Victoria has topped its average April rainfall over the past four days.
Melbourne's CBD received 44.4 millimetres while 61mm fell in north-eastern suburban Doncaster.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Gippsland's Latrobe Valley recorded 70mm, with 65mm in nearby Moe.
Senior forecaster at the Bureau of Meteorology Terry Ryan said the Gippsland flood warnings would ease throughout the day as the low pressure system near Wilsons Promontory moved further east.
"The (April) average is around 50mm; if you add the rain we had on Saturday night and a bit on Sunday it would be above that average," Mr Ryan said.
State Emergency Service spokesman Lachlan Quick told ABC radio the SES had 130 call-outs overnight, mainly in Melbourne's east.
