After 2003, dykes were broken down and the area partially re-flooded, bringing 40% of the original marshes back to life.
Now the situation has gone into reverse, shrinking the wetlands back to roughly 30% of their former size and it could get worse if predictions of another year of low rainfall prove correct.
"The current reduction is a problem, it's not normal," said Ministry of the Environment water engineer Hazim al-Dalli.
"We can see its impact on water quality, on biodiversity in the marshes, affecting the inhabitants, who are leaving their areas. We can even see its effect on the water levels of the Tigris in Baghdad."
The most immediate cause is low rainfall, though it's far from being the only problem
"The drought is indeed very serious," UN Environment Programme (UNEP) expert Hassan Partow told the BBC by email.
"The 2007-2008 season was one of the worst droughts on record, and snowfall in the catchments feeding the Tigris and Euphrates has also been limited."
We can see the effects of global warming on the level of our rivers, and on the dried-up parts of the marshes now
"All predictions are that the drought will continue over the 2008-2009 winter, with rainfall levels well below average.
"For the marshes, which are fed by a snow-driven hydrology, the spring snowmelt in March/April is critical, and so it is too early to tell what the flood will bring this year. But the signs don't look great."
Even if rain and snowfall were above normal, the proliferation of dams and irrigation schemes have choked off much of the supply, and muted the annual snowmelt floods.
"This pulse cycle has been disrupted by the dams built in Turkey, Syria and Iraq itself, but mostly Turkey," wrote Azzam Alwash, director of Nature Iraq, who has been deeply involved in efforts to restore the marshes.
"The natural flow system is not going to return until and unless the dams outside Iraq are actively managed as part of a basin-wide coordinated management of the Tigris and Euphrates."
"We need to make sure that there is a just and equitable distribution of the water resources and improved efficiency of usage."
Iraq has water-sharing agreements with Syria, Turkey and Iran. But getting its allocation during drought years is difficult.
The marshes are a wonder of nature but have been at the centre of conflict
Many new dams are being constructed which also need to be filled, further reducing the supply.
Turkey has some of the biggest projects, but Iran's damming of the Karkheh river, which feeds directly into the marshes, and its construction of a mud barricade along the border running through the big Huwaiza marsh, have disrupted natural flows.
There are dam and irrigation projects in northern Iraq that also threaten consequences further downstream.
As if all this weren't enough, climate change also seems to be kicking in.
"We can see the effects of global warming on the level of our rivers, and on the dried-up parts of the marshes now," said Hazim al-Dalli of the Environment Ministry.
"The evidence that these are only preliminary signs of worse to come is quite strong, and the government of Iraq needs to seriously begin developing contingency and adaptation plans to deal with climate change," added Hassan Partow of UNEP.
But despite all the bad news, experts appear to believe the marshes are not living their death-throes.
For one thing, the wetlands show extraordinary resilience in bouncing back from previous periods of drought as part of a natural cycle.
Why Iraq's southern marshes are under threat
The reedbeds on which much of the ecology - and the Marsh Arabs way of life - depend, may appear to die off when the water dries up.
But their rhizomes - horizontal root-stems buried underground - remain viable for long periods, and throw up fresh shoots when the floods return.
Mr Alwash is optimistic the demands of dams and irrigation projects can be survived.
The Iraqi Ministry of Water Resources has adopted a master plan for the construction of 17 regulators at key points to allow water to be retained in winter and released in spring, creating an artificial flood pulse as would happen with snowmelt if nature were not being obstructed.
"This is a crucial step that not only will assure the restoration of a major portion of the marshes, but the continued increase in areas recovered," Mr Azzam said.
He also believes that in the long run, agriculture based on excessive and wasteful exploitation of water upstream will have to adopt efficient modern irrigation techniques, or be doomed by a rising buildup of salts.
"If they do not evolve their irrigation, they will die from salination, and the marshes can live on relatively salty water, albeit in a different biodiversity scheme than exists today," he said.
In the short term, the marshes seem destined to face at least another year of hardship.
But with proper water-sharing agreements between the countries involved, and advanced management plans for water use both upstream and in the marshes themselves, the future beyond might not look so bleak.
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