The reliability-based risk assessment and structural design model (REBAD) introduced in this paper, is a worthwhile tool in the preliminary design of maritime structures which are portrayed by vast failure consequences and significant resource expenditures. REBAD model in which the Second-Order Reliability Method (SORM) is utilized together with a cost-optimization algorithm, is implemented to Mersin yacht harbor which is constructed near the city of Mersin located on the Turkish coast of Mediterranean Sea. SORM is established on a more correct approximation of the failure surface than the first-order method. The failure mode probability is predicted by approximating the failure surface by a quadratic surface with the identical curvature at the design point. First, REBAD is implemented to the main breakwater by utilizing the Hudson failure function to determine the size of armor units, then failure mode response functions were obtained for the fixed exceedance probability of several damage levels. Combining with the hydraulic model study carried out by Ergin and Ozhan (1994) and REBAD outcome, the trunk section of main breakwater and design functions were determined. The second order reliability-based sensitivity study was also carried out to systematically compare limit state equations of Hudson and Van der Meer. Authors concluded that, Van der Meer failure function is a more reliable design function for this case study which illustrated the affect of uncertainties encountered in Turkey on the design practice of rubble mound breakwaters. Since REBAD enabled the first application of reliability-based design practice for coastal structures in Turkey, it is the commencement for the development of a national reliability-based design standard of maritime structures.