Hamilton was hardest-hit by the wet weather; 47 mm of rain had fallen by 2 p.m.
Cars stalled on flooded thoroughfares, including Centennial Parkway and Burlington Street. Minor accidents piled up across the city as a result of the poor conditions.
Pearson International Airport had only recorded 12 mm of rain by Tuesday afternoon, but locally higher amounts caused chaos on roads north of Toronto.
In Vaughan, cars were submerged up to their door handles in some low-lying areas.
Local media reported a sinkhole opened up at Bathurst Street and Glengrove Avenue in north Toronto, forcing officials to close Bathurst in both directions.
The heavy rain also knocked out power to neighbourhoods in Markham and Pickering.
The less-than-ideal weather didn't stop Niagara resident Christine Arsenault from completing her swim across Lake Ontario Tuesday.
For Arsenault, a single mother of two, completing the 50-kilometre swim was the fulfillment of a lifelong dream. Arsenault raised funds for a new open water recreation program for low-income children, to be offered through the Welland International Flatwater Centre.
Arsenault was not alone in facing tough weather on her journey -- on Saturday, 17-year-old Rebekah Boscariol completed the grueling swim despite a stormy forecast.
Southern Ontario has dealt with waves of severe weather since the weekend. On Sunday, a line of severe thunderstorms rolled along the Erie shores, prompting a tornado warning in Elgin County. Heavy rain clogged sewers in the Greater Toronto Area.
On Monday, lingering atmospheric instability caused weak funnel clouds to develop over Kitchener.
More storms fired up along a cold front as it crossed the Huron Shores Tuesday evening.
With files from the Canadian Press