Physical processes in the world’s oceans span an enormous range of spatio-temporal scales, from ocean circulation at the global scale down to dissipation and mixing at the centimeter scale. It is impossible to simulate all of these processes using one model due to the shear computing power that would be required. Thus, different ocean models focus on specific processes and hence different spatio-temporal scales. At the largest scales are the global ocean circulation models, such as the Parallel Ocean Program (POP), which is used primarily to simulate seasonal or climactic processes (i.e., the El Niño Southern Oscillation [ENSO] or thermohaline circulation). At the intermediate scales are the regional ocean models, such as the Princeton Ocean Model (POM), the Regional Ocean Modeling System (ROMS), or the MIT General Circulation Model (MITgcm), which are well suited to modeling regional processes such as the Gulf Stream or the California Coastal Current. Indeed, these models are not necessarily limited to regional circulation studies; they have been applied extensively to simulate global circulation and, at the smaller scale, coastal processes, such as upwelling and internal waves. Ocean models that are specifically designed to simulate this end of the spatio-temporal spectrum are referred to as “coastal ocean models,” which, like their regional modeling counterparts, are not necessarily limited to, but are best suited for, the coastal region, which includes estuaries. Models that are specifically designed for coastal and estuarine processes include the Stanford Unstructured Nonhydrostatic Terrain-Following Adaptive Navier-Stokes Simulator (SUNTANS), DELFT3D, or the semi-implicit TRIM model of Casulli (1999). Coastal and estuarine processes distinguish themselves most significantly from regional and global processes in that they result from the interaction of ocean currents with complex boundaries and steep bathymetry. Models that simulate even smaller-scale processes, such as wind-waves, do not compute the three-dimensional circulation, but instead focus on computing time-averaged effects that can be included in larger-scale coastal circulation models, such as Simulating WAves Nearshore (SWAN), a two-dimensional wind-wave model.