Niligou Reservoir, a typical reservoir in the eastern region of Jilin Province, is subordinate to Niligou River, which is located in the Changbai Mountains in eastern Jilin, with abundant plant and animal resources and well protected biodiversity in the basin, but there are also some related problems such as fragile ecosystem of forest wetland. This paper carried out a health assessment of Niligou River, including water quality monitoring, aquatic organism monitoring, and riparian zone investigation. According to the requirements of the Technical Guidelines for River and Lake Health Assessment, 13 assessment indexes were selected to build a river and lake health assessment index system. By sorting and analyzing the monitoring and investigation data, we got a clear picture of the ecological environment status and existing problems of Niligou Reservoir. Based on the actual situation of Niligou River, we evaluated the hydrologic integrity, chemical integrity, morphological and structural integrity, biological integrity and sustainability of social service function, and put forward corresponding countermeasures according to the results, in order to provide a technical support for the health treatment of rivers and lakes in Jilin Province