Heavy rains flooded Toronto's Union Station, shutting down the station and stranding thousands of passengers in the downtown core during the Friday rush hour.

Fire and other emergency crews responded to the flooding shortly before 1 p.m. after a mixture of rain and sewer water flooded the tracks and prompted officials to shut down power to the key commuter line.

A heavy stench was also reported at Union Station. Officials later said the flooding was due to a storm sewer back up, mixed with fresh water from the rain.

Passengers were stranded on the platform at Union Station for several minutes, and a passenger and a driver were stranded in a streetcar in the tunnel of the Queen's Quay Station at Union Station.

Firefighters carried a number of passengers to safety as the water reached 30 centimetres in some areas of the station.

TTC service to the downtown core was turned back from Osgoode Station to Bloor Station as a result of the flooding.

The closures lasted through the Friday afternoon rush hour.

Commuters waited in the rain and wind, forming long lines to board the packed shuttle buses that would take them to Bloor Street.

By 5 p.m., crews had cleaned up some of the mess, but TTC CEO Andy Byford said there was still a ways to go before the station would be able to open.

Crews had to complete pumping, do electrical testing of elevators, escalators and train tracks, and then get everything cleaned before the station would reopen, Byford said.

"This was foul water, so we have to make sure everything is sanitized and the station is safe to open," he told CP24.

Mayor Rob Ford also toured the damage at the station Friday afternoon, commending Byford and the TTC for a job well done.

"In the amount of a couple hours its amazing how fast Andy (Byford), and these employees, got it cleaned up and rectified," Ford said.

The station finally reopened and full subway service resumed shortly before 11 p.m.

While the subway was closed, both Go Train and Via Rail service from Union Station remained open.

A record amount of rain is expected to drench the Greater Toronto Area Friday.

Environment Canada issued a special weather alert warning that a low pressure system laden with moisture could bring between 30 millimetres and 50 millimetres of rain to the Golden Horseshoe area.

Brisk and gusty winds are also expected to accompany the rain.

And Environment Canada is warning motorists of potentially dangerous driving conditions.

"Motorists should be prepared for occasional low visibility in heavier rain which will make driving conditions difficult," the weather agency said in a release.

CP24 meteorologist Bill Coulter said that if rainfall in the GTA touches the top end of the range predicted by Environment Canada a number of records could be washed away.

If the top end of that range is reached the amount would not only surpass May's total rainfall of 44.4 mm but could also break a June 1 rainfall record of 40.6 mm set in 1947.

"A very wet and windy day is on tap for southern Ontario as a low moves in from the American mid-west, drawing moisture up from the Gulf of Mexico," Coulter said.

The rains are not expected to let up until Monday when Environment Canada is calling for sunny skies.