Based on the criterion layer consisting of hydrology and water resources, physical structure, water quality, biology and social service function, etc. and the index layer consisting of 14 indexes, the river health of Nierji Sancha River Estuary in the downstream of Nenjiang River in the year of 2011was assessed. The results show that, affected by human activities, the score of Nenjiang river health assessment index is 59 and the river is in the sub healthy status. Agricultural development, water conservancy construction, overfishing and other human disturbances are the main factors contributing to eco environmental changes of river downstream. Countermeasures of river health management including ecological operation of water conservancy project, riparian restoration and management, water quality restoration, habitat restoration, wetland ecosystem restoration were put forward.