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Dead fish, including smelt, flounder, giant bullies, trout and inanga, littered the edges of the Kaikorai Stream and estuary at the Brighton Rd bridge on Saturday afternoon, Otago Fish & Game chief executive Ian Hadland said.
He visited the estuary after hearing reports of the dead fish at 4pm.
Any remaining fish appeared stressed, Mr Hadland said.
The water was very warm to the touch.
And though he was surprised by the biodiversity among the dead species, there were any number of reasons the fish could have died.
"It’s not a healthy stream," he said.
"It’s a sad indictment over how we’ve treated our estuaries over the years.
"It only takes one act to set a whole series of things in motion."
The stream drained a large residential catchment, there were light industrial sections in its middle reaches, and at the bottom it flowed past the Green Island Landfill, he said.
Local residents he spoke to were concerned the water levels were lowered for work to be done in the stream recently.
However, due to the stream’s underlying health, it could have been three sunny days in a row that led to the uninhabitable conditions, Mr Hadland said.
The estuary caught any contaminants put into the stream over the years, he said.
All of the nutrients trapped in the sediment could be brought back into the water column with only the slightest agitation.
It was the second major fish kill reported this year, but Mr Hadland said this incident was different from January in nearby Silverstream when low oxygen levels and high temperatures were thought to have caused the deaths of hundreds of eels and trout.
An investigation into that incident was ongoing, Mr Hadland said.
He understood the Otago Regional Council visited Kaikorai Stream at the weekend and that water sampling had taken place.
The council did not respond to a request for comment yesterday.