The main scope of this work is to contribute to the understanding of the complex hydrodynamic and morphodynamic processes that take place in coastal zones protected by single or multiple submerged breakwaters. The morphological response of such a system was studied both numerically and experimentally. In particular, a compound numerical model was developed in order to simulate the wave propagation, the wave-induced currents, the coastal sediment transport, the bed erosion and accretion, and finally describe the cross-shore profile and the coastline evolution in the lee of a system of permeable submerged breakwaters. The behaviour of such a system has not been described so far in a general and quantitatively consistent manner. The integrated model includes the combination of a higher order Boussinesq-type wave model with a sediment transport and a geomorphological model. Laboratory experiments were also performed focusing on measuring the morphology evolution of a sandy sloping beach in the lee of a permeable submerged breakwater. A thorough validation of the model is presented in order to check the efficiency of its various modules. Finally, the effect of some significant geometric and wave parameters was studied numerically in order to draw some guidelines for the optimal design of the aforementioned structures.