Much of central and eastern Victoria are under an advice warning, although a move-to-higher-ground alert remains for those in Ballan near the Werribee River, upstream of Lerderderg River.
The Bureau of Meteorology said on Saturday heavy rain bursts and potentially damaging winds and storms were also possible in parts of NSW as a band of heavy weather swept the southern states.
There was an watch and act warning, since downgraded, for parts of Geelong on Saturday afternoon.Â
Walking paths and suburban Melbourne roads were flooded on Saturday morning, forcing the cancellation of markets and even Parkrun events.
The Otway Ranges, southwest of Melbourne, and Gippsland were facing 24-hour rain totals up to 90 millimetres, with isolated falls up to 150mm possible in elevated regions.
Six-hourly totals up to 70mm were forecast, with conditions not expected to ease until late Saturday.
Gippsland was also likely to be hard hit, with 24 hour totals between 50 and 80mm likely and isolated falls up to 110mm possible, with conditions easing Sunday morning.
"This is on top of the rain you've already had in the last few days, so I'll say it again, the soils are already saturated," senior meteorologist Angus Hines said.
More than 100mm had already fallen in parts of the Otways, with heavy rain continuing on Saturday afternoon.
"Another 30 to 50mm on top of last night's deluge could certainly fall there," Mr Hines said.
The rain was centred around a low pressure system situated over the Murray River on the NSW-Victorian border.
In NSW, a severe thunderstorm warning was issued for the Illawarra and parts of south coast, central and southern tablelands, the central west slopes and plains.
Locations possibly affected included Orange, Goulburn, Dubbo, Nowra, Bowral and Bathurst.
The severe weather is expected to clear by the end of the weekend.
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