As a coastal city with rapid urbanization and high-intensity human activities, Shenzhen, China has carried out a series of comprehensive treatments for water pollution control and ecological restoration in recent years. However, the restoration effect is mainly reflected in the improvement of water quality and riparian landscape, and there is still a big gap in reaching the river’s ecological restoration goals. Therefore, it is necessary to make a full investigation and evaluation of river aquatic systems that focuses on the restoration of aquatic communities and ecosystem health. We surveyed forty-seven sampling sites in nine basins to investigate water quality and aquatic organisms (algae and macroinvertebrates) during the low-water period in 2019. Under the guidance of the EU Water Framework Directive (WFD), the urban river ecosystem health assessment system, with a total of twenty indicators from six criteria layers, was established. We addressed the bioremediation objectives in this system and aquatic organism indicators as high-weight characteristic indicators. The results showed that the degradation of the river ecosystem in Shenzhen is serious, which is mainly reflected in the simple structure of the aquatic biological community and the low biodiversity. Only one “healthy” sample site, accounting for 2% of the total sampling sites; six sites of “sub-health” level, accounting for 13%; twenty-four “poor” sample points, accounting for 51%; sixteen “extremely poor” sample points, accounting for 34%. From the perspective of spatial distribution, the river ecological status of Daya Bay Basin and Dapeng Bay Basin is good, which is at the level of “health” to “sub-health”; the Guanlan River Basin, Maozhou River Basin, Shenzhen River Basin, Shenzhen Bay Basin, Pingshan River Basin, and most of the Longgang River Basin are of “poor to extremely poor” grade; the Pearl Estuary basin is of “extremely poor” grade. This assessment system can be used as an effective tool to monitor the ecological health status, especially the enhancement of biodiversity and ecosystem function of rivers. Moreover, it could provide important decision-making guidance for river management affected by high-intensity human activities.
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