Despite all efforts and massive investments, the restoration of mangroves has not always been successful. One critical reason for this failure is the vulnerability of young mangroves, which cannot grow because of hydrodynamic disturbances in the shallow coastal water. For a comprehensive study bridging ecological and engineering principles, a portable community-based reef is proposed to shield mangroves from waves during the early stages of their growth. A series of field observations were conducted on Amami Oshima Island (Japan), to observe the growth of young mangroves and their survival rate under moderate wave conditions. The evolution of young mangroves was also observed in the laboratory under a controlled indoor environment. At the research site, it was confirmed that, after six months of germination, young mangroves could withstand normal high waves. Laboratory-grown plants were lower in height and had fewer leaves compared with the native mangroves on Amami. Based on these results, an economical reef system was designed. For this purpose, the Ahrens formula for the design of a low-crested reef breakwater was revisited. The results showed that a 50-cm-high reef constructed with 15-kg stones can protect mangroves that are a few months old and effectively promote early mangrove growth.