Most incised valleys become more organized seaward through tributaries merging with the main trunk valley. Late Quaternary incised valleys on the Mississippi and Alabama inner continental shelf branch seaward, although they do coalesce towards the shelf break where they feed shelf-edge deltas. To link fluvial systems with their associated previously mapped incised valleys on the shelf, and evaluate the contribution of small coastal-plain valley systems to the lowstand systems tract, high-resolution seismic data and cores were collected from Mobile Bay, eastern Mississippi Sound, and the Mobile bay-head delta. These data show four unconformity-bounded stacked units, and this study focuses on the upper two regionally mappable units. The upper two unconformities were sampled in core as exposure surfaces, and, on the basis of stratigraphic position, depth of incision, and 14C dates, are interpreted as sequence boundaries. The shallowest sequence boundary (A) formed in response to the Oxygen Isotope Stage 2 sea-level lowstand, while the underlying sequence boundary (B) formed in response to an earlier lowstand (Stage 6?). A map of Sequence Boundary B shows a network of seaward-branching valleys, 20–35 m deep and 0.6–7.7 km wide, that extend across Mobile Bay and Mississippi Sound. These valleys, which are bounded by well-developed terraces, are extensions of the piedmont Mobile fluvial system and the coastal-plain Fowl and La Batre fluvial systems. A map of the Stage 2 Sequence Boundary shows that all systems generally reoccupied their previous valley positions and are separated by interfluve plateaus. Valley fill between Sequence Boundary B and the Stage 2 Sequence Boundary is generally composed of a basal unit of alluvial sediments overlain by bay-head delta deposits; however, Stage 2 to 1 valley fill is composed entirely of central-basin sediments. The presence of bay-head delta deposits on the inner shelf indicates this depositional environment backstepped across the estuaries to modern positions. Backstepping likely occurred as the low-gradient paleovalleys were inundated, resulting in rapid rates of transgression. Fluvial gradients measured on Sequence Boundary B and the Stage 2 Sequence Boundary, below the modern Mobile bay-head delta plain and the estuaries, are very low (1.3–0.3 m/km). The Mobile bay-head delta and upper Mobile Bay are confined by steep topography, which opens basinward into the low-gradient shorelines surrounding lower Mobile Bay and Mississippi Sound. During falling sea level, channel branching likely occurred as the low-gradient fluvial systems extended basinward beyond the confined topography. These channels incised as sea level fell below the steeper shelf break during the lowstand. Stage 2 valley morphology is partially influenced by the position of the underlying Stage 6 valleys. Both coastal-plain and piedmont valley systems exhibit compound fill, indicating that differentiation between these types of incised valleys cannot be based on valley-fill architecture alone.