In this study, a series of laboratory experiments were carried out to investigate the weak reflection of regular and random water waves over a train of protruded permeable shore structures. A cylindrical slit type breakwater and the alternatives are employed and compared for reflecting and transmitting capabilities of incident waves including wave forces. A series of random waves were generated by using the Bretschneider-Mitsuyasu frequency and directional spectrum. Measured spectrum of irregular waves without breakwaters is verified by comparing with those of the input waves generated. Weak reflection is occurred at the breakwater center of the peak frequency. If the row of breakwaters is fixed at three layers and the relative height of breakwater is fixed at 0.6, around 45% of incident wave energy is reflected to offshore. It is also found that the transmission of directional random waves increases as the maximum frequency parameter increases. A very good agreement is observed. Reflection coefficients of permeable submerged breakwaters are less than those of impermeable breakwaters. The upside-down L shape is recommended for a small fishery harbor mooring in terms of reflecting capability and of practical application. The final design was applied to the wharf of a small beach of Seolly, near Namhae at the southeast coast of Korea.