During the recent prolonged Millennium drought (2001-2009) the shoreline of Lake Alexandrina receded. At Clayton Bay, on the Goolwa Channel, the jetties were left high and dry. All the while the sea dykes could have been opened and the lake filled with seawater as once happened naturally each autumn, and for longer periods during drought.
That Lake Alexandrina is now brimming with freshwater has nothing to do with the government’s water reform agenda, but rather the breaking of the drought with flooding rains.
Once upon a time when there was drought the Murray River did run dry.
Water was never more than two feet deep while we carted timber, and for a long time in autumn 1915 was perfectly dry, the river having stopped running in February or March.” Russell McDonald, Riversdale, Central Murray Valley
Then dams were built so surplus water could be stored. During the recent protracted Millennium drought (2001-2009) the river did not run dry, there was a continual supply of water from the Hume Dam and the water quality was good.
Then the drought broke and the River Red Gum forests flooded again.
During the drought it was feared that the Murray River might never flood again. But the drought broke with flooding rains – as it always does.
Never mind that so many commentators claimed the dams would never fill again. They filled to overflowing.
A simple chart of annual rainfall in the Murray Darling illustrates that there is no “declining rainfall” in the Murray Darling.
The Murray Darling Basin received the highest rainfall on record in 2010, even more rain than recorded in the flood year of 1956. 
It was once feared that because of rising river salinity levels, Adelaide’s drinking water would become salty.
Murray River salinity has been recorded on a daily basis at Morgan since 1938. 
The peaks in salinity in 1967/1968 and 1982/1983 corresponded with years of low river flow because of drought.  However, during the recent drought river salinity levels continued to fall despite reduced inflows. This is a consequence of improved on-farm drainage management and salt interception schemes. 
It is often claimed in the popular press that Lake Alexandrina has been a freshwater lake for 7,000 years.
In fact, the Lower Lakes formed when the Southern Ocean burst through a coastal dune formation flooding an areas of natural subsidence. This occurred between 6,000 and 7,000 years ago when sea levels were 1-2 metres higher than they are today. [6,7]
Studies of fossil foraminifera – tiny protozoa with shells of calcium carbonate – indicate that the lakes had a maximum marine influence 5,255 years ago and a maximum freshwater influence 3,605 years ago. 
The period of maximum freshwater influence coincided with a period when the Murray River’s mouth was closed because climatic conditions in the catchment were generally drier. 
The narrow breach in the coastal sand bar-dune system, now officially the Murray River’s mouth, was closed when the first European visited the area in 1830.
Charles Sturt described in detail how his men were unable to maneuver their boat from Lake Alexandrina to the Southern Ocean because they were “blocked by sandbars”.
During the recent drought a sand-dredge worked to keep the narrow inlet open. As soon as the drought broke, the dredge was no longer needed.
There is a fear that without the barrages the lakes would become hypersaline, in reality, without the barrages, the natural tidal prism would facilitate scouring of the Murray’s mouth and enable the Southern Ocean to roll in each autumn. 
During autumn 2011, the barrages were open and despite flooding rains upstream causing strong flows through the Mouth, every spring tide caused flow reversals with a corresponding increase in salinity in Lake Alexandrina. On May 22, 2011, an intense low pressure system associated with a west to southerly wind of up to 40 knots blew in and salinity levels increased to over 35,000 EC units upstream of the Mundoo, Boundary Creek, Ewe Island and Tauwitcherie barrages. 
Robert Bourman and his Adelaide University colleagues describe the dramatic change that occurred with the construction of the barrages:
Originally a vibrant, highly productive estuarine ecosystem of 75,000 ha, characterized by mixing of brackish and freshwater with highly variable flows, barrage construction has transformed the lakes into freshwater bodies with permanently raised water levels; freshwater discharge has been reduced by 75 percent and the tidal prism by 90 percent. 
During the recent drought the barrages acted as dykes; water levels dropped and Lake Albert dried-up exposing potential acid sulphate soils. These soils are harmless as long as they remain undisturbed and waterlogged, but when exposed to oxygen, sulphuric acid forms. 
The development of acid sulphate soils can be avoided by restoring the Murray River’s estuary and letting the area fill with seawater during drought.
During the drought water levels in the narrow Goolwa channel were allowed to fall to one metre below sea level with the barrages acting as dykes keeping out the Southern Ocean.
1. Australian Bureau of Meteorology, 2011. Australian climate variability and change – Time series graphs
2. Murray Darling Basin Commission, 2011. River salinity data
3. Close A, 1990. River Salinity, In The Murray (Edited by Norman Mackay and David Eastburn), pages 127 to 146, Murray-Darling Basin Commission
4. Murray Irrigation Annual Reports, 2003 to 2010.
5. Harriss-Buchan A, 2011. “Muddying the waters”. Indaily blog.
6. Lewis SE, Wust RAJ, Webster JM, Shields GA, 2008. “Mid-late holocene sea-level variability in eastern Australia”, Terra Nova 20:74-81
7. Bourman RP, Murray-Wallace CV, Belperio AP, Harvey N. 2000. “Rapid coastal geomorphic change in the River Murray Estuary of Australia”. Marine Geology, 170, 141-168
8. Cann JH, Bourman RP, Barnett EJ. 2000. “Holocene Foraminifera as Indicators of Relative Estuarine-Lagoonal and Oceanic Influences in Estuarine Sediments of the River Murray, South Australia”. Quaternary Research, 53, 378-391
9. Sturt C, 1833. Two Expeditions into the Interior of Southern Australia. Smith, Elder and Co. Publishers, London
10. Jensen A, Good M, Tucker P, Long M, 2000. River Murray Barrages: Environmental Flows. Department of Environment Heritage and Aboriginal Affairs, Government of South Australia
11. Marohasy, J. 2011. End the Barrage of SA Spin, June 26, 2011. http://www.mythandthemurray.org/end-the-barrage-of-sa-spin/
12. Department of Environment and Resource Management (Queensland), 2009. “Managing Acid Sulfate Soils”, Facts Sheet.
13. Wood, A. 2007. Poor man river: Memoirs from the River Murray Estuary. ISBN 9781921207167