The reliability-based model applied in this paper, provides a valuable tool in the design of coastal structures which are characterized by large failure consequences and substantial capital expenditures. Therefore, the implementation of the model to the design of rubble-mound breakwaters has an utmost importance especially in countries such as Turkey, where the use of natural stone for breakwaters is very common due to its economy. The purpose of the present paper is to describe the model by implementing it to Mersin Yacht Harbor which will be constructed near the coastal city of Mersin located on the Mediterranean Sea, and compare the results of the reliability-based model which utilizes the failure functions of Hudson and Van der Meer, with the deterministic design. Mersin Yacht Harbor construction project is a public investment administrated by the Ministry of Transportation. This study is the first application of the reliability-based design for breakwaters in Turkey (Balas, 1996). In the reliability-based model, the hydraulic stability of the main armor layer which is the most important failure mode as dislocking of the armor units under the wave attack, is described to compare the effects of failure mode response functions derived from Hudson and Van der Meer equations.