets forth the relations among databases which work together in this system.