In 2006 a Vietnamese Engineering Consultancy Company carried out a design study of a Naval Base at the location of the South of Doson Peninsula in Vietnam. A deterministic approach applied to the conceptual design of the breakwater system of the Naval Base resulted in a cross-section with a big armour layer and a rather low crest level. This paper applies an economic optimisation approach to derive the optimal geometry for the breakwater system. Results show that when considering total costs over the lifetime of the breakwater system, the block size can be reduced and the crest height can be increased. Some failure to the armour layer can be accepted while the wave transmission and overtopping should be limited in accordance with their related costs.