Ecologist working with NSW's North West Local Land Services Phil Spark, said they've tried protecting the nests but that's all been undone due to the high waters.

"We put fences around their nests and exclude foxes from them," he said.

"And because the river keeps coming up and down, it keeps flooding the fences and shearing them out.

"The fox fencing works well when the season allows it, but in years like this, it's very difficult."

It's a serious problem for the endangered turtles, which have an ageing population that could be wiped out if the older turtles are unable to run a successful nesting season, according to Mr Spark.

"Basically they're all old. They're dominantly old and those old ones have a limited lifespan," he said.

"And when they die they're just not being replaced by the juveniles that normally would."

Mr Spark said the turtles have just entered peak nesting season, which will last for another week or so until mid November.

With the persistent threat to their nesting, Mr Spark said they're trying to build an insurance population by trapping females.

He said left to themselves the young turtles have struggled to survive.

"We have a permit to raise 2500 through the university's [University of New England] incubator," he said.

"We induce them, put their eggs in the incubator and then hatch them out and release them."

The hatchlings would then probably be released in about late February, Mr Spark said.

However, it's been a race against time to trap the turtles, as Mr Spark said they tend to lay earlier in years like this.

"We trap them each year, but this year so far the rivers have been uncooperative," he said.

"And that's a bit of a problem if we're trying to collect eggs and the window of opportunity is slim."

"You want to get the eggs from the females that are ready to lay, but they can all go and lay and you can miss the boat really easily."

And even when they do manage to trap turtles and release the hatchlings, they are very vulnerable.

Mr Spark said they can't tell yet how many of them are surviving, so he won't be counting his turtles before or even for a while after they hatch.

"At this point in time there's not clear indication that we've managed to increase the population," he said.

"They're all still pretty small turtles and we're not catching those age classes much.

"They stay hidden in the vegetation and in the bottom of the river."

As such, he said it's going to take a few more years to be able to tell if the population is turning around.

However, there is some hope on the horizon, as Mr Spark said Kentucky Creek seems to be a bit of a haven for the species.

"Kentucky Creek, it's the exception. It's actually got a really good mix of age classes," he said.

He'd originally been trying to trap turtles along the Macdonald River before trying his luck on a section of the creek near Uralla in NSW's Northern Tablelands.

"And that was much better because it's a dam and there wasn't any strong current," he said.

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But according to Mr Spark it's still a bit strange they seem to be doing well there.

"It's got us puzzled really, because it's a very different habitat to the [MacDonald] river and we're wondering where they actually nest there," he said.

"There's a lot of thick vegetation around it and at a glance it looks as though there's too much vegetation from the point of view of getting sufficient sunlight to incubate the eggs."

But not being one to look a gift turtle in the mouth, Mr Spark and his team are now on a mission to find similar havens.

"We're looking for more dams that are in drainage lines and creeks where the turtle does already occur, that might replicate the habitat in Kentucky Creek," he said.