In this paper, we propose a reliability-oriented design of a linear generator-based prototype of a wave energy conversion (WEC), useful for the production of hydrogen in a sheltered water area like Mediterranean Sea. The hydrogen production has been confirmed by a lot of experimental testing and simulations. The system design is aimed to enhance the robustness and reliability and is based on an analysis of the main WEC failures reported in literature. The results of this analysis led to some improvements that are applied to a WEC system prototype for hydrogen production and storage. The proposed WEC system includes the electrical linear generator, the power conversion system, and a sea-water electrolyzer. A modular architecture is conceived to provide ease of extension of the power capability of the marine plant. The experimental results developed on the permanent magnet linear electric generator have allowed identification of the stator winding typology and, consequently, ability to size the power electronics system. The produced hydrogen has supplied a low-power fuel cell stack directly connected to the hydrogen output from the electrolyzer. The small-scale prototype is designed to be installed, in the near future, into the Mediterranean Sea. As shown by experimental and simulation results, the small-scale prototype is suitable for hydrogen production and storage from sea water in this area.