The NSW Department of Primary Industries said fish including bony herring, Murray cod and perch had died on the lower Darling-Baaka River, in the far west, along with carp.
The deaths were likely caused by low oxygen levels as floods recede, a situation made worse by fish needing more oxygen because of the warmer weather, the department said.
Bony herring were a boom-and-bust species, the department said, which thrive in floods but are more susceptible to stresses when water flows return to normal.
Local nature photographer Geoff Looney found huge clusters of dead fish near the main weir at Menindee on evening of Thursday, March 16.
"The stink was terrible. I nearly had to put a mask on," Mr Looney said.
"I was worried about my own health. That water right in the top comes down to our pumping station for the town.
"People north of Menindee say there's cod and perch floating down the river everywhere."
Mass kills have been reported on the Darling-Baaka River in recent weeks.
Tens of thousands of fish were found at the same spot in late February, while there have been several reports of dead fish downstream towards Pooncarie, near the borders of South Australia and Victoria, since February 20.
Enormous fish kills occurred on the river at Menindee during severe drought conditions in late 2018 and early 2019, with locals estimating millions of deaths.
The department's investigation involving scientists and Murray-Darling Basin experts found those events were also caused by a lack of dissolved oxygen, amid very low or non-existent water flows, high temperatures and blue-green algal blooms.
Mr Looney said there should be an inquiry into water management and fish deaths.
"It's getting ridiculous," he said.
Several state and federal departments are responding to the latest mass kill.
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