While the Lower Lakes have been predominantly freshwater and estuarine, with occasional incursions of seawater during droughts, this situation only applies to the relatively recent times. We certainly know that the whole area was once covered by the sea during times of higher sea level, and this is when the fossiliferous limestone was laid down.
There is also evidence from paleoecology that the Lakes were at least partly salty in the 6000 years prior to the barrages: http://www.theaustralian.news.com.au/story/0,25197,24877670-5013169,00.html
This is from the work of respected environmental scientist, Peter Gell, who believes that to allow seawater to enter the lakes could be a short term, reversible solution and would support a healthy marine ecosystem.
There is a suggestion from satellite photos that the River Murray formerly ran out into the sea just south of Pt Augusta where there appears to be a large relict delta. If this were the case, then the low lying lands which became the Lakes would almost certainly have been totally saline. What geological or other event caused the River to change its course at Morgan to run to the south is unknown.
by Elizabeth Gordon-Mills, Phd