Assessing the hazard of inundation due to extreme storm surges in low-lying coastal areas and fragile ecosystems has become necessary and important. In this study, Xincun Lagoon and Li’an Lagoon in the Lingshui area of Hainan, China, were selected as the study areas, a high-resolution storm surge inundation numerical model was established, and the model reliability was tested. Based on data on typhoons affecting the study area from 1949 to 2022, the typhoon parameters for the extreme storm surge scenario were set and used for model numerical simulation and hazard assessment. The results revealed that in the extreme storm surge scenario, the average maximum tidal level, average maximum flow velocity, maximum inundation area, and average maximum inundation depth in the lagoon area were 2.29 m, 1.03 m/s, 14.8124 km2, and 1.20 m, respectively. Under the extreme storm surge scenario, a flow velocity of 2.0 m/s off the coasts of the lagoons could damage coastal aquaculture facilities, harbors, and ecosystems, while an inundation depth exceeding 1 m along the coasts of the lagoons could lead to the salinization of inundated land and severely affect the safety of residents. The hazard analysis of storm surge inundation in the land area of the lagoons revealed that hydrographic nets and coastal wetlands are the major land types inundated by storm surges, with the two accounting for approximately 70% of the total inundation area. According to China’s technical guidelines, the hazard levels of the inundated land area of the lagoons are mostly level 3 (moderate hazard) and level 2 (high hazard), together accounting for approximately 90% of the total inundation area. If the government deems the measures feasible based on strict estimation and scientific evaluation of economic benefits and disaster prevention, planting mangroves in coastal wetlands and/or establishing adjustable tidal barriers at narrow entrances to lagoons could minimize disaster losses.
