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The estuary—located in the joint zone between river and ocean—has created unique ecosystems and rich biodiversity due to its complex habitat conditions. As the critical period for the growth and reproduction of estuarine organisms, the flood season is also crucial for estuary sluice to play a role in flood control and drainage. This study aims at proposing an ecological scheduling scheme that comprehensively considers the adverse factors brought by draining of the estuarine sluice to maintain different ecological functions of the Jiaojiang River estuary. A two-dimensional mathematical model in MIKE 21 was used to ascertain the change of salinity and nutrients in the study area, and results were analyzed to understand the impact of draining on estuarine organisms. Based on an analysis of the change and redistribution of salinity and nutrients, the sea area could be divided into three parts during the operation of the estuarine sluice: nearshore area with low-salt and high eutrophication, medium mixed salinity under nitrogen limitation area and high-salt under phosphorus limitation area. The aquaculture area was alternately situated in the mesohaline (>5.0‰–18.0‰) and polyhaline (>18.0‰) zones. The after-effects of salinity change—including the lowest value and the sharp change of salinity, especially the sharp change of salinity (11.8‰–12‰) caused by large-volume discharge—would affect the growth of organisms to a certain extent, but would not be lethal. Moreover, a high-incidence red tide area was determined to be formed within 8–14 km away from the estuarine sluice after the sluice opening, and the area of this zone was firmly related to the opening schemes. The study suggested that the proposed sluice should choose the mode of draining frequent with the small flow at neap tide in order to reduce the stress of sluice construction and operation on mariculture organisms and phytoplankton in Jiaojiang River estuary on the strength of the ecological restoration measures for estuary and riparian zones.

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