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Hydrodynamic modelling of Australia's lower Murray River demonstrates the response of a large coastal plain estuary to the mid-Holocene (7,000-6,000 yr BP) sea-level highstand. The approximately two metre higher-than-present sea level during the highstand forced the estuarine limit upstream generating an extensive central basin environment extending more than 200 kilometres from the river mouth (143 kilometres upstream of the modern tidal limit). The geomorphic history of the region does not conform to conventional estuarine facies models as, for much of the Holocene, the lower Murray River acted as a landward, gorge-confined extension of the Murray estuary. The incredibly low relief of this coastal plain system drove significant saline incursion and limited current velocities across the estuary facilitating deposition of a laminated silt-clay sequence which our results suggest may be regionally extensive. Variations to discharge, barrier morphology, or the estuary's bathymetry result in minimal change to the estuarine palaeo-environment. The shift to the present-day fresher water distribution in the Murray estuary requires a fall in sea level to present-day conditions. The dominance of sea level as the controlling factor on this estuarine palaeo-environment highlights the significant potential impact of climate change induced sea-level rise to coastal plain estuaries.