Abstract: Lagoons are a significant type of surface water body in coastal zones, receiving dual inputs from tidal currents and freshwater, and are widely distributed in coastal regions worldwide. Xiaohai Lagoon, located in eastern Wanning City, Hainan Province, covers a current water area of approximately 43 km² and is the largest lagoon in China. Over the years, socio-economic development has caused serious water environment issues, such as siltation, reduced tidal capacity, and ecological degradation in Xiaohai Lagoon. Comprehensive management has thus become urgent. However, balancing improvements in water dynamics with the preservation of salinity stability remains a challenging task for Xiaohai Lagoon. In this study, we integrated on-site monitoring, theoretical analysis, numerical simulation, and physical model experiments to investigate the evolution mechanisms of dynamic landforms in this barrier lagoon, simulate salinity variations under weak tidal and strong wave conditions, and propose key technologies for estuary gate protection and tidal channel pattern reconstruction The research simulated changes in the water dynamics and salinity patterns of the lagoon under various condition combinations, such as widening the entrance from 150 m to 180–350 m and reconstructing the southern branch channel with a bottom width of 60–120 meters. A plan was proposed to enhance the hydrodynamic force and water quality of Xiaohai Lagoon, which included widening the estuary gate to 280 meters, restoring the southern channel with a bottom width of 100 meters, and partially removing the estuarine sandbar. This plan has been successfully implemented in engineering practice to improve the hydrodynamic conditions and water quality of China’s largest lagoon. The results indicated that the geomorphic system of the Xiaohai tidal channel had remained relatively stable. However, since 1984, it has undergone significant changes due to intensive human activities. The aquaculture industry in Xiaohai expanded rapidly; the salt mounds of three islands in the tidal fork were reclaimed, and the southern tidal fork was blocked. Consequently, the northern fork became the sole tidal channel connecting the lagoon to the open sea. Severe siltation developed at the estuary. Following project implementation, Xiaohai Lagoon's hydrodynamic force improved significantly, with the average flow velocity at the inlet increasing from 1.4 m/s to 1.9 m/s. Furthermore, the inflow (outflow) volume rose from approximately 0.14×10⁸ m³ (0.155×10⁸ m³) to 0.188×10⁸ m³ (0.21×10⁸ m³), marking an increase of over 30% in tidal capacity after the removal of fishing platforms. The average half-exchange time with the open sea decreased from 50 days to approximately 30 days. In addition, external pollution was brought under control, and the water quality of Xiaohai improved from poor Class IV to Class II, indicating a significant enhancement of the lagoon’s water environment and an increase in its self-purification capacity. The primary salinity regime of the lagoon changed only slightly (with an increase of less than 5%), effectively maintaining the stability of the open-lake salinity habitat pattern and supporting the survival of native species under the enhanced water exchange conditions. This laid a solid foundation for subsequent ecological projects, such as the restoration of Xiaohai’s seagrass beds. The research promoted substantial improvements in the water environment and generated notable social, economic, and ecological benefits, providing essential support for the high-quality development of the Xiaohai Basin.