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 accretionary wedge. 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 forearc and accretionary wedge. 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 a less mafic composition, related to a previous period of intermediate-rate spreading.