Construction work coupled with heavy rainfall caused Friday’s Union Station flood and the ensuing commuter chaos, says the City of Toronto.

Last Friday’s deluge marked the second time in three months the same contractor played a role in flooding the station and paralyzing the busy Yonge-University subway line.

The city is in the midst of reconstructing a large sewer as part of a massive Union Station revitalization.

“To enable construction of the new lowered sewer, a section of the existing sewer was removed and pumps put in place in order to install maintenance holes at one of the future connection points,” the release states. “During the heavy rainstorm, sanitary and storm water overflowed from the open section of sewer at this location ...”

The contractor and the project manager are taking steps to avoid a repeat, the city said, including having two more pumps standing by. The exposed sewer is to be capped by Friday.

TTC spokesperson Brad Ross confirmed that EllisDon Construction is doing the work. Its removal of part of the sewer, with pumps standing by, was fully approved, he said, blaming the flooding on heavy rain that overwhelmed the city’s storm sewer system.

“There was a big surge in the system and that exposed sewer was the outlet,” he said.

The city and TTC are still trying to figure out exactly what went wrong, however, he added later, and the investigation is continuing.

The flooding made the station look like a partially drained swimming pool and paralyzed the Yonge-University line between Bloor and Osgoode stations. The TTC put 118 shuttle buses into service to transport thousands of passengers.

GO trains and the 509 streetcar were also disrupted by the stinky-smelling mess, which took 11 hours to clean up.

In early March, an EllisDon crew accidentally hit a water main on the job site, flooding the station with nearly a metre of water at track level.

That halted service between Bloor and Osgoode Station for most of a Saturday.

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City spokeswoman Wynna Brown said Wednesday she did not know if the city plans to take legal action, or some other action, against the contractor to recover costs from the most recent cleanup and transit diversions.

Messages left with EllisDon officials were not returned.