The invention discloses a polluted water environment three-dimensional rapid display method and a system. The method comprises: sensing information of each water area by a corresponding sensor, and transmitting data back at regular time, storing information sensed by sensors to a database; establishing a case library in accordance with five types of the national water quality standard; dividing a water environment three-dimensional scene, and establishing a scene tree based on a BSP tree structure with a water area target knot as an organization unit; conducting view frustum culling based on a bounding volume hierarchy of the scene tree; determining the grade of water quality based on the data sensed by sensors; looking for corresponding cases in the library based on the determination result, and displaying water quality graphics; and looking for water quality information by clicking. The method and the system of the invention obviate the need for experts to observe water quality on site, realize rapid display of polluted water environment three-dimensional graphics, can conduct automatic selection of corresponding water quality graphics, and enable experts to roam in the water environment three-dimensional scene and observe, look for real-time information of current water area, and facilitate experts' research on polluted water environment.