Bristol Bay lies along the northern side of the Alaska Peninsula and extends nearly 600 km southwest from the Nushagak lowlands on the Alaska mainland to near Unimak Island. The bay is underlain by a sediment-filled crustal downwarp known as the north Aleutian basin (formerly Bristol basin) that dips southeast toward the Alaska Peninsula and is filled with more than 6 km of strata, dominantly of Cenozoic age. The thickest parts of the basin lie just north of the Alaska Peninsula and near Port Mollar, are in fault contact with older Mesozoic sedimentary rocks. These Mesozoic rocks form the southern structural boundary of the basin and extend as an arcuate belt from at least Cook Inlet to Zhemchug Canyon (central Beringian margin).

Offshore multichannel seismic-reflection, sonobuoy seismic-refraction, gravity, and magnetic data collected by the USGS in 1976 and 1982 indicate that the bedrock beneath the central and northern parts of the basin comprises layered, high-velocity, and highly magnetic rocks that are locally deformed. The deep bedrock horizons may be Mesozoic(?) sedimentary units that are underlain by igneous or metamorphic rocks and may correlate with similar rocks of mainland western Alaska and the Alaska Peninsula. Regional structural and geophysical trends for these deep horizons change from northeast-southwest to northwest-southeast beneath the inner Bering shelf and may indicate a major crustal suture along the northern basin edge.

Bedrock and crystalline rocks beneath the Bristol Bay basin may be part of the extensive peninsular terrane that is believed to have accreted to southern Alaska in late Mesozoic or early Tertiary time. Development of the basin by extensional subsidence of Mesozoic basement rocks and infilling by a Cenozoic sedimentary section probably initiated in earliest Tertiary time. Subsidence was probably most rapid in Oligocene and Miocene time, based on sediment thicknesses in the St. George basin COST 2 and Gulf Sandy River (Alaska Peninsula) wells.

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