A numerical study, based on a density-dependent variably saturated groundwater flow model, was conducted to investigate flow and salt transport in a near-shore aquifer under intensified wave conditions caused by offshore storms. Temporally varying onshore hydraulic gradients due to wave set-up were determined as the seaward boundary condition for the simulated aquifer. The results showed a rapid increase in influxes across the aquifer-ocean interface in response to the wave event followed by a more gradual increase in effluxes. The upper saline plume first widened horizontally as the wave set-up point moved landward. It then expanded vertically with recirculating seawater pushed downwards by the wave-induced hydraulic gradient. The time for the salt distribution to return to the pre-storm condition was up to a hundred days, and correlated strongly with the time for seawater to recirculate through the aquifer. The pathways of recirculating seawater and fresh groundwater were largely modified by the wave event. These pathways crossed through the same spatial locations at similar times, indicating significant salt/freshwater mixing. The flow and salt transport dynamics were more responsive to wave events of longer duration and higher intensity, especially in more permeable aquifers with lower fresh groundwater discharge. Despite their larger response, aquifers with higher permeability and beach slope recovered more rapidly post-event. The rapid recovery of the flows compared with the salinity distribution should be considered in field data interpretation. Due to their long-lasting impact, wave events may significantly influence the geochemical conditions and the fate of chemicals in a subterranean estuary.