Falls of up to 50mm in some parts of the city were reported overnight.
Victoria SES confirmed there had been 99 calls for assistance between 6pm on Saturday and 7am this morning.
About 60 of those were about building damage, and the rest were flooding-related.
But there were no reports of flood rescues being carried out.
The SES also confirmed a landslide had been triggered by the flooding in Pascoe Vale South.
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A minor flood warning is in effect for the Yarra River.
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A “stay informed” warning exists for the Watts River, as well as the Yarra River from Warrandyte to Abbotsford.
The Bureau of Meteorology has forecast a high chance of rain again today, but said showers should be easing.