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UPDATE 1.45pm: The worst of the rain is likely over for Bendigo today and the chances of a thunderstorm has been described as "very unlikely".
Bureau of Meteorology duty forecaster Gary Missen said the rain band is still continuing across central Victoria.
"There are more showers to come in the afternoon in Bendigo," he said.
"Once it clears later on, there might be light rain but not much after.
"There is very little chance of thunderstorms in Bendigo, maybe a five to 10 per cent chance."
There is also a small chance of rain tomorrow but the heavy rain seen earlier today and on Friday is unlikely to return.
UPDATE 11.15am: Heavier rain is beginning to fall in Bendigo.
A severe weather warning for heavy rainfall still remains in place for people in the Northern Country, North Central, North East, South West and Central forecast districts, of which includes Bendigo.
The Bureau of Meteorology advises that heavy rain and isolated thunderstorms may lead to flash flooding over parts these forecast districts.
"A low pressure system southwest of Mt Gambier, will continue to deepen and move eastwards to be south of Warrnambool by this evening while an associated surface trough moves across Victoria," the warning from the Bureau of Meteorology reads.
"The low will move away to the southeast of Tasmania Wednesday."
The severe weather warning for the Mallee and Wimmera forecast districts has been cancelled.
How much rain have you had at your place? We'd love to know your rainfall totals - find us on Facebook, tweet us at @BgoAddy or email ashley.fritsch@fairfaxmedia.com.au
UPDATE TUESDAY 7.10AM: A severe weather warning for heavy rainfall and potential flash flooding remains current for parts of the Mallee, Wimmera, Northern Country, North Central, North East, South West and Central forecast districts.
To find out which forecast district you are in, click here.
Heavy rainfall and thunderstorms are likely to extend into central districts by midday, the warning reads.
A flood watch is current for the Campaspe, Loddon, Avoca and Wimmera basins. Minor flooding is considered a possibility for these catchments.
Forecast high humidity and heavy rainfall has also prompted a brown rot warning for stone fruit growers in the north central and central forecast districts.
The State Emergency Service advises that people should:
Don't drive, ride or walk through flood water.
Keep clear of creeks and storm drains.
For emergency help in floods and storms, ring your local SES Unit on 132 500.
MONDAY: THE Bureau of Meteorology is predicting between 40 and 50 millimetres of rain could fall on Bendigo on Tuesday.
If accompanied with thunderstorms, the rain could cause more flash flooding in prone areas of the city.
Duty forecaster Stuart Coombs said a storm cell was likely to pass over Bendigo during the morning.
"From midnight to midnight, we have a prediction of 44 millimetres of rain for Bendigo," he said.
"As the trough moves through, heavy rain could fall within the space of an hour or two, possibly causing water over roads.
"That probability will be exacerbated if a thunderstorm comes through with the rain."
The rain is associated with the same air mass that produced more than 100 millimetres of rain in an hour in parts of Bendigo on Friday.
Rain is likely to start falling in the early morning and intensify by mid-morning. In late afternoon the weather system should have passed through Bendigo, Mr Coombs said.
"The rest of the week should be good for Bendigo, giving the city a bit of a respite from the heavy rain," he said.
North Central CMA produced an anecdotal rainfall map from Friday's heavy rain.
It showed the heaviest falls in Marong, Maiden Gully and Golden Square, which each recorded more than 100 millimetres.
The system moved in a southeast direction.
Huntly and Lockwood recorded significantly lower rain.
The two areas were on the outskirts of the rainfall totals, which intensified on the city itself.