Rescue efforts in recent weeks have resulted in more than 600 freshwater crayfish and native fish being removed from river between Swan Hill and Robinvale-Euston.
But fish continue to be found dead along the river, prompting concerns about what effect blackwater is having on fish populations heading into the next fishing season.
An emergency alert for the Murray River exists up to Robinvale and prohibits entry onto the river.
Ozfish Unlimited Murray Darling Basin manager Braeden Lampard said this had made the search to rescue fish harder.
He said it was akin to “finding a needle in a haystack”.
“There are some sections of the Murray River that are about a (kilometre) wide and … you may only come across one or two (native fish) every 500 metres,” Mr Lampard said.
“We’re really relying on the input from the community because they are out (by) the water probably more often than we are.”
Mr Lampard said with dissolved oxygen levels just above deadly, volunteers were trying their best to rescue as many fish as possible.
“We’re currently sitting between that critical zone between two to four,” he said.
“Anything below four starts getting dangerous for native fish. And anything below two is deadly.”
He said native fish, which showed signs of discolouration, had been spotted exhibiting other signs of stress.
“The native fish start to go to the top of the water column,” he said.
“That’s unnatural behaviour for them.
“They’re basically in survival mode. All they’re trying to do is basically minimize their movement.”
Mr Lampard said peak floodwaters moving downstream had spelled the end of many fish and volunteers had seen Murray cod, and silver and golden perch, dying in the vicinity of Swan Hill.
He said more images on social media showed stressed native fish at Nyah Nyah, Tooleybuc, Wood Wood and Robinvale-Euston.
The emerging fish kills have thrown the outlook of the next fishing season into doubt and Mr Lampard said he had received repeated queries from recreational fishers about the short-term future of the fish population.
But he said it was “extremely difficult” to put a number on how many fish were affected and what impact fish deaths had on current breeding numbers.
“A lot of the big breeders of cod are dying,” he said.
“I’m just hopeful that these native fish have gone through their breeding cycle before they died.”
