Intertidal wetlands such as salt marshes are complex hydrological systems characterized by strong, dynamic interactions between coastal surface water and groundwater, driven particularly by tides. We simulated such interactions with a focus on 3D, variably saturated pore water flow in a salt marsh with a two-layer soil configuration (with a low-permeability mud layer overlying a high-permeability sandy-loam layer), which is commonly found in natural marshes. Simulated intra-tidal groundwater dynamics exhibited significant flow asymmetry with non-zero mean flow velocities over the tidal period. The tidally averaged flow led to 3D pore water circulation linked strongly to the marsh topography, over a range of spatial scales: near the creek bank, around the creek meander and over long marsh sections inclined towards the main channel. Time scales associated with these circulations differed by orders of magnitude. Under the simulated conditions, the creek served as the main outlet of the pore water circulation paths, especially those with infiltration taking place in the upper marsh surface areas away from the main channel. Water infiltrating the soil in the lower marsh surface areas away from the creek tended to discharge to the main channel directly. These flow characteristics have important implications for mass and nutrient transport and transformations in the marsh soil. Since the origin of pore water in the marsh soil is largely the coastal surface water, the travel paths and times revealed by the particle tracking are key factors that determine the (modified) chemical composition of the recycling water at the circulation outlet, which in turn affects the net exchange between the marsh and coastal surface water. Our study highlights the hydrological complexity of intertidal marshes and the need for further research on interactions among marsh morphology, hydrology and ecology, which underpin the functionalities of these wetland systems.