In this paper, we simulate the sea bottom modifications produced by the presence of a T-head groin. We present a simulation model of sea bottom modifications composed of two sub-models: a two-dimensional phase-resolving model that simulate the variation of the fluid dynamic variables inside the wave; a second sub-model to simulate the sea bottom modifications, in which the suspended sediment concentration is calculated by the wave-averaged advection-diffusion equation. The fluid motion equation and the concentration equation are expressed in a new contravariant formulation. The velocity fields from deep water up to just seaward of the surf-zone are simulated by a new integral contravariant form of the Fully Nonlinear Boussinesq Equations. The new integral form of the proposed continuity equation does not contain the dispersive term. The Nonlinear Shallow Water Equations, expressed in an integral contravariant form, are solved in order to simulate the breaking wave propagation. The momentum equation, integrated over the turbulent boundary layer, is solved to calculate the near-bed instantaneous flow velocity and the intra-wave hydrodynamic quantities. Starting from the contravariant formulation of the advection–diffusion equation for the suspended sediment concentration, it is possible to calculate the sea bottom modification. The advective sediment transport terms in the advection-diffusion equation are formulated according to a quasi-three-dimensional approach