Orbost in East Gippsland has experienced major flooding with many roads shut and residents urged to move to higher ground.
Agricultural land surrounding the town has been impacted, according to secretary of the local chamber of commerce Garry Squires.
He said the town has had a difficult few years due to drought, fires in 2019, the impacts of the COVID-19 pandemic and now floods.
"The communities are very resilient but it is tough," Mr Squires told AAP.
"There's lots of things happening and it affects people economically and certainly the inconvenience of the whole thing."
Possible thunderstorms have been forecast in eastern parts of the state and northern Melbourne for the rest of Thursday.
Residents in Echuca along the Murray River have noticed a stench coming from stagnant water which engulfed dozens of homes on the "wrong side" of a levee built to protect the town from the worst of the disaster.
Resident Michelle McLeod believed the the "vile" smell came from overwhelmed sewerage systems and rotting animals caught up in floodwater.
"We opened the window the other day to let a bit of fresh air in and had to shut it straight away and light candles," Ms McLeod told AAP.
Authorities said the Murray peaked earlier in the week but Ms McLeod noticed an extra 10cm of water had crept up on her property on Wednesday.
She was concerned the clean up would not be able to begin for several days and was unsure whether authorities would be able to assist her.
Moderate flooding continues along the Avoca, Campaspe, Goulburn and Loddon rivers as well as creeks near Euroa and Benalla.
Victoria's Emergency Management Commissioner Andrew Crisp said the severe weather would continue in all parts of the state well into summer.
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