With the two-dimensional hydrodynamic and water quality models of Lingdingyang estuary in South China, the marine water environment response to slotting at the root of the jetty in Dachan Bay, a typical study area in the eastern Guangdong-Hong Kong-Macao Greater Bay Area, was analyzed based on the changes of tidal current field, water e-folding time, and pollution zone. Results showed that the tip area of Dachan Bay was relatively closed with slow current, where water pollution was serious under the impact of land sewage discharge. After slotting, the fluctuation tidal power in the tip area of the bay was increased, the water e-folding time was obviously shortened, and the ranges of the pollution zone were significantly decreased due to the occurrence of the new tidal channel. With the increase of the slotting width, the proportion of the pollution zone in the tip area of the bay sharply decreased at first and then changed slightly. To improve the water environment and economic effectiveness of the project, it is considered that the reasonable slotting width should be 60~100m.