In this study, a wave-damping rate was derived for waves propagating over a multilayered, permeable seabed of finite depth. For a single-layer bed, a monogram is presented for the relationship between the wave-damping rate and the relative water depth for various depths of the permeable bed. The derived damping rate was used in the extended mild-slope equation to calculate wave dissipation over the permeable bed. For a single-layer bed, the result from the extended mild-slope equation model was compared with the result from the integral equation method and showed good agreement. The extended mild-slope equation model was also used to examine the wave transmission over a permeable shoal with a various number of layers, each with a different permeability. In general, short waves are more influenced by the permeability of the shoal than long waves unless the water depth is so great that the influence of the permeable bed on the surface water waves disappears. For a multilayered bed, the influences of the permeability of the upper layer on wave dissipation and transmission are more significant than those of the lower layers.