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In coastal marsh ecosystems, porewater salinity strongly affects vegetation distribution and productivity. To simulate marsh porewater salinity, an integrated, spatially explicit model was developed, accounting for tidal inundation, evaporation, and precipitation, as well as lateral and vertical exchanges in both surface waters and the subsurface. It was applied to the Duplin River marsh, Sapelo Island, USA, over a 3-year period, which covered both drought and wet conditions. Simulated porewater salinity in the low and high marsh correlated with Duplin River salinity, with evapotranspiration and precipitation leading to substantial variations in porewater salinities across seasons, in particular in the high marsh. The model revealed substantial interannual variability in marsh soil conditions, and—due to its process-based approach linked to external forcings—can be used to explore effects of sea level rise and changes in hydrological forcings on marsh soil conditions.