The European Union, in its Framework Strategy for A Resilient Energy Union, as described in the "Clean Energy for all Europeans" package of measures, marked its energy priorities for transition to a low-carbon, secure and competitive economy. Following this direction, the paper deals with the exploitation of one of the most significant and extensively available energy sources, that of nearshore waves. More specifically the paper emphasizes in the optimal design of Overtopping Breakwater for Energy Conversion systems, known as OBREC, using a novel and very effective, meta-heuristic optimization technique, the Harmony Search Algorithm. The proposed methodology is based on the combined application of wave propagation equations that simulate the compound wave field near coastal structures where the waves are subjected to the combined effects of shoaling, refraction, diffraction, reflection-total and partial-and breaking, with an optimization algorithm, aiming at the identification of the optimal dimensions of an OBREC reservoir. In order to demonstrate the effectiveness of the methodology, the port of Heraklion in the island of Crete in Greece, is used as a case study. The results of the application are very promising and strongly support the statement that the proposed methodology provides a new concept in the design of OBREC systems.