Coastal regions often suffer from intertwined issues of seawater intrusion and soil salinization due to various factors. Although the application of rainwater infiltration measures in sponge city construction have shown effectiveness for stormwater control and water resource management, their role in addressing coastal ecological issues and the potential to identify optimal permeation thresholds to simultaneously mitigate these coastal challenges remains unexplored. This study developed an integrated modeling approach, including a rainfall infiltration model, variable density solute transport model, and statistical soil salinization model, to assess the impacts of different rainfall infiltration levels on seawater intrusion and soil salinization in Zhuanghe, China. The models were calibrated and validated using monthly observational data and extensive field sampling measurements. Scenario simulation analyses quantified sponge city implementation increased rainwater infiltration by 2.752 × 10