Most domestic small rivers and streams due to industrialization and urbanization have managed by concrete structures. The environmental functions of the river and stream are disappearing and urban streams play only the role of drainage systems. Also, the researches to restore natural streams are something yet to develop and not established the restoration for ecological functions of a small stream. Therefore the researches are required to develop ecological engineering system for watershed management system to handle various pollutants with restoration for ecological functions of a small stream. To develop this, the ecological engineering system for watershed management system could be developed with ecological conservation. In addition, ecological engineering system for watershed management system should be prior to conserve the habitat of biological resources and water conservation and applied to the original shape of streams. Also, it should be designed to restore the micro-topography of stream, the habitat of plant population in watershed. It is needed to develop the integrated researches to restore a small stream ecosystem.