The North Central Catchment Management Authority (NCCMA) has closed off fishways leading to the Gunbower Creek, after millions of juvenile carp found their way into the waterway and onto farms in the Cohuna area.
Authorities say recent floods caused a large carp breeding event in creeks and rivers across much of the southern Murray Darling Basin.
Now the NCCMA has advised fishways at the Koondrook Weir and Hipwell Road offtake have been closed.
"We are working with Goulburn-Murray Water to protect against further carp movement into Gunbower Creek and keep it a haven for native fish, such as Murray Cod and Silver and Golden Perch," the NCCMA said in a statement.
"We're investigating ways to remove carp, below the Koondrook Weir, at the natural junction of the creek and the Murray River."
Read more: The horse has bolted with the European carp
But a leading environmentalist said authorities were warned, in 2019, that such a mass spawning event could occur.
Central Murray Environmental Floodplain Group environmental committee chair Geoff Wakeman said while the Gunbower Creek originally contained some carp, flooding had triggered a mass breeding event and allowed the juvenile fish to enter both ends of the waterway.
"There are thousands of carp, I have never seen anything like it, and they are just going up the fish ladders," Mr Wakeman said.
"They could have shut the fish ladders in the first place - there was no need to keep them open."
The carp were breeding in the Gunbower Forest.
"There was a 2019 report done for the CMA saying that there was a danger the carp were going to breed in the forest - if you ask any of the locals, they will tell you shallow, warm water is the ideal carp breeding spot," he said.
Once in the creek and channels the carp would continue to breed up, he said.
"The horse is gone; there are going to be thousands of carp in the creek, they are just going to grow - they can't be cleaned out."
Cohuna dairy share farmer Heather Campbell said the property she worked on had experienced a "Carpageddon", as the fish flooded into paddocks from the irrigation channels.
She said she was still seeking advice as to what might happen if cattle ate the dead carp.
"The main issue is if dead fish make it into people's silage stacks," she said.
"People try to keep out dead rabbits and foxes and now we have fish - obviously dead animals in silage can be a botulism risk and you can kill a whole herd that way."
The biggest problem for the property's 200 cow herd was if single animals were "dumb enough to eat a dead fish.
"Cattle can both be extraordinarily smart and extraordinarily stupid, sometimes in the same day - so you look at them and think 'which one of you is dumb enough to eat a dead fish?"
The carp on her property appeared to be coming from Kow Swamp - "our water is fed from there, as is most everywhere else in the district," she said.
"From what I've heard, if you don't let them [the carp] through, you won't get much water through, either."
She said farmers with permanent pasture could not plough the dead carp into the soil.
"If you know anything about that pasture, you don't do anything to permanent pasture, you just chuck fertiliser on it," she said.
Cohuna dairy farmer John Keely said the carp were "just everywhere in the water".
"It doesn't matter whether you pump them out, or they go through the slip gates, you've got fish," he said.
"Anyone that is irrigating is going to have 'em, because the channels are just chock-a-block full of them."
Goulburn Murray Water Incident and Recovery manager Peter Clydesdale said instances of carp deaths had been widespread since the October floods.
They had been more noticeable in the west of region in recent weeks due to the receding water levels.
"Where possible, we have released small amounts of water from our storages to 'flush' channels and improve water quality for stock and domestic customers."
A spokesman for the Department of Energy, Environment and Climate Action said farmers should exclude livestock from areas contaminated with decomposing fish.
If drinking water had similar contamination, farmers should provide an alternative source for livestock.
Dead fish should be removed before re-introducing livestock due to the potential to impact on animal health, or re-introduction of livestock delayed until the fish have fully decomposed.
"Obviously we can't do that," Ms Campbell said.
"A thousand fish pick up is a bit more than a 52-card pick up."
It was not possible to wait for the fish to compost, because other types of feed were scarce because of the floods.
Agriculture Victoria encouraged affected farmers to call 136 186 to seek advice on biosecurity, animal welfare and food safety.
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Andrew Miller
I'm a general reporter with Stock & Land, with a special interest in irrigation issues. I completed my cadetship, with the Age, in 1980. Over my career, I've worked for ABC radio news (Mt Isa, Qld) and at provincial and suburban newspapers.
I'm a general reporter with Stock & Land, with a special interest in irrigation issues. I completed my cadetship, with the Age, in 1980. Over my career, I've worked for ABC radio news (Mt Isa, Qld) and at provincial and suburban newspapers.
