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Council chief executive Ian Hadland, of Dunedin, said rotting grass and vegetation lying beneath ponded floodwater was known to decrease water oxygen levels as it broke down.
"There are dead and decomposing fish everywhere and dead worms all over the stream bottom — it’s a tragic sight."
A stench of rotting fish and vegetation emanated from a section of Silverstream, near Riverside Rd.
"It’s in a bad state — man alive."
The conditions, combined with heat, were the "perfect recipe" for creating an environment without oxygen to form, Mr Hadland said.
Oxygen levels in the lower Silverstream remained "very low" last week. The levels were "borderline lethal for fish".
An Otago Regional Council spokesman said water samples had been taken to rule out other causes for the deaths of the fish species.
Analysis of the samples in a laboratory continued this week, he said.