Architecture of late Quaternary incised-valley fills is commonly attributed to the interplay between sea-level rise, sediment supply, and hydrodynamic processes. Inundation of fluvial terraces is commonly overlooked as an autocyclic mechanism for formation of parasequences. If the rate of sea-level rise and sediment supply is constant, architecture of terraced incised-valley fills will likely show backstepping parasequences. The control that variable antecedent topography has on architecture of incised-valley fills is examined in the Trinity incised valley, Texas. The Trinity valley is characterized by a series of downward-stepping terraces, and the Galveston Estuary formed above this irregular antecedent topography. Flooding surfaces, recognized in core by a decrease in sedimentation rates and a change from delta-plain to central-basin facies, formed at ~ −14 m, 8,200 cal. yr BP and ~ −10 m, 7,700 cal. yr BP, matching depths of the relatively flat fluvial terraces. Flooding surfaces formed rapidly and represent entire reorganization of the estuarine complex. Across the −10 m flooding surface, the river mouth and bay-head delta shifted landward at a rate of ~ 6.5 km per century and the associated barrier shoreline was stranded on the inner continental shelf, forming Heald Bank. Flooding surfaces formed as the rate of sea-level rise was decreasing, and are not associated with a decrease in sediment delivery to the estuary. As sea level inundates relatively flat fluvial terraces, rates of transgression rapidly increase, resulting in a sudden increase in accommodation space and an associated landward shift in coastal facies. Backstepping parasequences are inherent to the architecture of terraced incised-valley fills.