Summary: An integrated computational structure for non-cohesive sediment-transport and bed-level changes in near-shore regions has been developed. It is basically composed of: (1) three hydrodynamic sub-models; (2) a dynamic equation for the sediment transport (of the Bailard-type); and (3) an extended sediment balance equation. A shallow-water approximation, or Saint-Venant-type model, is utilized for the computation and up-to-date field currents, initially and after each characteristic computational period. A Berkhoff-type wave model allows us to determine the wave characteristics in deep water and intermediate water conditions. These computations make it possible to define a smaller modeling area for a nonlinear wave-current model of the Boussinesq-type, including breaking waves, friction effects and improved dispersion wave characteristics. Bed topography is updated after each wave period, or a multiple of this, called computational sedimentary period. Applicability of the computational structure is confirmed through laboratory experiments. Practical results of a real-world application obtained around the S. Lourenço fortification, Tagus estuary (Portugal), with the intention of preventing the destruction of the Bugio lighthouse, are shown.