In the Low reaches of Yangtze River and the estuary region, there are rich fish species and high autochthonous species. The economic species that has an obvious fishing season characteristic almost distributes in this area, and the species number of the economic fish and fish catchability ranked first in the whole basin. In recent years the fishery ecological function has been weakened by many factors, such as river-lake disconnection, seawater intrusion, habitat fragmentation and hydrological changes due to the hydraulic engineering, and fish catchability, natural fishery resources, species diversity and idioplasm resources were also influenced seriously. In this paper, the development and status of hydraulic engineering and characteristics of fishery resources in the lower reaches of the Yangtze River have been introduced, basing on some important hydraulic engineering, such as waterpower projects, migration engineering, navigation engineering, bridge construction, and sand digging. Existing and latent impacts of hydraulic engineering on fishery resources and fishery ecological environment have also been discussed. Suggestions on design of hydraulic engineering and compensation methods for fishery ecology have been given. Responsibilities and obligations that the fishery department should take were pointed out. At last the urgent research tasks of protection of fisheries resources and environments in lower reaches of the Yangtze River were put forward.