The weather agency issued a special weather statement projecting isolated thunderstorms in southern Ontario and a general rainfall for eastern Ontario regions.
Flooding was reported on some city streets, including on Lakeshore Boulevard.
Go Transit issued an email alert reporting some access restrictions to Union Station due to flooding.
"With Mother Nature not on our side this afternoon we have some flooding inside Union Station which will make for a challenging commute this evening," the email said.
Go Transit said that some escalators were out of service and that there was no elevator access to platforms 4 and 5. A stairway leading from those platforms to the York Street West Teamway was also closed.
Passengers were also told that the VIA Concourse walkway, which can be used to access platforms 8 and 9, has been closed.
A moist air mass and an upper disturbance over southern Ontario was forecast to produce heavy downpours while showers moving in from New York were expected in eastern Ontario.
Drivers are reminded to exercise caution on the roads, as thunderstorms can create slippery conditions and low visibility. Keep checking the Environment Canada Weather Office for updates as the agency continues to monitor the situation.