A simulation-based framework for the prediction of ship maneuvering in deep and shallow water is presented. A mathematical model for maneuvering represented by coupled nonlinear differential equations stemming from Newtonian mechanics is derived. Hydrodynamic forces are modeled by multivariat polynomials, and therein included are coefficients representing ship-specific hydrodynamic properties which are determined by way of captive maneuvering tests using Computational Fluid Dynamics (CFD). The development and evaluation of efficacy of the proposed framework encompasses verification and validation studies on numerical methods for maneuvering and flows around ships in shallow water. The flow field information available from numerical simulations are used to discuss hydrodynamic phenomena related to viscous and free surface effects, as well as squat.