Almost 60 years after Hurricane Hazel taught Toronto not to allow homes in ravines, another storm vividly demonstrated the vulnerability of the transportation corridor running up the Don Valley.

In the most dramatic example, a GO Transit train carrying more than 1,000 people was stranded because the rails had disappeared into rising flood waters that brought aboard small wildlife – including a snake – and forced a prolonged rescue involving scores of police.

A basic tenet of railroading is that trains don't proceed if water is hiding the rails. There's a fear of debris, explained Greg Percy, vice-president for GO capital infrastructure, but there's a more serious issue as well.

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"If it destabilizes the ballast that holds the rail then the rail has a chance to move apart, and that's a derailment risk," he said Tuesday.

The Don Valley is the route for key road and rail links that funnel tens of thousands of commuters in and out of the downtown each day.

But on Monday evening the system was overwhelmed after a freak storm hit at the height of rush hour. As well as the train being stranded, the Don Valley Parkway (DVP) had to be closed overnight due to flooding, the second time this year it was shut because it was awash.

As the region mopped up, officials said there was no simple way to protect the corridor from these sorts of extreme weather events, which climatologists say are likely to increase. Both the city and Metrolinx said they are working with the Toronto and Region Conservation Authority in small ways to reduce the impact of flooding. More radical solutions are not on the table.

Mr. Percy said that dredging the Don River or elevating a stretch of the track are both possible solutions, but added that each option poses its own problems and that neither is being actively considered.

Jacqueline White, acting director for Toronto and East York of the city's transportation services division, said that there's not much to be done about the DVP's inherently vulnerable location.

"In terms of being able to prevent the flooding, there's not really anything specific that has been identified at this point," she said. "I mean, basically, we've got a river right beside a road. And once the river gets up past a certain level, it's higher than the road."

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On the rail line running up the valley, the commuter train ran into problems only minutes after leaving Union Station. The previous train had made it through without problems but atypical rain lashing the city, coupled with saturated ground from earlier precipitation, led to rapidly rising waters.

The train's engineer decided it would be unsafe to continue and began the brake-test procedure that must be done before reversing, GO's Mr. Percy explained. But, by the time that was done, the rails behind were covered as well, leaving the engineer without options.

Passengers unhappy to hear the announcement that they would go back to Union were now told that they were indefinitely trapped.

"There was one guy who decided to open the door and swim through and try to get onto the road," said Julia Li, who takes the GO train from Richmond Hill to her job at a downtown bank. "Everyone at that point thought he was kind of crazy for doing that. But you know what? He was one of the smartest guys … I'm guessing he got home all right and would have sat down, ate dinner, watched us on the news. But, yeah, it would've been dangerous."

Scores of people were eventually rescued by Toronto police in a major operation that involved ferrying them to dry land in inflatable boats. The rest walked out after the water gradually receded.

"We knew there was a thunderstorm warning coming, but that's not unusual," said Metrolinx spokeswoman Anne Marie Aikins. "It was really an unpredictable amount of rain."