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Coseismic slip on the Patton Bay splay fault system during the 1964 Mw9.2 Great Alaska Earthquake contributed to local tsunami generation and vertically uplifted shorelines as much as 11 m on Montague Island in Prince William Sound (PWS). Sudden uplift of 3.7–4.3 m caused coastal lagoons along the island's northwestern coast to gradually drain. The resulting change in depositional environment from marine lagoon to freshwater muskeg created a sharp, laterally continuous stratigraphic contact between silt and overlying peat. Here, we characterize the geomorphology, sedimentology, and diatom ecology across the 1964 earthquake contact and three similar prehistoric contacts within the stratigraphy of the Hidden Lagoons locality. We find that the contacts signal instances of abrupt coastal uplift that, within error, overlap the timing of independently constrained megathrust earthquakes in PWS—1964 Common Era, 760–870 yr BP, 2500–2700 yr BP, and 4120–4500 yr BP. Changes in fossil diatom assemblages across the inferred prehistoric earthquake contacts reflect ecological shifts consistent with repeated draining of a lagoon system caused by >3 m of coseismic uplift. Our observations provide evidence for four instances of combined megathrust‐splay fault ruptures that have occurred in the past ∼4,200 years in PWS. The possibility that 1964‐style combined megathrust‐splay fault ruptures may have repeated in the past warrants their consideration in future seismic and tsunami hazards assessments. During the Mw9.2 1964 Great Alaska Earthquake, both the subduction zone and the crustal faults connected to the subduction zone (called splay faults) slipped, lifting shorelines up to 11 m on Montague Island in Prince William Sound (PWS) and contributing to local tsunami generation. The sudden uplift cut off tidal connection to coastal lagoons on Montague Island's northwest coast, producing a change to a drier, freshwater environment. The sudden environmental change created a clear sedimentary change from pre‐earthquake lagoon silt to post‐earthquake rooted soil in the stratigraphy of a study site known as Hidden Lagoons. Using the stratigraphic evidence of the 1964 uplift as a guide, we investigated deeper into the subsurface of Hidden Lagoons to see if there were previous instances of subduction zone and splay fault activation. We discovered three previous stratigraphic boundaries marking times when earthquakes uplifted the land. Changes in the species of diatoms across these boundaries show that the marine lagoon system was repeatedly drained by earthquakes causing over 3 m of uplift. These uplift events match the timing of four of the eight known prehistoric subduction zone earthquakes in PWS, suggesting that splay faults have slipped with the subduction zone multiple times over the past ∼4,200 years. We find widespread stratigraphic evidence for the 1964 M9.2 earthquake and three prehistoric earthquake contacts on Montague Island, AlaskaStratigraphic and diatom analyses suggest ruptures of splay faults may have occurred in conjunction with 4 of 8 documented Alaska‐Aleutian subduction zone earthquakesHazard assessments may want to consider the tsunami potential with possible future 1964‐style combined megathrust‐splay fault ruptures We find widespread stratigraphic evidence for the 1964 M9.2 earthquake and three prehistoric earthquake contacts on Montague Island, Alaska Stratigraphic and diatom analyses suggest ruptures of splay faults may have occurred in conjunction with 4 of 8 documented Alaska‐Aleutian subduction zone earthquakes Hazard assessments may want to consider the tsunami potential with possible future 1964‐style combined megathrust‐splay fault ruptures