Indonesia is an archipelago with a long coastline which provides many economic, social, and cultural advantages. Therefore, it is necessary to protect coastal areas from erosion. Mangroves as a form of natural coastal protection, are economically and environmentally feasible in many coastal areas. However, before mangroves can grow into strong trees which require two years of plantation, the ocean waves will damage them. To solve this problem, a natural coastal protection system using main natural protection (mangroves) as well as a temporary artificial structure (bamboo poles with green mussels) is proposed. This study aims to quantify wave height reduction using various mangroves and bamboo pole configurations. The laboratory experiments were conducted in a wave flume using physical models of mangroves as the main natural protection and bamboo poles with green mussels as the temporary artificial structure. Various wave conditions, including extreme waves, were generated during the laboratory test. This paper focuses on wave transmission over the natural coastal protection system to determine the most effective configuration of bamboo poles with green mussels. The results show that the most effective configuration model is to use 50 mm between the poles’ columns and rows and a breakwater width of 800 mm.