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Abstract A shallow sub‐seafloor seismic model that includes well‐determined seismic velocities and clarifies sediment‐crust discontinuities is needed to characterize the physical properties of marine sediments and the oceanic crust and to serve as a reference for deeper seismic modeling endeavors. This study estimates the seismic structure of marine sediments and the shallow oceanic crust of the Alaska‐Aleutian subduction zone at the Alaska Peninsula, using data from the Alaska Amphibious Community Seismic Experiment (AACSE). We measure seafloor compliance and Ps converted wave delays from AACSE ocean‐bottom seismometers (OBS) and seafloor pressure data and interpret these measurements using a joint Bayesian Monte Carlo inversion to produce a sub‐seafloor S‐wave velocity model beneath each available OBS station. The sediment thickness across the array varies considerably, ranging from about 50 m to 2.80 km, with the thickest sediment located in the continental slope. Lithological composition plays an important role in shaping the seismic properties of seafloor sediment. Deep‐sea deposits on the incoming plate, which contain biogenic materials, tend to have reduced S‐wave velocities, contrasting with the clay‐rich sediments in the shallow continental shelf and continental slope. A difference in S‐wave velocities is observed for upper oceanic crust formed at fast‐rate (Shumagin) and intermediate‐rate (Semidi) spreading centers. The reduced S‐wave velocities in the Semidi crust may be caused by increased faulting and possible lithological variations, related to a previous period of intermediate‐rate spreading.