An aminostratigraphy of Lake Illawarra and St Georges Basin, two wave-dominated barrier estuaries in southeastern Australia, has been derived on the basis of the extent of aspartic acid racemisation in the Holocene fossil molluscs Anadara trapezia and Notospisula trigonella. Relative ages were also assigned to Late Pleistocene fossil molluscs on the basis of the extent of racemisation of the slower racemising amino acids valine, leucine, and proline. Aminostratigraphy indicates that remnant Last Interglacial deposits within both incised valleys form a substrate over which Holocene estuarine sediments have been deposited and form a core for the Holocene barrier. Results from this study also indicate that the early geomorphological evolution of wave-dominated barrier estuaries formed in broad and relatively shallow, incised valleys is different from previously published models of Holocene barrier estuary evolution that explain successions in narrow, drowned valleys. Divergence from previous models is seen with the deposition of a near-basinwide shell-rich transgressive sandsheet deposited as rising sea levels breached remnants of Last Interglacial barriers during the most recent postglacial marine transgression (PMT; ca. 12,000–7000 Cal BP). Subsequent development of the estuaries follows the previously developed models with the Holocene barrier and central mud basin accumulating over the initial transgressive sandsheet. The aminostratigraphic framework derived from this study will serve as a geochronological template for future studies in wave-dominated barrier estuaries on the southeast coast of Australia.