The sight prompted the keen fisherman to call the Bay of Plenty Regional Council to report the unusual event.
"I've never seen anything like that happen in the Tauranga Harbour ever and I've fished the harbour for decades," Mr Hardy said.
Mr Hardy said the huge number of dead creatures and the location near an industrial area made him suspect it was some sort of toxin which had killed the fish.
Bay of Plenty Regional Council pollution prevention officer John Morris confirmed at least 100 recently spawned young mackerel were dead in the stream. They appeared to have been blown towards the southern end of the estuary by the wind, he said.
Mr Morris said it was more likely to be a natural event than a pollution incident as only one species was involved. The regional council was investigating and had called in experts to check the site.
Biologist Dr Ian McLean was also concerned to learn of the occurrence and expected the regional council would conduct a thorough investigation.
"Surely the first thing the regional council would do would be check what's happening in the industrial area. To say it's only one species so it has to be natural, what a pile of rubbish."
Mr McLean said there were occasionally instances where there were unexplained die-offs of fish but that should not be the first assumption.
The industrial area and the area above it needed to be investigated to ensure there was no toxins leaking, he said.