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The field of seawater desalination faces some challenges. For example, at present, site selection and layout of water intakes and outlets are often not carefully considered. This can easily result in the degradation of water quality due to coastal sea pollution and sudden brine discharge, which can be hazardous and can negatively impact marine development and activities such as aquaculture. By using the MIKE21 numerical simulation software, this paper establishes a two-dimensional mathematical tidal current model of the engineered sea area and a mathematical convection diffusion model after brine discharge. The tidal current field of the Laoshan Bay waters and the salinity field distribution after brine discharge in different water intake-outlet arrangement schemes in desalination plants are calculated and analyzed. In view of the various control factors affecting the layout and location selection of water intakes and outlets, combined with the current situation of marine development and utilization, calculation results and layout advantages and disadvantages of the primary schemes are compared and analyzed, the scheme with the best water intake-outlet layout is recommended, and relevant optimization suggestions are presented.