Abstract: With the development of social economy and acceleration of urbanization, the lagoon has become a part of human water resources utilization. Because of the influence of domestic sewage and industrial wastewater discharged and human activities, most lakes are polluted in different degree. Numerical simulation of lake water ecology could quickly and accurately establish lake hydrodynamic model, analyze hydrodynamic characteristics and variation rules, provide scientific basis for lake environmental protection work, and provide the basis for environment management and monitoring departments to provide water quality status quo and simulation prediction analysis, so as to make better scientific decisions. The hydrodynamic and salinity distribution of the lakes under the condition of connectivity were studied, and furthermore the impact of the project to the aquatic plants was analyzed to provide a basis for scientific decision-making of the "Ling Shui County double lakes" (the two lagoons of Xincun Port and Li'an Port) connectivity project in Hainan Province. It can provide a reference for the numerical simulation of lagoons.