The interactions of physical processes between estuaries and upstream river floodplains are of great importance to the fish habitats and ecosystems in coastal regions. Traditionally, a hydraulic analysis of floodplains has used one- or two-dimensional models. While this approach maybe sufficient for planning the engineering design for flood protection, it is inadequate when floodwaters inundate the floodplain in a complex manner. Similarly, typical estuarine and coastal modeling studies do not consider the effect of upstream river floodplains because of the technical challenge of modeling wetting and drying processes in floodplains and higher bottom elevations in the upstream river domain. While various multiscale model frameworks have been proposed for modeling the coastal oceans, estuaries, and rivers with a combination of different models, this paper presents a modeling approach for simulating the hydrodynamics in the estuary and river floodplains, which provides a smooth transition between the two regimes using an unstructured-grid, coastal ocean model. This approach was applied to the Skagit River estuary and its upstream river floodplain of Puget Sound along the northwest coast of North America. The model was calibrated with observed data for water levels and velocities under low-flow and high-flood conditions. This study successfully demonstrated that a three-dimensional estuarine and coastal ocean model with an unstructured-grid framework and wetting-drying capability can be extended much further upstream to simulate the inundation processes and the dynamic interactions between the estuarine and river floodplain regimes.