The Snohomish River is one of the largest rivers to discharge into to the Puget Sound estuarine system. The tidal circulation, mixing and salt intrusion processes in the Snohomish River estuary are complex due to the presence of a large intertidal region, multiple distributary channels, and a sharp gradient of bottom elevation from the estuary to the fjordal depths of Puget Sound. To accurately simulate the tidal mixing and salt intrusion in such a complex system, a high-resolution model grid in both horizontal and vertical directions is required to represent the details of the geometry and bathymetry changes in the study domain. In this paper, a finite volume, unstructured coastal ocean model, FVCOM, was used to simulate the estuarine physical processes specific to the current state of the Snohomish River estuary, which consists of a number of dike-trained channels forming a uniquely braided system. The model was calibrated against observed data for a neap-spring tidal cycle collected during fall of 2006. Model simulations were carried out to study the tidal mixing, baroclinic flow, tidal residuals, salinity stratification and intrusion in the Snohomish River. Model results demonstrated that successful simulation of the physical processes in a complex braided estuary are feasible with a finite volume, unstructured model such as FVCOM.