“We’ve seen multiple thunderstorms hitting those same areas,” Mr Carlyon said.
The latest downpour capped off a busy two days for SES units across the state.
From 2.20pm Sunday to 6.40pm Monday, crews had attended 1897 calls for help.
The Malvern unit was inundated with 804 requests, while the Manningham unit was also kept busy with 338.
There were 1306 requests for assistance for incidents of building damage, 211 for flooding and 150 for traffic hazards.
At peak hour on Monday the Sandringham line was suspended with buses replacing trains between Elsternwick and Sandringham due to flooding over the lines at North Brighton. There were major delays too on the Williamstown line.
Minor delays were also recorded on the Sunbury line (due to an ill passenger) as well as the Alamein and Belgave lines. Trains are suspended between Dandenong and Pakenham due to an earlier fatality.
Metro Trains warned that the buses it had ordered may take over an hour to arrive to retrieve sodden commuters.
The BOM also warned there could be flash flooding and hail in regional areas including Mildura, Swan Hill, Bendigo, Echuca, Seymour, Castlemaine, Morwell, Traralgon, Sale, Moe, Bairnsdale and Orbost.
It said a severe thunderstorm over Mount Moornapa, West Gippsland, dropped 51mm of rain in an hour earlier in the afternoon, with 61mm recorded since 9am.
“Be aware that in fire-affected areas, rainfall runoff into waterways may contain debris such as ash, soil, trees and rocks,” the BOM said in its warning.