A program of geophysical mapping and vibracoring was conducted to better understand the geologic evolution of Apalachicola Bay. Analyses of the geophysical data and sediment cores along with age control provided by 34 AMS ¹⁴C dates on marine shells and wood reveal the following history. As sea level rose in the early Holocene, fluvial deposits filled the Apalachicola River paleochannel, which extended southward under the central part of the bay and seaward across the continental shelf. Sediments to either side of the paleochannel contain abundant wood fragments, with dates documenting that those areas were forested at 8,000 ¹⁴C years B.P. As sea level continued to rise, spits formed of headland prodelta deposits. Between ∼6,400 and ∼2,500 ¹⁴C years B.P., an Apalachicola prodelta prograded and receded several times across the inner shelf that underlies the western part of the bay. An eastern deltaic lobe was active for a shorter time, between ∼5,800 and 5,100 ¹⁴C years B.P. Estuarine benthic foraminiferal assemblages occurred in the western bay as early as 6,400 ¹⁴C years B.P., and indicate that there was some physical barrier to open-ocean circulation and shelf species established by that time. It is considered that shoals formed in the region of the present barrier islands as the rising sea flooded an interstream divide. Estuarine conditions were established very early in the post-glacial flooding of the bay.