Scientists say salinity levels are falling in the lower reaches of the Murray and many bird and fish populations are increasing.
One native species thought to have been extinct is benefiting from a captive breeding program but concern remains that some plant species have failed to return after years of drought.
The southern purple-spotted gudgeon can be hard to find. Although colourful, they are thin and only grow up to 12 centimetres.
In 2002, a remnant population was collected from wetlands near Mannum in South Australia for a breeding program.
Chris Bice, an ecologist at the South Australian Research and Development Institute, said - at the height of the drought - those wetlands dried up.
"We monitored that population during the drought to see how the population was going and I think over two years we caught maybe two individuals and then for a year or two straight we caught no fish whatsoever," he said.
"So we were quite confident in saying that population was probably gone from the wild, so the only population was in a couple of aquariums essentially."
Those aquariums are in the Institute's research centre at West Beach in Adelaide, where about 500 gudgeons are being monitored before being returned to the Murray-Darling river system next month.
Mr Bice says extra flows to the river system have created conditions for the species to survive.
"We feel that there is some water back in the system at the moment and it probably has a reasonable amount of security behind it at the moment and, as long as habitat conditions come back to a level where we think they'll be adequate for the fish, we think that, yeah, it's time to release them back in the wild," he said.
Mr Bice said there would be risks in releasing the aquarium-raised fish into the wild.
"They've actually become used to captive conditions I suppose, so they're not quite used to things like predation from birds and other fish and simply surviving out there in the big, wide world is one of the biggest risks I suppose," he said.
"Pinning down the reason why this species declined in numbers in the first place is quite difficult, but undoubtedly it probably has to do with river regulation and decreases in flows to the lower part of the river and potentially also the impact of introduced species on this fish. We've basically altered the river quite a lot from its natural state and undoubtedly those are the reasons why the species declined.
"It's certainly not out of danger at all. In terms of where it sits on an endangered list currently, it's still in a very precarious state and it needs to move a lot further from here before it gets to a stage where we'd be quite happy about its future."
Associate Professor David Paton from Adelaide University said water quality had improved along many areas of the lower Murray in SA.
"The Coorong has had a recovery of its salinity, largely because of significant volumes of water arriving at that region," he said.
"For some of the organisms living within the water column, various fish and some of the aquatic invertebrates, there's been a recently rapid recovery.
"But there are other components of that system that have not shown any recovery at all despite the return of appropriate salinities."
All but gone
Professor Paton said Ruppia tuberosa, a local native plant, had been affected by years of drought and was now virtually non-existent in the Coorong.
"The longer the plant is away, the harder is it for various organisms that depend on those plants to also be there and the notion of having a healthy, resilient system has to start being addressed within the Murray-Darling Basin Plan," he said.
"At present, the Murray-Darling Basin Plan is all about the delivery of water and assumption that if you get the hydrology right, salinities and so forth, the biology will actually be fine.
"Well the biology is not fine, it hasn't been fine and there needs to be a much greater focus on repairing the damage, before one even thinks about what one even thinks about what might be the status quo in terms of the volumes of water that one could tolerate being returned and/or removed from the system."
Professor Paton says there were difficulties in returning the plant to its earlier levels.
"The dilemma is there is no actual seed bank, substantial seed bank that can then be used to then restock this system and get it re-established and so it will take many years to slowly build this population of plants back, to get it back to the dominance that it once had," he said.
© ABC 2012
17:45 EST It's been a wet and wild 48 hours in parts of Western Australia with some parts of the grain growing region receiving over 65 millimetres of rain and wind gusts of almost 100 kilometres an hour.