The inland waters of the Puget Sound, Washington, USA, and Georgia Basin, British Columba, Canada, is a complex system of high energy river inputs to lower energy large basins with direct connection to the open ocean through the Straits of Juan de Fuca. High energy systems acting as transport mechanisms for coarse sediment interact with low energy regions with transport deposition of finer sediments to create the vertical stratigraphy of the seafloor. In regions of high energy the seafloor expression is dominated by a rougher seafloor with more geomorphic features of coarser material, while low energy regions are expressed in a seafloor of uniform lamination. This research investigates the link between the surface expression of seafloor roughness and the underlying vertical structure of sediment deposition. Using a high resolution bathymetric surface derived from multibeam sonar synchronized with low frequency sub-bottom acoustic profiles, the depth of acoustic penetration is correlated with a focal calculation of seafloor roughness. Areas of lower acoustic impedance have a larger range in penetration, with lower ranges of penetration persisting in areas of high acoustic impedance. High acoustic impedance is indicative of harder sediments, such as sand, and low acoustic impedance indicates softer sediments, such as mud. The research is a comparative study between a high energy system adjacent to the mouth of the Elwha River and the low energy protected region of South Possession Sound. The research illustrates the strong link between seafloor geomorphology and the terrestrial sources of sediment input and mitigation of sediment transport energy.