Work will begin after Easter on the removal of European weeds that are choking the Moorabool River.
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Crack Willow - or salix fragilis - has infested public land at Bolwarrah Weir in Bunding - a popular fishing spot 7km north of Ballan.
"The Corangamite Catchment Management Authority will revegetate the site with indigenous species.
"Seven thousand grasses and tussocks and 4,500 stems will be planted across the 51-hectare site," Project Officer Angus Donaldson said.
"Public access will be restricted at areas of the site for safety reasons, as large earthmoving equipment moves in.
"Sections of the site that don't have heavy machinery or don't have materials that risk public safety will stay open."
While the site is close to one of Central Highlands Water's biggest water storages - Moorabool Reservoir - it actually flows into Bostock Reservoir - a Barwon Water asset on the other side of the freeway.
Geelong-based water authority Barwon Water said the works would improve river health of the Moorabool - which was classed in 2005 as the most degraded river system in the state.
"As with our East Barwon willow removal project, this work will have environmental benefits from improved water quality and waterway health," Chief Scientist Will Buchanan said.
"It also created a better habitat for animals and fish in and along the river."
The works will include a 12-month maintenance program that focuses on willow re-emergence, blackberry control and revegetation maintenance.
The work is due to get going from Monday April 17.
The Living Moorabool Flagship project is part of a $248 million State Government program to preserve Victorian waterways.