A supermarket lost part of its roof and the casualty ward of Bacchus Marsh and Melton Regional Hospital was swamped with water during the brief but intense storms.

Water also came through the roof of Stoney's Pub in Grant Street and many shop fronts in Main Street.

David Morrison, of the Bureau of Meteorology, said the official reading at Bacchus Marsh Golf Club was 47millimetres of rain over a 24-hour period from 9am Wednesday to 9am Thursday. He said there were unofficial reports of up to 70millimetres of rain at Bacchus Marsh central.

SES regional manager Stephen Warren said there were 95 requests for assistance in Bacchus Marsh on Wednesday. A further 47 requests were reported by the SES the next day.

"We had volunteers from Bacchus Marsh, Ballarat, the CFA and Moorabool Shire Council, and put in a level two incident control centre," he said.

Teams were in place to help with clearing channels to divert water away from main streets.

They also provided aid with storm damage at the Bacchus Marsh Village shopping centre.

"The ceiling at the shopping centre collapsed in the section in front of Aldi," Mr Warren said.

"The centre was evacuated and closed but there were no injuries."

Bacchus Marsh Secondary College met a similar fate, with two lightning strikes and flash flooding causing substantial damage.

Principal Robyn Hunter commended the behaviour of students, who had to be kept indoors.

The storms also caused damage to the school's computer network.

"All our switches that act as a surge protector are gone - $40,000 worth of equipment was damaged and if you include the electrical whiteboards, it is around $50,000," she said.

Ms Hunter said the Department of Education was assisting with the clean-up and repair of carpets, shade sails and the area where lightning struck the roof of the school.

She said matters were made worse when the main drain from the south of Grant Street burst and flooded the entrance to the school.

Mr Warren advised residents to reduce the impact of future property damage by looking at ways to prevent water entering their homes.