Abstracting overmuch water from rivers to provide services like hydropower has greatly damaged river ecosystem. Therefore, restoration of the degraded river ecosystem is very urgent. A lot of methods have thereby been proposed, and partial restoration of natural flow is a kind of prescription in reality. During the restoration process, to monitor or evaluate the health of river is very important and necessary. Traditional methods to assess the condition are structural or physicochemical ones and their powers are limited. Therefore, in our study, we tried to employ some functional indicators, which are critical parts of the ecosystem, to monitor the river health based on a reference-control-impact (RCI) design. Results showed that the partial restoration of flow was effective and the functional indicators were better than the traditional ones.