Flash flooding hits Victoria again

Homes have again been flooded and transport routes disrupted in Victoria's ongoing flood emergency, with more people now able to access disaster relief.

Residents on the Mornington Peninsula were warned to stay indoors and away from floodwaters as a severe thunderstorm caused havoc on Monday.

Seven homes flooded above floor level at Balnarring and about 300 of the 650 calls for help across the state were from concerned peninsula residents.

Mount Martha and Mornington were hit with 40mm to 50mm of rain in the space of a few hours and about 38 inland water rescues were made.

The effects were also felt north and west of Geelong, with six homes flooded at Lethbridge and authorities investigating the cause of a train derailment at Inverleigh, cutting off freight rail between Melbourne and Adelaide.

Major to moderate flood warnings have been issued for several waterways across the state but Emergency Management Commissioner Andrew Crisp said he did not expect rivers to rise as high as they did in late October or impact as many communities.

Major flooding at Albury-Wodonga in the state's northeast has receded but it's expected that water will flow west to Yarrawonga on Thursday and then on to Tocumwal.

Northeast Victoria also experienced significant rainfall over the weekend, including at Mount Hotham which received 144mm in 48 hours.

More than 85 warnings have been issued across Victoria and almost 450 roads remain closed.

Showers and possible hail have been forecast south of the ranges from Tuesday, while isolated thunderstorms could hit northern Victoria before wild weather ramps up again next weekend.

"There's still some time to go before this flood emergency is over in Victoria," VICSES chief operations officer Tim Wiebusch told reporters on Monday.

The state's Environmental Protection Authority issued a fresh plea for communities in northern Victoria to stay away from flood waters after finding low levels of the bacteria E. coli in major waterways at Swan Hill, Rochester and Echuca.

"Just because E. coli levels are low does not mean that there is no risk to health," the authority's chief environmental scientist Mark Taylor said.

"Floodwater should be treated as contaminated water as it can be contaminated from naturally occurring sources as well as overflowing sewage or septic tanks, or agricultural or industrial wastes and chemicals."

Water testing will be expanded to look for traces of other contaminants including pesticides, arsenic and copper.

From Monday, communities in East Gippsland, Mildura, Hindmarsh, Towong and the Southern Grampians can apply for federal and state flood assistance.

Employees and sole traders in those areas are eligible for 13 weeks of income support while authorities and primary producers in those regions can access hardship grants to cover the clean-up or other associated costs.

Residents impacted by floods in the Yarra Ranges in Melbourne's east can also now access one-off payments of $1000 per adult and $400 per child.

Federal Emergency Management Minister Murray Watt said the money was intended to help with short term recovery while authorities consider what long term help is needed.

VICSES has received more than 13,500 requests for assistance in the past month since severe flooding hit Victoria.