This thesis presents the implementation of fully three-dimensional sediment transport and morphological updating formulations within a proven three-dimensional hydrodynamic flow solver. The thesis briefly discusses the formulations used to model both suspended and bed-load transport of non-cohesive sediment, and describes the implementation of a morphological updating scheme which incorporates novel approaches to morphological acceleration and dry bank erosion. Approaches used to model the three-dimensional effects of waves on coastal hydrodynamics and of three-dimensional currents on waves are also discussed. Results of several validation studies are presented and the model is shown to perform well in a series of simplified theoretical, laboratory, and full scale test cases. Application of the model and acceleration techniques to the complex and dynamic entrance to Willapa Bay, WA, USA is also discussed. Model processes are validated against the results of an extensive field measurement campaign, and diagnostic morphological model simulations are performed for two historical periods of contrasting morphological development. Input reduction and morphological acceleration techniques used to perform 5-year simulations of Willapa Bay are critically analysed and a new generic method to select a representative morphological tide for coastal environments containing significant diurnal tidal energy is presented.