Intertidal wetlands 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 three-dimensional, variably saturated pore water flow in a creek-marsh system that bordered a tidally dominated main channel. 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 pore water circulation with three dimensionality 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. Particle tracking revealed that 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 linked with infiltration into the upper marsh surface areas away from the main channel. Local net efflux, influenced by the creek channel curvature, varied along the creek but produced a total discharge largely proportional to the creek length. Water infiltrating the soil in the lower marsh surface areas away from the creek tended to discharge directly to the main channel. However, the total discharge to the main channel was much less than that into the creek. This 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.