The evolution of the Matagorda/Lavaca Bay complex demonstrates that although eustasy was an important control on incised valley flooding during the Holocene, antecedent topography, climate change, and barrier migration significantly impacted the resulting stratigraphic architecture. With the acquisition of 110 km of high resolution seismic data and 100 m of sediment cores, lithofacies and seismic facies of both bays were mapped in detail revealing 4 abrupt changes in depositional environments. These changes occur across major flooding surfaces at 9600, 7700, 7000, and 5000 yr and include the backstepping of deltaic and estuarine deposits as well as the onset and termination of spit accretion. Comparison of the evolution of Matagorda Bay with other Gulf Coast bays reveals that, with the exception of the 9600 yr event, flooding events were diachronous across the Gulf Coast, implying that climatic and autocyclic forcing mechanisms played a larger role in coastal evolution than previously recognized.