An enormous, toxic blue green algal bloom has infested the estuary for nearly two months, killing tens of thousands of native fish and devastating the ecology of the river.

At a meeting at the town's community hall on Wednesday, organised by the Peterborough Residents' Association, a number of locals spoke of their frustration that recommendations from a comprehensive 2005 report on the river hadn't been implemented.

"That 2005 report had strong recommendations for the river and if they had been properly implemented we wouldn't be in this situation," Peterborough's Barb Mullen told a group, including representatives of the Corangamite Catchment Management Authority, Wannon Water and dozens of fellow residents.

Paaratte eel fisherman Zac Taylor said he remembered blue green algae appearing in the river as far back as 1997, but the health of the river had become "worse and worse and worse" and the current conditions were by far the worst he had seen there.

"There are more dead fish in there this morning, which obviously isn't good," he said, adding it wasn't just native fish that had been wiped out.

"The worms are dead, and the crabs, the native minnows are all gone."

Mr Taylor said it was nearly a decade since he had seen baby bream in the river, and four years since he had seen any baby perch.

Corangamite Catchment Management Authority chief executive John Riddiford addressed the meeting to hear from locals and offer his thoughts on possible solutions.

He conceded authorities "need(ed) to do better".

"I know there were concerns about the alacrity of the response to the fish kill and particularly the stock death," he said.

He said the herd of cows found dead in the river had spurred the dairy industry into action because it had harmed their reputation.

"They know they need to get their act together," he said.

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Mr Riddiford spruiked the CCMA installing 42km of fencing along the Curdies over the past four years at a cost of $1.1 million, with another 13km scheduled this year.

But at that pace it could take a century to fence the entire catchment. Mr Riddiford said "resource constraints" were an issue.

"To have effective mitigation against blue green algae the program needs to be significantly expanded," he said.

At a separate meeting last Friday night, Member for Polwarth Richard Riordan spoke about the need for authorities to work closely with dairy farmers to find out how they could be supported to fence off and revegetate their river frontage.

Many residents focused on the lack of an overarching coordinating body for the river, but the most glaring deficiency appeared to be a lack of funding and political will.

The Department of Environment, Land, Water and Planning was aware of the meeting but did not send a representative. PRA chair Ron Irvine asked Mr Riddiford why DELWP had been so reluctant to assist with the crisis.

"That's a question I've put to them and it's a question I think you should put to them too," Mr Riddiford said.

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