Wetland-estuarine-shelf interaction processes in the Plum Island Sound and Merrimack River system in the Massachusetts coast are examined using the high-resolution unstructured grid, finite volume, primitive equations, coastal ocean model. The computational domain covers the estuarine and entire intertidal area with a horizontal resolution of 10–200 m. Driven by five tidal constituents forcing at the open boundary on the inner shelf of the eastern coast of the Gulf of Maine, the model has successfully simulated the 3-D flooding/drying process, temporal variability, and spatial distribution of salinity as well as the water exchange flux through the water passage between the Plum Island Sound and Merrimack River. The model predicts a complex recirculation loop around the Merrimack River, shelf, and Plum Island Sound. During the ebb tide, salt water in the Plum Island Sound is injected into the Merrimack River, while during flood tide, a significant amount of the freshwater in the Merrimack River is forced into Plum Island Sound. This water exchange varies with the magnitude of freshwater discharge and wind conditions, with a maximum contribution of ?30%–40% variability in salinity over tidal cycles in the mouth of the Merrimack River. Nonlinear tidal rectification results in a complex clockwise residual recirculation loop around the Merrimack River, shelf, and Plum Island Sound. The net water flux from Plum Island Sound to the Merrimack River varies with the interaction between tide, river discharge, and wind forcing. This interaction, in turn, affects the salt transport from this system to the shelf. Since the resulting water transport into the shelf significantly varies with the variability of the wind, models that fail to resolve this complex estuarine and shelf system could either overestimate or underestimate the salt content over the shelf.