Low level flood advice remains in place for the region.
Flood warnings got as high as watch and act on Saturday as the region was belted with close to 50mm of rain.
Locals are being urged to avoid the Barwon due to concerns about water quality.
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Authorities say sewer overflows and flood runoff could have impacted the water quality and will issue more advice throughout the week as testing results come in.
Advice levels have decreased since the weekend, but continue to cover much of the city and down towards the Otways.
The Surf Coast and the Bellarine are largely clear of warnings.
