The Otago Regional Council was investigating the fish deaths.
Kaikorai Valley College teacher Dr Simon McMillan, who has been involved in work to improve the stream, said it was disappointing to discover the dead fish but it was not the first time such an incident had happened.
"There are regular happenings in the stream all the time, like clay spills which increase the turbidity."
He did not know what had caused the deaths.
The discovery meant changing his lesson to talk to his pupils about pollution and its effects, he said.
Otago Fish and Game operations manager Ian Hadland said ranger Steve Dixon had investigated and found fish dead in pools from a stretch about 1.5km above the college, south.
People had gone to much time and effort to clean up the degraded stream, so it was very concerning another incident had happened, Mr Hadland said.
"It's a crying shame."
Fish and Game would wait for the outcome of the regional council investigation.
