Interruption of cargo handling is often induced by the resonance between a mooring system and long period waves in some large harbors facing to oceans. A new type seawall with a wide permeable rubble layer is proposed to reduce the reflection of long period waves and to prevent the cargo handling damages. A detail study on the mechanism of long period flow motion inside the permeable rubble layer is necessary to design the seawall with less reflection rate of the long period waves. Only experimental and analytical studies are done so far on the mechanism of water flow inside the permeable rubble layer. In this paper, a field test was conducted on the variation of water surface and flow velocity inside a permeable rubble layer in a newly constructed seawall at “Mabori” coast, Yokosuka, Japan. The stormy and long period waves have been completely dissipated by the water penetration into the rubble layer of the sea wall. The observed results demonstrate that the change of wave energy derived from the wave height and flow velocity inside the rubble layer is approximately represented in the Dupuit-Forchheimer law.