The Holocene stratigraphy of Mobile Bay, Alabama, was mapped using a combination of high-resolution seismic data and sediment cores to refine changes in the bay's evolution during this time. The base of the Holocene-era stratigraphy is an erosional surface formed during the last glacial maximum. Overlying Holocene deposits are primarily estuarine mud that has a finely laminated weak acoustic signature. One exception is a thin unit, R1, with varying reflection amplitude that can be traced throughout the southern part of the bay. The continuity of the unit throughout the southern part of the bay suggests a baywide change in sedimentation that was perhaps driven by rapid retreat of the bay-head delta in response to a sudden rise in sea level or an abrupt change in accommodation space due to basin geometry. Along the southern edge of the bay, the R1 unit increases in thickness and reflector amplitude towards Morgan Peninsula. The peninsula itself underwent a period of erosion and narrowing between 4,300 to 3,000 years before present, and the variation in reflector amplitude and the geometry of this part of the R1 unit appear to reflect a period of increased overwashing of the peninsula during this period. Average estuarine sedimentation rates decreased after the formation of the R1 unit, and the decrease coincides with a decline in the rate of sea-level rise. A similar change in depositional style at approximately the same time in neighboring Apalachicola Bay suggests a change that affected the northeastern Gulf of Mexico region and not just Mobile Bay.