The Otago Regional Council said this week it was unaware of the mess.
The Dunedin City Council said it did not know where the "disappointing" contamination came from — but it was not the nearby Green Island landfill.
Michael Dick, of Dunedin, said he was kayaking up the Kaikorai Stream last week to do some duck-shooting when he saw an "incredible" amount of rubbish in the water, including "hundreds of tyres".
Photographs Mr Dick took last week, which he supplied to the Otago Daily Times, show a wheelie bin, tyres, road cones and other detritus clogging the waterway.
He noticed rubbish last year on a similar outing, but this year while the water was low, "there’s a lot more".
It was not visible from the Waldronville Bridge, in Brighton Rd, but "just out of sight of the road, it gets worse and worse".
"It's out of the public's eye.
"The further up you go, the worse it gets, so the public don't really get to see it."
ORC compliance manager Carlo Bell said the council was not aware "of any issues in recent times" and had not received a complaint related to the waterway since 2023.
The council was unable to comment on the source but appreciated the concerns about rubbish in the environment.
"Staff will visit the site," he said.
"We can’t be sure where these items have come from, but we’re very confident it is not from the Green Island landfill. The landfill is a well-managed facility designed to prevent waste from polluting the environment.
"Most tyres arriving at the Green Island landfill are sent to Christchurch for recycling, and old kerbside recycling bins are sent back either to the manufacturer for recycling into new bins or to ‘Future Post’ to be recycled into fenceposts," the spokesman said.
A hearing for the DCC’s continued use, closure and aftercare of the Green Island landfill is scheduled for next week.
The privately-owned Fairfield landfill closed in 2017.
The ORC lists the waterway as a regionally significant wetland.
