The discovery on Wednesday follows the death of a woman in the area on Boxing Day after a campground was hit by a flash flood.
Police launched a fresh search after being told the deceased woman was believed to have been camping with a man.
Neither have been formally identified and a report will be prepared for the coroner.
A number of vehicles in the campground area were underwater and several people were safely rescued from a nearby bridge, police have been told.
A 44-year-old Bunyip man was killed earlier on Tuesday after a branch fell at his property at Caringal, in eastern Victoria.
Authorities have also renewed warnings for people to stay alert around waterways after the rescue of a woman and her pet in Melbourne.
Madi, 29, was walking her dog Minka along Werribee River in the city's west about 1.30pm on Boxing Day when the pooch jumped in.
"I kind of kicked into mum mode and started running downstream after her trying to get her to swim to me but the current was too strong for her to actually be able to cross," Madi told reporters.
She jumped in after Minka but then struggled to get out of the river, which was swollen and surging after days of heavy rain.
"I just lost my mind and made the decision to go in the water, which I think is just what you do if your dog's in that much trouble," she said.Â
"I quickly realised I wasn't going to be able to get her out with me."
She pulled Minka onto a small island and clung onto a tree until someone walking near the river called for help.
Water Police and Search and Rescue members pulled Madi and her dog Minka onto the riverbank. (HANDOUT/VICTORIA POLICE)
Five water police officers, two search and rescue members, SES volunteers and local police came together to rescue the pair.
Acting Sergeant Nicole Bath said the river was flowing quickly and carrying debris when they found the woman and her dog.
"(We were) quite concerned with the rate of the flow of the water and how cold she would be, waiting there for some time," she said.
She said rescuers tethered themselves and put Madi in a life jacket to pull them to safety.
Madi and Minka did not suffer any serious injuries in the ordeal.
Acting Sgt Bath had a warning for all Victorians as water levels continue to rise following heavy rain since Christmas.
"We'd like to just reiterate that message of safety around all waterways and particularly for floodwaters," she said.
Much of the state was on flood watch on Wednesday but conditions are tipped to improve.
Swimmers have been warned to stay alert as the weather gets better and check water quality, as rain has swept contaminants across Port Phillip Bay and into the ocean.
Victoria's Environmental Protection Authority said beach conditions along the Bellarine Peninsula, much of Melbourne and the Yarra River were likely to remain poor on Thursday.
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