Based on solving the Navier–Stokes equation, this paper establishes a numerical model of wave propagation and breaking on porous coral reef topography, which simulates the propagation and deformation process of regular and irregular waves on coral reef–lagoon topography, and analyzes the influence of different hydrodynamic factors on waves in reefs and lagoons. By analyzing the characteristics of solitary wave deformation on porous media reefs and comparing with the physical experiment's results, it can be found that the numerical wave flume in this paper has good accuracy in wave generation and propagation. This paper focuses on the comparative analysis of regular and irregular wave deformation on coral reef–lagoon topography. It is found that when the wave propagates on the reef flat, the larger the wave height, the more obvious the wave height and wave setup after breaking. The larger the wave height and period, the more significant the energy dissipation after the wave passes over the coral reef. Inundation water depth affects the value of wave setup, when the water depth increases the transmitted wave height increases, and the value of wave setup decreases; the wave setup increases at low tide level. The larger the porosity of the coral reef, the smaller the transmitted wave height, and the more the energy dissipated by friction. At low water level, wave reflection is obvious, wave height decreases in the lagoon, and energy dissipation increases.

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