Farmer John Blackie said he had not seen anything like it in nearly four decades on the farm.
He was initially sceptical of the Otago Regional Council's reasoning, but after a visit to Owhiro Stream with an ORC staff member yesterday, had accepted the explanation.
Mr Blackie's daughter Tinelle found the dead eels and a giant kokopu on Wednesday.
Otago Regional Council environmental monitoring and operations director Jeff Donaldson said this summer was the hottest since 1999, causing problems for fish.
From a visual inspection, the water did not appear to have been polluted. Its temperature, about 18degC, was not enough to be lethal, but dry weather caused the stream to pool and go underground in places, and exposed parts of the eels' natural habitat.
The Otago Daily Times visited the stream on Wednesday with Mr Blackie, Tinelle Blackie and lambing drafter Ross Stevens.
Mr Stevens did not accept heat would cause the deaths, as eels could survive in very little water and the stream was still flowing well in most places.
He said he had seen a film on the water in some parts of the stream and believed it could have been polluted.
''I cannot honestly believe that the heat killed those eels. That is absolute [rubbish],'' he said. ''They're just walking away from a problem.''
Otago Fish and Game council operations manager Ian Hadland told the ODT yesterday the Owhiro Stream was one of the most polluted streams in the region, largely because of stormwater discharge.
It was possible the heat, on top of the stream's underlying poor health, had caused the deaths, but he could not be sure.
''When streams are under strain, like they are at the moment, if you add temperature you're adding another element to it which just might be the tipping point.
''My experience is that eels are one of the most tolerant species that are in fresh water, they are almost the last to leave ... when things get really dire.''
Eels were sensitive to certain pollutants, he said.
