Spatial and temporal salinity variations in surface water and pore water commonly exist in salt marshes under the combined influence of tidal inundation, precipitation, evapotranspiration, and inland freshwater input. Laboratory experiments and numerical simulations were conducted to investigate how density gradients associated with salinity variations affect pore water flow in the salt marsh system. The results showed that upward salinity (density) gradients could lead to flow instability and the formation of salt fingers. These fingers, varying in size with the distance from the creek, modified significantly the pore water flow field, especially in the marsh interior. While the flow instability enhanced local salt transport and mixing considerably, the net effect was small, causing only a slight increase in the overall mass exchange across the marsh surface. In contrast, downward salinity gradients exerted less influence on the pore water flow in the marsh soil and slightly weakened the surface water and groundwater exchange across the marsh surface. Numerical simulations revealed similar density effects on pore water flow at the field scale under realistic conditions. These findings have important implications for studies of marsh soil conditions concerning plant growth as well as nutrient exchange between the marsh and coastal marine system.