Urban lakes serve multiple functions including flood storage, water supply, landscape tourism, and ecological maintenance, possessing significant ecological, environmental, and socio-economic value. Yangtze River Basin hosts approximately 355,000 urban lakes, accounting for over 65% of the nation"s total water area. These lakes exhibit strong ecological functions. Currently, urban lakes in the Yangtze River Basin face prominent challenges such as high non-point source pollution loads during flood seasons, pollution risks associated with ecological water supplementation safety, and weak resilience of aquatic ecosystems. Addressing these issues requires an integrated approach that considers the holistic nature of urban lake ecosystems and the systemic characteristics of the river basin. Advancing coordinated water environment and aquatic ecosystem management under a source–sewer–treatment plant–river–lake integrated framework. This study provides a systematic review of the research status and development needs related to the coordinated governance of water environment and aquatic ecosystems in urban lakes of the Yangtze River Basin. It synthesizes recent progress in domestic and international research as well as practical engineering applications, and offers an in-depth analysis of the major challenges currently constraining coordinated governance: (1) In certain urban areas, the issues of pollutant accumulation during dry seasons and the episodic release of contaminants during rainfall events remain prominent. Notably, storm-induced non-point source pollution has increasingly become a key constraint on the sustained improvement of urban water environments; (2) The critical challenge for using effluents from municipal wastewater treatment plants as ecological replenishment for urban lakes lies in achieving water quality and aquatic ecosystem compatibility between reclaimed water and receiving lake bodies; (3) The ecological resilience of lake ecosystems remains weak, and watershed-level systematic governance is still insufficient. Based on this analysis, we summarize targeted strategies and key tasks centered on "pollution source identification and perception - efficient external source control - water supplementation safety - habitat restoration and reconstruction - system optimization and configuration - integrated platform management," aiming to accelerate new achievements in the ecological environment governance of urban lakes in the Yangtze River Basin and provide scientific and technological support for national ecological civilization construction and green development strategy implementation.