A low-pressure system is expected to arrive in the area from the U.S. Midwest on Saturday and will "spread rain across southern Ontario from west to east through the day," the federal agency said in the alert issued on Friday. An isolated thunderstorm is also possible on Saturday.
Heavy northeasterly winds gusting between 50 and 70 kilometres per hour are also forecast for Saturday.
Rain is expected to continue through Sunday afternoon in most areas "and may be heavy at times," the alert goes on. Between 30 and 60 millimetres of rain could fall in the region from Windsor to the Golden Horseshoe, and between 20 and 40 millimetres of rain could fall over central and eastern Ontario.
In a bit of good news for cottagers, areas to the northeast of Georgian Bay could receive less rain.
"This unseasonably strong low pressure is expected to track just south of the Lower Great Lakes into the Northeastern United States by Sunday," the alert says, adding: "This is a track that is quite uncommon during the summer."
The GTA has already been hit with stormy weather this week that disrupted public transit and knocked out power.
After between 30 and 50 mm of rain fell Monday night and into Tuesday morning, some city intersections lacked working street lights for the morning commute. Flooding also disrupted Go Transit service from Richmond Hill to Union Station, and closed some city roads.
Toronto Water told CBC News on Tuesday that it received 54 calls about sewer backups during the storm.