In order to improve the risk communication and emergency disposal capacity of trans-boundary water pollutions, a river basin risk communication model has been developed based on Multi-Agent, combined with WebGIS technology, which coordinate the relationship among government departments, the related enterprises and the general public. By the cooperation of the distributed agents, the risk information of trans-boundary water pollutions was communicated and published rapidly and effectively, leads to quick action in the state of emergency, realize the effective risk communication and decision making.