Estuarine and coastal hydrodynamic processes are sometimes neglected in the design and planning of nearshore restoration actions. Despite best intentions, efforts to restore nearshore habitats can result in poor outcomes if water circulation and transport are not properly addressed. Land use constraints can lead to selection of suboptimal restoration alternatives that may result in undesirable consequences, such as flooding, deterioration of water quality, and erosion, that require immediate remedies and costly repairs. Quantitative models designed for application to the nearshore environment can minimize uncertainty about restoration goals, such as recovery of tidal exchange, supply of sediment and nutrients, and establishment of fish migration pathways. A high-resolution circulation and transport model of the Puget Sound, in the state of Washington, was developed based on an unstructured grid framework to define the complex shoreline using a finite volume coastal ocean model. The Puget Sound model is intended to assist with nearshore habitat restoration design and analysis, and to answer the question, “Can we achieve beneficial restoration outcomes at small scale, as well as estuary-wide?” Examples of restoration projects in the area illustrate the model’s capacity to simulate important nearshore processes such as circulation in complex multiple tidal channels, wetting and drying of tide flats, and water quality and sediment transport.