Kaikorai Valley College pupils discovered the dead trout floating in the stream during a lesson.
Otago Regional Council resource management director Selva Selvarajah said investigators visited the site on the day of the complaint and again the next day to investigate potential discharges from stormwater pipes and other sources.
"They couldn't find an indication any such discharge occurred."
Staff took water quality samples which showed the oxygen levels were extremely low and the alkalinity levels were slightly elevated, he said.
"That is unusual for the site."
The results meant there might have been an incident of "biological activity" in the area.
"We cannot rule out algae activity."
A plant-based source could have activated overnight, when temperatures were slightly elevated, depleting oxygen, resulting in the death of fish, Dr Selvarajah said.
"It's a very unusual occurrence."
In the past when there had been similar incidents of fish deaths, the council had been able to track down the source, he said.
