Myrtleford appears to have copped the brunt of thunderstorms which swept across the Alpine region late Saturday night and early Sunday morning.

Myrtleford SES controller, David Coates, said unit volunteers attended four calls for assistance Saturday evening, with another five call-outs on Sunday morning.

"The worst case of damage was to the pony club's shed at the Myrtleford Recreation Reserve, where the roof was partially removed: but because the incident wasn't considered to be an emergency, it didn't require any action from us," he said.

"There were a number of trees down on roads or in yards around the area, but fortunately there was no damage to homes or other properties."

Mr Coates said the only other major incident was heavy rainfall flooding a home, caused by uncleared gutters.

Myrtleford residents and visitors were fortunate to have attended the month's Saturday Farmers' Market earlier that morning, before half of one of the tallest trees in the Piazza came down in the storm.

Council arborists were busy on Sunday cutting down the other half, as it was deemed the safest option going forward, with teams shredding and finalising the safe removal of the debris on Monday morning.

According to the Bureau of Meteorology, the storms' heaviest rainfall was as Falls Creek with 68.8mm.

Mt Hotham had 32.2mm, Harrietville 29.2mm, Myrtleford 28mm, Rosewhite 22.4mm, Bright 19.8mm and Eurobin 17mm.