Yesterday Environment Minister Peter Garrett ordered an environmental assessment into the flooding of South Australia’s parched lower lakes with saltwater.

We are certainly facing a dilemma, it is widely called a crisis, and locals call it Australia’s greatest environment disaster.

One doesn’t have to venture far into South Australia to realise that it is a dry part of Australia and that water issues are critical to its social, economic and environmental well-being. The internationally renowned wineries and the productive riverland are obvious modern icons of the SA landscape that have reached their present status on the back of the use of that state’s scarce water resources. So too are the Coorong and the Lower Lakes an icon — at a national and international scale.

From 1865, in response to pastoralists in the south-east, frustrated at the difficulty of getting produce past flooded valleys to Adelaide, the SA government began construction of an extensive drainage system to direct excess freshwater to the ocean. This diverted more and more water away from the Coorong, one of the natural outlets of this surplus winter rain. Then, in 1917, initially for the purposes of navigation and ultimately for the regulation of supply for irrigators and domestic use, plans were put in place for a vast series of barrages across the Murray system.

Lock 1 was completed at Blanchetown in 1922 and many more were commissioned after, culminating in the creation of an extensive line of barriers at the river mouth, most constructed on a natural rise of cemented shells that represented an old dune front. Development of water resources from the 1950s, mostly in Victoria and NSW, ultimately reduced the river flow through the system to much less than half its natural average. So, from early in history, and advancing at an accelerating rate, the system has been modified, and, being at the end of the system, the Coorong and Lower Lakes have suffered most.

By the time the lakes were nominated as sites of international significance under the Ramsar protocol, in 1985, they were already substantially modified. While remaining productive in terms of bird and fish numbers, the site qualified easily. The lakes, denied tidal flushing by the barrier system, had become largely fresh and were described as such in the listing. The Coorong was described as a saline to hypersaline, reverse estuary (more saline inland that at the mouth), while recent sediment evidence has shown it to be estuarine and brackish for 7000 years. In the Coorong’s case, the Ramsar description triggered a restriction being placed on the release of freshwater from the east; exacerbating its increasingly saline status.

Not surprisingly such intense abstraction and regulation of flows in the lower Basin lead to a choking up of the Coorong and lakes. This has lead to the accumulation of sediments and salts though the system. The mouth closed in the early 1980s, and has remained effectively so in recent years despite the efforts of dredges. Where water levels have been kept high, sulphate salts, denied exposure to oxygen, have reduced to sulphides buried in the sediments. Latterly, shifts in climate since the last large flood event in the 1970s, and more recently a significant drought, has reduced river flows and lake levels such that the sea is now half a metre or more above the level of Lake Alexandrina. The barrages, designed to hold river flow for consumptive use and to keep out the sea to retain its quality, is now exclusively a tidal barrage.

To further escalate the management challenge, Lake Albert, lying like an appendix on the eastern side of Lake Alexandrina, is drying risking the exposure of the accumulated sulphides. Simple secondary school chemistry tells us that adding oxygen to sulphides produces sulphuric acid. Further, while acidity is potentially harmful in itself, at a pH below 5, metals are released from clay particles liberating them into the environment to be dispersed by water or wind. School chemistry students also know that the smell from sulphides is particularly unappealing.

So, the acidification of Lake Albert has become the number one priority in the management of the system. The short term solution is to keep a veneer of water over the sediments to minimise the oxygenation of the sulphides. To date, this has been achieved by the pumping of scarce Lake Alexandrina water into Lake Albert. Under the premise that the lakes have always been fresh, and prompted by this “robbing Peter to pay Paul” scenario, there have been loud calls for the allocation of environmental flows to the Lakes.

Under the National Water Initiative, these lakes are entitled to a one sixth share of the 500 GL (billion litres) p.a. to be allocated to “the environment”. Some have bid for 700 GL p.a., to be released out the mouth, to re-establish a healthy system. At present water prices, this would constitute one of Australia’s largest environmental restoration programs — the opportunity cost being the denial of freshwater to most other wetlands in the Basin — unless a case for a larger allocation can be successfully argued at the national level.

The present debate then centres on whether fresh water is available, whether it would all evaporate en route to the lakes if the decision were made to send it, and what is the cost to the tax payer on the water market if we did. Not surprisingly, given there is a large volume of water bursting to enter the lakes, available at little or no cost, the emerging fall back position is to release sea water into the lakes to avoid acidification. The risk of this is to switch the lakes from freshwater to estuarine systems. There is some comfort in the evidence from sediment records, supported by hydrological modelling, that Lake Alexandrina at least, has been partly estuarine for most of its long term, pre-barrage existence.

So, the release of sea water would return the lake to its natural ecological character, which is somewhat different to that described in its Ramsar listing. With boundary conditions different now however, there is the risk that the volumes of water required to flush out the tidal waters remain distant in time and space. It may be decades before a fresh regime returns, seriously challenging the capacity of the modern freshwater system to recover when flows return.

So, at the end of the day, the issue remains about the lack of water in the system. We have been sailing far to close to the wind for far too long, maximising our profits from the system and minimising our capacity to adapt to variability and change. And change is certainly upon us. This is certainly a dilemma, it is widely called a crisis, and locals call it Australia’s greatest environment disaster. To add salt to the wound, consider a 50-140 cm sea level rise and a 5-25% reduction in river flow under climate change scenarios. The Environmental Effects Statement announced today will seek a short term fix, but, in addition to that, we desperately need a longer term solution.

Peter Gell is Professor of Environmental Science & Director of the Centre for Environmental Management at the the University of Ballarat and Adjunct Associate Professor, Geographical & Environmental Studies at the University of Adelaide.