When the estuaries of south-western Australia were first flooded by the Holocene marine transgression about 7000 years before present (BP), most were enclosed by limestone barrier dunes. Coastal sand drift built bars and flood-tide deltas in the narrow entrances, but until about 3500 years BP the estuaries remained tidal-dominated systems with a diverse marine-estuarine fauna. Now the bars/deltas so obstruct the small tides that estuary water is fresh in winter and marine to hypersaline in summer; the estuaries are river-flow-dominated systems and the ecosystems are characterised by a restricted euryhaline estuarine biota. Some estuaries are still permanently open, their bars/deltas never close, and some am seasonally open, their bars open with river flow in winter and close in summer. Other estuaries am normally closed, their bars remain closed for several years and break with episodic flood flow, or are permanently closed coastal salt lakes with bars that never or rarely break: they can become grossly hypersaline and may dry up altogether. An hypothesis to explain this Holocene transformation of the estuaries attributes it principally to sedimentary processes in an environment where river flow is highly seasonal, tides are microtidal, there was a fall in sea level, and there are differences in the volume and periodicity of flow and the degree of shelter to the entrances from the prevailing south-west winds and swell.