Abundant water resources have facilitated the completion and operation of numerous large-scale water conservation projects. However, the operation of cascade hydropower stations has changed the natural hydrological regime of rivers, thereby affecting the integrity and stability of downstream benthic animal habitats. To quantitatively evaluate the impact of infrastructure development, we proposed a coupling of hydrodynamic and habitat models, with benthic animals as indicator species (because they are highly sensitive to hydrological changes). This study established a physical habitat model of benthic animals in the upper reaches of the Yangtze River, from the Xiangjiaba to Zhutuo sections by coupling the MIKE21 hydrodynamic model with a habitat model. This model coupled the changes in hydrological conditions and ecological processes to quantitatively reflect the effects of flow changes on river habitat quality, which can be used to predict the effects of hydrological changes on water ecosystems and provide fundamental information for ecological flow and scheduling decisions. Our results showed that by jointly regulating the suitable outflow of the Xiangjiaba Reservoir and the inflow of the Tuojiang, Minjiang, and Hengjiang rivers (three tributaries with water conservancy projects), the minimum flow in the non-flood season and the maximum flow in the flood season could be controlled more precisely. This increases the suitable habitat area for benthic animals as well as improves the stability of their habitat. This study fills the gap in the physical habitat model of benthic animals in the upper reaches of the Yangtze River as well as enriches the research ideas of ecological flow regulation. Moreover, this indicates the first application of the physical habitat model to the joint ecological flow regulation of the main tributaries, thus opening new directions for the application of the physical habitat model.
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