Up to 10mm of rain fell overnight on Thursday followed by storms on Friday.

More than 10mm fell from 9am throughout the day, followed by wind gusts of up to 74km/h.

The strongest winds were found in the high country reaching over 100km/h at Mount Hotham.

Outside of the Alpine region, Wangaratta copped the brunt of the force with winds reaching 91km/h.

The wild storms caused damage throughout the Border and North East as SES volunteers responded to about 100 call-outs.

Albury Unit controller Scott Richter said their crews attended six incidents involving flash flooding, fallen trees and roof damage to houses.

“Most of the flash flooding was early on, they tend to come down fairly rapidly once the rain stops,” he said.

“Mungabareena would have been closed, the water there comes up fairly quickly.

“Our guys had to sand bag near some homes to divert the water away.”

South of the Border, North East SES crews received 93 call-outs across the region since midnight.

State media duty officer Jacque Quaine said about 80 per cent involved fallen trees on roads, buildings and property.

“They were pretty evenly spread –  Euroa, Wangaratta, Wodonga and Yackandandah were the hardest places hit,” she said.

“With the number of trees down in the North East, drive to the conditions and be very aware there could be trees across the road.”

The storm was enough to bring trains to a halt after one of the V/Line services struck a tree branch over the track.

The 12.05pm Melbourne to Albury train and the 5.20pm return service were both replaced by coaches.

Despite the cool change, Bureau of Meteorology duty forecaster Christie Johnson warned there could still be some warm days left before winter.

“We are in that in-between season now, so it's not unusual to get fronts coming through,” she said.

“In 2009 we had a run of six days over 30 from March 19, last year we had a few days over from 19th until the 23rd. We can get 30 degree days in the second half of March.”