Salt marsh encroachment is a visible indicator of saltwater intrusion into the root zone in low-lying coastal areas. The rate of salt marsh migration does not track directly with sea level, however. Field observations from 1998 to 2022 at Sapelo Island, Georgia (USA), show that salt marsh migration occurred during droughts. Drought has the potential to affect salt marshes in multiple ways, including reduced infiltration of rainwater and reduced discharge of fresh groundwater from adjacent uplands to the marsh. To test these possibilities, we instrumented the field site in 2018 to record hydraulic head (every 20 minutes) and groundwater salinity (sporadically) in the root zone. We then developed a two-dimensional numerical model to simulate groundwater flow and salinity below the salt marsh from 1998 to 2022. Simulations revealed recurrent winter freshening of groundwater in the root zone in the high marsh, caused by winter expansion of the freshwater lens. In drought years, the simulated freshwater lens failed to expand, leading to higher salinities during the spring growth period. These kinds of seasonal variations in the size of the freshwater lens have implications for seasonal patterns in submarine groundwater discharge and salt water intrusion.