Coastal saltwater intrusion (SWI) is one key factor affecting the hydrology, nutrient transport, and biogeochemistry of coastal marsh landscapes. Future climate change, especially intensified sea level rise (SLR), is expected to trigger SWI to encroach coastal freshwater aquifers more intensively. Numerous studies have investigated decadal/century scale SWI under SLR by assuming a static coastal landscape topography. However, coastal marshes are highly dynamic systems in response to SLR, and the impact of coastal marsh evolution on SWI has received very little attention. Thus, this study investigated how coastal marsh evolution affects future SWI with a physically-based coastal hydro-eco-geomorphologic model, ATS (Advanced Terrestrial Simulator). Our synthetic modeling experiments showed that it is very likely that the marsh elevation increases with future SLR, and a depression zone is formed due to the different marsh accretion rates between the ocean boundary and the inland. We found that, compared to the cases without marsh evolution, the marsh accretion may significantly reduce the surface saltwater inflow at the ocean boundary, and the evolved topographic depression zone may prolong the residence time of surface ponding saltwater, which causes distinct subsurface salinity distributions. We also found that the marshland may become more sensitive to the upland groundwater table that controls the freshwater flux to the marshes, compared with the cases without marsh evolution. This study demonstrates the importance of marsh evolution to the freshwater-saltwater interaction under sea level rise and can help improve our predictive understanding of the vulnerability of the coastal freshwater system to sea level rise.