State parliamentary secretary for water Harriet Shing launched the Rivers of Warrnambool Flagship Project as the newest initiative in a state-wide catchment improvement program worth $248 million.

Ms Shing said the project would bring "a lasting benefit for the communities where waterways are the lifeblood of our cities and rural and regional towns".

She said the rehabilitation work would also extend to Brucknell Creek, but investment in the Hopkins River would only focus on its lower reaches.

The Merri River is only short, beginning near Bushfield and encircling the western half of Warrnambool before entering the Southern Ocean at Stingray Bay.

The Hopkins River is much longer, with its source north-east of Ararat. Almost all of the 271km waterway is in either poor or very poor condition according to government studies.

Much of the investment will be spent on restoring natural bush and vegetation along the banks of the rivers, which prevents runoff from surrounding farmlands getting into the water.

Less than five per cent of the Hopkins River has natural bushland, prompting small revegetation projects along some areas of the river in recent years.

Ms Shing said the Glenelg Hopkins Catchment Management Authority would work with Eastern Maar Aboriginal Corporation and the Merri Alliance to manage the project.

She said the government would also invest $400,000 in the Merri Connections Project, which will help fund walking paths, seating and launch areas for watercraft along the Merri River.

The project was adopted in August 2020 by Warrnambool City Council to develop the green corridor around the western fringe of the city.

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