Low oxygen and high temperatures appear to have caused the deaths of hundreds of eels and trout in Dunedin's Silverstream.
Mosgiel angler Bevan Campbell, who alerted Fish & Game Otago and the Otago Regional Council, said he had never seen anything like it.
Both agencies were on site last night.
Trout used the lower Silverstream as a refuge when the Taieri River was in flood and dirty, Campbell said.
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Otago Fish & Game chief executive Ian Hadland said the likely cause of death was warm, low-oxygen inflows of ponded floodwater from surrounding farmland.
''We have taken oxygen levels in the lower Silverstream today and they are still very low - borderline lethal for fish - and it's down to near zero in one of the drains leading into the stream.
"There are dead and decomposing fish everywhere and dead worms all over the stream bottom. It's a tragic sight."
Rotting grass and vegetation beneath ponded floodwater was known to decrease water oxygen levels as the material broke down.
That, in combination with heat, was a perfect recipe for an anoxic environment to form, he said.
"The Otago Regional Council are taking water samples to rule out other sources, but the cause of the fish kill looks to be simply a result of a natural flood event at the warmest time of the year," Hadland said.