Although many significant policies and legislation have been put forth by the Chinese government aiming toward "ecological civilization" for the aquatic environment, in practice, the situation is still undesirable. A pioneering multi-year study has since been conducted on the East Tiaoxi River (a major tributary of the renowned Yangtze River), focusing on fish distribution, influencing factors and habitat requirements, and river health as well. This revealed certain key species, hotspot protection areas, negative impacts of local anthropogenic activities, and inappropriate perceptions and practices of conservation and restoration. We found that not all fish species were equally conserved and that the supposedly ecological engineering measures were initiated without regard for ecological integrity. Our exemplary study appreciates scientific basis and truly ecological notion, and urgently advocates comprehensive and continuous basin-scale scientific investigation of fish biodiversity, and "ecological river"-oriented conservation and restoration action for the Yangtze River Basin and broader areas of China.