The weather advisory was issued after funnel clouds were reported in the Niagara region late this morning, the weather agency said. A waterspout was also reported over Lake Nipissing today.
"Treat any funnel cloud sighting seriously," Environment Canada said Saturday. "Should a funnel cloud develop nearby, prepare to take shelter. These funnel clouds usually appear with little or no warning."
"These types of funnel clouds are generated by weak rotation under rapidly growing clouds or weak thunderstorms. This weak rotation is normally not a danger near the ground. However, there is a chance that this rotation could intensify and become a weak landspout tornado."
Toronto could also be hit with heavy rain this afternoon that could lead to localized flooding.
"Total rainfall amounts will vary significantly, however local amounts of 50 to 100 mm are possible," Environment Canada said.
The weather agency said local rainfall rates of 25 to 50 mm per hour are possible.