Abstract Storm surges severely salinize coastal aquifers, yet post‐storm subsurface hydrodynamics remain poorly understood. We investigated surge inundation in unconfined tidal aquifers, revealing that subsurface flow recovers much faster than salinity distributions. Immediately post‐storm, submarine groundwater discharge rapidly increases to greatly exceed the pre‐storm level under extreme surge scenarios. Concurrently, downward surge infiltration creates a transient hydraulic barrier, forcing the saltwater wedge to temporarily retreat seaward, depending on surge height. Furthermore, we reveal the upper saline plume overshoot effect, as infiltrated storm water continues to migrate downward and seaward. This overshoot is exacerbated in micro‐tidal, low‐permeability aquifers. Understanding these asynchronous responses is critical for predicting groundwater quality and managing coastal resources under intensifying storm events.