Thousands of fish died at once of natural causes in Sydney, authorities believe

The NSW Environment Protection Authority believes natural causes are most likely to blame for the deaths of thousands of fish in Sydney last week.

Thousands and fish and prawns were found floating in Haslams Creek flowing into Homebush Bay last Thursday.

On Sunday, thousands more were found dead on the Parramatta River in Rydalmere.

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In both cases, low dissolved oxygen levels were detected in the water by the EPA.

"Preliminary investigations indicate low oxygen levels were not caused by chemical pollution and were more likely due to natural causes," the EPA said in a statement about the Haslams Creek fish kill.

"Observations by EPA Officers indicate low oxygen causing fish to die."

The fish kill at Haslams Creek was cleaned up by the Sydney Olympic Park Authority.

Preliminary investigations at Rydalmere have indicated the low oxygen levels were also due to natural causes.

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"Observations by EPA Officers indicate low oxygen levels were caused by high intensity storms that washed organic matter into the waterway, which combined with elevated water temperatures, has caused the fish deaths," the EPA statement said.

"It is difficult to provide exact numbers but EPA officers estimate a few thousand fish have died, potentially up to 4000, in the Parramatta River at Rydalmere."

The clean-up has been hindered by the need to collect the fish without trampling the mangroves.