UPDATE 6.30PM | Ballarat is no longer in the line of fire for severe weather.
The Bureau of Meteorology has cancelled a severe weather warning for the Mallee, South West and Wimmera districts however Ballarat has also been put outside the warning area.
BOM senior forecaster Dean Stewart said Ballarat would likely be spared the forecast storms.
“It looks like Ballarat has avoided all the action today, the trough of low pressure is still very close to Ballarat so whilst it’s likely the storm activity in the area has moved further eastwards there’s still a very slight chance of storms of developing.”
Mr Stewart said even Melbourne, which had experienced some of the heavier rainfall in the state, had “huge” variances within the city.
Meanwhile Melbourne has seen heavy rains and widespread flash flooding, forcing the suspension of some train lines and a warning from Metro Trains for commuters to avoid travel across the network.
Lines to the SES had reached maximum capacity shortly before 6pm with 430 jobs across the state.
“The nature of thunderstorms is some areas will cop it and you don't have to be far away from a thunderstorm and you might miss out on a heavy downpour.
“There were quite heavy falls in the Melbourne area but even in the Melbourne area we had huge variations.”

EARLIER | Get ready Ballarat, a severe weather warning has been issued for much of the state with meteorologists predicting heavy rainfall and severe thunderstorms.
Severe thunderstorms are likely to produce heavy rainfall that may lead to flash flooding in the warning area over the next several hours, the bureau of meteorology has warned.
Locations which may be affected include Horsham, Bendigo, Seymour, Maryborough, Ballarat, Geelong, Melbourne and Traralgon.
The State Emergency Service advises that people should:
Keep clear of creeks and storm drains.
Don't drive, ride or walk through flood water.
Be aware that in fire affected areas, rainfall run-off into waterways may contain debris such as ash, soil, trees and rocks.
Be alert that in areas recently affected by fires, heavy rainfall increases the potential for landslides and debris across roads.
- Stay indoors if possible.
- Avoid using the phone during the storm.
- If you are outside, avoid sheltering under trees
- Listen to the radio for storm updates
- Switch off your computer and electrical appliances
The next warning is due to be issued by 2:55 pm.
If severe thunderstorms develop in the Melbourne Area, a more detailed Severe Thunderstorm Warning will be issued to people in this area.
Warnings are also available through TV and Radio broadcasts, the Bureau's website at www.bom.gov.au or call 1300 659 217. The Bureau and State Emergency Service would appreciate warnings being broadcast regularly.