The increase in storm surge events caused by climate change exacerbates adverse effects on seawater inundation in coastal areas. An accurate description of the water level curve is crucial for understanding the process of saltwater intrusion (SWI) resulting from storm surge. Most studies involving empirical surges as inputs to groundwater models, often simplify spatial and temporal seawater inundation processes, which may increase the uncertainty in vertical seawater intrusion. To address this gap, we employed a comprehensive modeling approach using storm surge model ADCIRC and numerical simulator HydroGeoSphere to reveal SWI dynamics during a historical storm surge event in a coastal farm, considering varying tidal-surge phases and typhoon intensities. Our findings indicate pronounced SWI variations even with consistently highest water level during a storm surge, contingent on prior tidal processes. The timing of typhoon landfall on an hourly scale yielded diverse water level curves, altering the function of SWI. Intriguingly, SWI exacerbates following a high tide with 31.2 % average salinity higher, highlighting the profound modulation effect of tidal levels on SWI. Local topography significantly influenced SWI dynamics. Ponds, for instance, retained elevated salinity levels for over 15 h, indicating a more prolonged exposure to salinity than roads. These findings underscore the importance of considering both tidal influences and topographical factors in understanding and mitigating SWI in coastal agricultural management.