In coastal marshes, low-permeability mud is often found overlying high permeability sandy deposits. A recently developed 3D creek-marsh model was used to investigate the effects of soil stratigraphy (a mud layer overlying a sandy-loam layer) on pore-water flow in the marsh. Simulation results showed significant modifications of tide-induced pore-water flow due to the layered soil. The presence of the lower sandy-loam layer with a relatively high hydraulic conductivity not only increased the pore-water flow speed but also changed the flow direction, particularly in the upper mud layer where enhanced vertical flow dominated. Particle tracking revealed large changes in the overall pore-water circulation pattern, and associated particle travel path and time due to the influence of the soil stratigraphy. While the amount of water exchange between the marsh soil and tidal water increased, the residence time of particles in both soil layers was reduced. Sensitivity analysis showed the importance of soil compressibility, capillary rise and hydraulic conductivity contrast between the soil layers in modulating the effect of soil stratigraphy. In particular, the total net influx and efflux across the marsh surface (including the creek/channel bank and bed) increased proportionally with the square root of the lower layer’s hydraulic conductivity. These results demonstrated the interplay of tides, marsh topography and soil stratigraphy in controlling the pore-water flow characteristics, which underpin solute transport and transformation as well as the aeration condition in the marsh soil.