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Using the improved 3-D ECOM model with a high resolution grid and incorporating various dynamic factors, the impact of the deep waterway project on the saltwater intrusion in the Changjiang Estuary was analysed. Salinity in the South Branch is shown to be influenced by saltwater intrusion downstream and from spillage of brackish water from the North Branch upstream. In the North Channel, the saltwater intrusion had been alleviated distinctly after the deep waterway project, because the dykes of the project blocked off the southward drift of the brackish water plumes under forcing by the northerly monsoon and the Coriolis force. The saltwater intrusion in the project area was intensified at the upper section and alleviated at the lower section. In the South passage, the saltwater intrusion was intensified as the background salinity increased and the river discharge decreased. The deep waterway project had an obvious impact on saltwater intrusion in the Changjiang Estuary. The impacts of the deep waterway project on planktons and benthos have been quantified and analyzed. The species number and biomass of planktons and benthos have decreased dramatically as compared with 20 years ago. The degradation of biodiversity at the Changjiang Estuary appears due to the cumulative impacts of eutrophication caused by human activities such as agriculture and sewage discharge, as well as land reclamation and estuarine engineering projects. [ABSTRACT FROM AUTHOR]