Abstract: The current study assessed the health status of the Yellow River ecosystem based on macrophytes, zoobenthos, fishes and their environments from investigation in Spring and Autumn, 2008 on 14 segments and 4 reservoirs on the mainstem. The results showed a high variation in health status among river segments with healthier segements concentrated in the middle reaches. The results of biological ansalysis reflected the spatial distributions of water quality and substrates of the river. Segments below Lanzhou were poor in water quality. The lower segments were better in quality but unstable in shore shapes. Segments of these two regions were therefore relative poor in eco-health. Comparatively, the middle segments were better in eco-health due to the light pollution and stable substrate. Regression analysis showed vital roles of hydrological and sediment processes in the development of biological assemblages. These findings support the importance and requirement to establish biological indexes to assess the eco-health and maintain the eco-health of the Yellow River.