The Environment Protection Agency (EPA) has issued a warning for the Yarrowee River after about 30 fish were found dead.
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"While this investigation is underway the community is advised to avoid contact with the water," EPA South West regional manager Carolyn Francis said.
"Additional testing is being undertaken and works to improve water quality are underway."
Dead Brown Trout along waterway near Sebastopol were reported late Monday.
The EPA conducted testing on a significant length of the river on Tuesday in response to the reports, but did not find any pollution.
The authority has reopened investigations after new information about a wastewater discharge from the Ballarat South Wastewater Treatment Plant was provided by Central Highlands Water (CHW).
CHW is licensed by the EPA to discharge treated water to the Yarrowee River under strict requirements.
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In a statement, the EPA said it will investigate the extent and impact of that discharge and associated compliance requirements.
"Regulatory notices and temporary alternative approvals to Central Highlands Water in response to the incident are now in place which will prevent any further discharge of poor quality water," the statement read.
Ms Francis said more information would be provided as soon as possible and that warning signage, which has been placed along the impacted area, would be removed when the area was safe again.
Ballarat woman Gretel Wilson was walking along the Yarrowee trail near Docwra Street this week when she spotted five dead fish along the creek.
"It's such a gorgeous creek and terrible to see," Ms Wilson said.
"I was shocked and surprised."
Residents can report fish deaths in Victoria to the EPA on 1300 372 842.
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