A dead cattle or dairy beast may have been lying metres upstream from a popular Ngunguru swimming hole for two weeks before the stench alerted neighbours.
Now it is too decomposed to be removed.
Environmental River Patrol director Millan Ruka said he found the decomposing carcass half submerged on the bank upstream from Coalhill Bridge after people reported the smell to him.
"It didn't take long to find it," he said.
Surfers sometimes stopped at the swimming hole by the bridge to wash the salt off their gear, kayakers paddled the river and picnickers often stopped there, Mr Ruka said.
"It is a health hazard if we get fine weather as the summer looms and people start to use the swimming hole.
"It is also a health hazard to those who gather kai moana down in the lower saltwater estuary."
Unfenced cattle on the Ngunguru River had been a problem for residents for some time, Mr Ruka said.
Northland Regional Council staff have decided not to remove the carcass because it is too rotten to move in one piece.
Nor could the council recover any removal costs. The cow carcass was so decomposed it no longer had an ear tag to identify its owner, consents manager Colin Dall said.
Trying to remove the remaining carcass would require machinery and was likely to cause more environmental impact than leaving it to break down.
Mr Dall said people should report incidents to the NRC's environmental hotline.
Meanwhile, Mr Ruka said he was concerned the NRC's proposed 2016 Draft Policy on water quality allowed beef and dairy support cattle to graze unfenced waterway banks as a "permitted activity" until at least 2025.
Mr Ruka said he had not heard the term "dairy support cattle" until a few months ago.
He believed it was contrived to put some dairy stock into the same category as beef stock to get around the fencing requirements in the Fonterra-supported Clean Stream Accord 2004/2012 and the Sustainable Dairying Water Accord 2013.
"They are dairy cattle. They might not yet be milking but they are dairy cows.
"Is this progress to clean up our waterways? No, it's a giant step backwards."