Up to 30 millimetres of rain is expected to fall in Bendigo today, the Bureau of Metereology has said.
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Senior forecaster Peter Newham predicted heavy showers for the region after 3pm and said residents could expect to see between 10 and 30 millimetres of rain.
The inclement weather is expected to ease by midnight.
Mr Newham said more showers and a thunderstorm are expected on Wednesday.
But the worst of the weather is thought to be heading east of Bendigo, with the bureau releasing flood watches for the state's north-east and for the Goulburn and Broken basins.
View flood warnings, flood watches, river height and rainfall information at http://www.bom.gov.au/vic/flood/.