Holidaymakers planning to hit the beach or splash in a river have been warned to check the water quality before taking a dip.
Recent storms likely washed pollution into Port Phillip Bay, with many beaches at Melbourne and the Bellarine Peninsula expected to be unsuitable for swimming on Thursday.
The Victorian Environmental Protection Authority has also issued an alert for poor water quality along the Yarra River from inner Melbourne to beyond Warburton.
However, front beaches along the Mornington Peninsula from just past Frankston to Portsea were tipped to be fair quality, meaning swimmers are urged to check for signs of pollution before heading in.
Contamination could include rubbish near the water's edge, flowing drains and water that looks murky or smells bad.
Much of the weather and flood threat for the state has now passed but people have been warned to stay vigilant around waterways.
Three people died during storms in Victoria over the Christmas break.
The bodies of a man and a woman were found at Buchan in the state's east after a camping area was hit with flash flooding on Boxing Day.
Earlier on Tuesday, a 44-year-old Bunyip man was killed after a branch fell on his property in Caringal, eastern Victoria.
A 29-year-old woman had to be rescued from the Werribee River in Melbourne after jumping in to save her dog.
She managed to pull the pet onto a small island and clung to a tree until a passerby called emergency services for help.
Neither animal nor owner were seriously injured and Victoria Police Acting Sergeant Nicole Bath warned all Victorians to be on alert following heavy rain since Christmas.
"We'd like to just reiterate that message of safety around all waterways and particularly for floodwaters," she told reporters on Wednesday.
