THE severe thunderstorms that hit large parts of Victoria on Saturday have abated but a severe weather warning remains in place for all districts.

On Saturday afternoon, storms descended across the state, dumping heavy rain in northern Victoria right down through Seymour, Healesville and as far south as Wilsons Promontory.

Earlier in the day, the Bureau of Meteorology had warned of damaging wind, flash flooding and large hailstones in north central Victoria and parts of the Mallee, Wimmera, Western District and in the north of the state.

Storms caused serious flash flooding in Bendigo and Melbourne was hit by destructive hail and rain in what's been described as a storm similar to a mini-cyclone, causing flooding, transport chaos, damaging buildings and forcing the cancellation of sporting events and the city's Moomba festival.

Soon after 9.30pm on Saturday, the Bureau of Meteorology cancelled its severe thunderstorm warning, saying that the storms were no longer ocurring.

"The immediate threat of severe thunderstorms has passed, but the situation will continue to be monitored and further warnings will be issued if necessary," the Bureau said.

"A severe weather warning remains current for all Victorian districts as areas of heavy rain and isolated thunderstorms are expected to continue overnight and during Sunday, that could result in localised flash flooding."

The State Emergency Service advises that people should keep clear of fallen power lines, secure any loose objects in the vicinity of their homes and keep away from creeks and drains.

It also says not to drive through flooded areas, stay indoors if possible and avoid sheltering under trees.