In this paper we propose a new model based on a contravariant integral form of the fully non-linear Boussinesq equations (FNBE) in order to simulate wave transformation phenomena, wave breaking, runup and nearshore currents in computational domains representing the complex morphology of real coastal regions. The above-mentioned contravariant integral form, in which Christoffel symbols are absent, is characterized by the fact that the continuity equation does not include any dispersive term. The Boussinesq equation system is numerically solved by a hybrid finite volume-finite difference scheme. A high-order upwind weighted essentially non-oscillatory (WENO) finite volume scheme that involves an exact Riemann solver is implemented. The wave breaking is represented by discontinuities of the weak solution of the integral form of the non-linear shallow water equations (NSWE). On the basis of the shock-capturing high order WENO scheme a new procedure, for the computation of the structure of the solution of a Riemann problem associated with a wet/dry front, is proposed in order to simulate the run up hydrodynamics in swash zone. The capacity of the proposed model to correctly represent wave propagation, wave breaking, run up and wave induced currents is verified against test cases present in literature. The results obtained are compared with experimental measures, analytical solutions or altative numerical solutions. The proposed model is applied to a real case regarding the simulation of wave fields and nearshore currents in the coastal region opposite San Mauro Cilento (Italy).