Anthropogenic activities have a tremendous impact on water ecosystems worldwide, especially in China. To quantitatively evaluate the hydrological alteration connected with aquatic lives and river ecological risks, we took the Beijiang River located in South China as the case study and used ecosurplus (defined as ecological carrying capacity exceeding ecological consumption)/ecodeficit (defined as ecological consumption exceeding carrying capacity) and Indicators of Hydrological Alterations to evaluate hydrological changes. The Ecologically Relevant Hydrologic Indicators were employed to select the key indices of Indicators of Hydrological Alterations, and the eco-environmental water demand calculation provide an effective way for the reservoir operation. Results showed that: (1) High flows contributed more to the ecodeficit, while low flows contributed more to the ecosurplus; (2) the ecodeficit in some parts of the river basin might exceed the ecosurplus after reservoir construction, especially along the main stream; and (3) the determination of eco-environmental water demand is a feasible way for improving the environment by controlling reservoirs. The current study can help guide the optimization of hydrological operation in the basin toward making the ecosystem healthier and has potential to further provide a reference for other basins in terms of hydrological alterations driven by anthropogenic activities.