A new scientific study has found native freshwater turtles are on the brink of extinction in South Australia, a concern predicted 30 years ago but little action has been taken since.

First published in the Scientific Reports in Nature journal this week, the researchers said rapid action was needed for conservation to be effective to save the dying species.

Researcher Ricky Spencer, Associate Professor of Ecology and Zoology at Western Sydney University, said the main driver for declining turtle populations was invasive foxes preying on turtle nests, but the impacts of marine disease and water quality issues were also significant contributors.

"We see foxes destroy turtle nests and they also eat the females throughout the catchment, but in South Australia we are probably now seeing the effects of water quality catching up with it [declining turtle populations]," Dr Spencer said.

"Ten years ago, during that millennium drought, we had mass mortality events because of water-quality-related diseases such as the marine tubeworm killing freshwater turtles.

Researchers say turtle populations are crashing and there are barely any baby turtles found along the Murray River system. ( Supplied: Sally Tsouta )

"Overall we are probably seeing between a 70–90 per cent decline of once 'common' native species.

"We are actually now not seeing any signs of activity or any turtles in some populations."

The researchers identified crashing turtle populations caused by the deaths of aging turtles and no juvenile turtle populations coming through due to nest predation, leaving no chance for populations to recover.

James van Dyke, senior lecturer in Biomedical Sciences at La Trobe University, said turtle populations in South Australia were most concerning and were like a "turtle aged care home".

"At some of our sites in Victoria and New South Wales, on a good night, we might catch 30 turtles, whereas on a good night in South Australia we would get one or two," Dr van Dyke said.

The researchers assessed populations of the broad-shelled turtle, eastern long-necked turtle, and the Murray River turtle in the Murray River and some of its associated waterways.

Researchers check a net at Lake Bonney for turtles as part of a catch and release study to monitor turtle numbers along the River Murray and its backwaters in South Australia. ( ABC Riverland: Catherine Heuzenroeder )

Why the river system desperately needs native turtles

The researchers said the recovery of turtle populations was essential to the health of the Murray River ecosystem, as the turtles were the "vacuum cleaners of the river".

"We just had the Menindee fish kill event … and the turtles are really important in terms of those ecosystem processes," Dr Spencer said.

"Any fish kill, turtles are the best cleaners and converters."

Researcher James van Dyke monitoring turtle numbers along the River Murray in South Australia. ( ABC Riverland: Catherine Heuzenroeder )

Dr van Dyke said the turtles were essential to the health of the river, recycling nutrients and contributing to the prevention of blue-green algae blooms.

"They eat pretty much anything, they eat a lot of vegetation and green algae, they eat a lot of dead stuff in the water, and they also eat a lot of insects and invertebrates."

Fear of tubeworms' return if dry conditions continue

Chairperson of the Alexandrina Wildlife Support Group Inc Deanne Smith was involved in the clean-up and rescue of turtles during the marine tubeworm infestation in the Murray River in 2008.

She said losing thousands of turtles was heartbreaking and they were fearful it could happen again soon.

"They are probably ready to do its thing again if conditions worsen," Ms Smith said.

"There are still active tubeworms just at the mouth of Sugars Beach on Hindmarsh Island, so it is a bit of a concern that it is so close to the River Murray.

A Murray River turtle encrusted with tubeworms, one of the worst marine diseases for freshwater turtles. ( Supplied: Deanne Smith )

"Prime conditions for tubeworms are stagnant, still water … from what I have seen lately, we still have quite high salinity, but we do have water movement in the Lower Lakes."

Dr van Dyke said infestations of tubeworms occurred during major droughts where salinity levels increased.

"The turtles will get tubeworms encrusting on their shells and you can have a lot of turtles die at once from that."

Dr Spencer said freshwater turtles could not handle high salinity levels and, if that did occur, turtles would be wiped out straight away.

Scientists call for action

The study found funding limitations, political constraints, and limited data often made effective action difficult, but the researchers said it was essential.

"The difficulty is we had 30 years to do something about it, because it was predicted by researchers 30 years ago," Dr Spencer said.

"What government agencies don't do well is to respond to these types of predictions.

"Usually the response occurs when populations are already declining.

Deanne Smith releasing turtles back into the river system after the millennium drought. ( Supplied: Deanne Smith )

"We saw the community outrage around the fish kill in the Murray-Darling in the Darling system recently and a lot of that obviously has to do with water storage and water use.

"We actually need to have proper discussion and almost reset the Murray-Darling river system … and turtles are a vital part of that."

Dr Spencer said it was not just about the fish.

"It needs discussion around key species in the Murray-Darling," he said.

"There are things that we can do and we certainly look at restoring populations and one of the beauties of turtles is that they live for a long time and the other thing is that they produce lots of eggs."

Ms Smith said in the Lower Lakes region it was important to look at the recovery of the environment, which she believed had not recovered from the millennium drought.