Rotary-drill cores from the Matagorda and Lavaca estuary complex sampled six distinct lithofacies, and high-resolution seismic data reveal four main seismic facies. The facies architecture of the bay indicates a history of Holocene flooding punctuated by major landward shifts in estuarine environments. Radiocarbon ages help to constrain the rate and timing of these flooding events and indicate significant reorganization of the estuarine environments at a decadal to century time scale. The Holocene evolution of the Matagorda and Lavaca estuary complex began ca. 11,600 yr B.P. with initial flooding of the portion of the ancestral Lavaca River incised valley that is now occupied by lower Matagorda Bay. Early flooding of the lowstand valley was punctuated by landward shifts in the river mouth, followed by episodes of fluvial aggradation. The most pronounced phase of aggradation occurred between ca. 11,600 and 9600 yr B.P., when sea level was rising rapidly, and a step in the valley floor slowed the rate of flooding. By ca. 9500 cal yr B.P., the deep, narrow part of the Lavaca incised valley had been flooded and was occupied by a bayhead delta. The river mouth shifted landward within Lavaca Bay between 8500 and 8200 cal yr B.P., followed by another landward shift in the delta between 7900 and 7700 cal yr B.P. These changes were mainly caused by variations in the rate of sea-level rise. The most dramatic change in the bay setting occurred between 7300 and 6700 cal yr B.P., when the bayhead delta stepped landward at least 30 km, establishing most of modern-day Matagorda Bay. This flooding event is attributed to a combination of rapid sea-level rise and to a reduction in sediment supply to the estuary that was associated with a change in the regional climate from cool and moist to warm and dry conditions. During the past 6700 yr, as the rate of sea-level rise decreased from an average rate of 4.2 mm/yr to an average rate of 1.4 mm/yr, the bayhead delta of the Lavaca River retreated slowly up the valley as the present-day outline of Lavaca Bay formed. The most significant change in the estuary setting during the past 6700 yr was the development of the present coastal barrier system, which led to gradual restriction of tidal exchange and associated changes in salinity.