During the process of urbanization, impermeable surface areas enlarge and rain runoff and peak discharges grow, rainstorm become more frequent. As more rain water and pollutants mixed with each other, more areas of urban runoff are polluted, causing significant change to aquatic organisms, especially fish, their population and structure. In order to balance the relations between urban development and river eco-environmental protection, avoid reappearance of mega rainstorm disaster like the one on July 21st in Beijing, we suggest protecting and safeguarding the structure and function of urban river ecological system from perspectives of urban planning, eco-environment improvement and integrated management over urban river system.