This chapter describes modeling of circulation and mixing in estuaries and coastal oceans. The most crucial factor limiting the development of a truly predictive circulation model is a lack of a comprehensive observational database for model initialization, boundary condition specification, and model result assessment. The estuarine and coastal ocean circulation model (ECOM) model is three-dimensional with prognostic variables being the three components of velocity, temperature, salinity, turbulence kinetic energy, and turbulence macroscale. The density, vertical eddy viscosity, and vertical eddy diffusivity are also calculated. The model responds to surface wind stress, heat flux, and salinity flux and to the specification of tidal forcing, freshwater discharge, and other lateral boundary conditions. The condition under which a given estuary may be well approximated by a two-dimensional vertical-plane model is obtained. It is found that in continental shelf regions in which baroclinic effects are important, fine cross-shelf grid spacing that resolves the baroclinic Rossby radius is required. It is suggested that numerical models with variable grid spacing would be most appropriate in this case.