Operations at Montreal's Pierre Elliott Trudeau Airport were briefly suspended earlier in the day due to freezing rain.
By mid-afternoon, dozens of flights were still delayed and several more had been cancelled as crews worked to reopen all the runways.
"Conditions are gradually returning to normal and will continue to do so throughout the day," a statement on the airport website said. "Thanks for your understanding."
Meanwhile, a computer software glitch at Toronto's Pearson International Airport saw all its check-in counters malfunction. Instead, passengers were checked in manually by airline staff, resulting in slowdowns.
The Greater Toronto Airports Authority said IT providers were trying to fix the problem.
"If you're flying tonight, confirm flight status with your airline and use web check-in or self serve kiosks to ease the check-in process," the airport tweeted.
The Toronto airport authority and the airlines have additional staff on duty.
The latest hold-up at Pearson follows the cancellation and delays of hundreds of flights, and dozens more in Montreal due to bad weather earlier in the week.
Toronto officials triggered a so-called ground stop early Tuesday, preventing North American flights from landing for more than eight hours.
Thousands of passengers ended up sleeping at the airport that night while mountains of luggage awaiting pickup grew.
Officials said Friday the baggage backlog had since shrunk and the rest of the personal cargo should be reunited with owners this weekend.
The GTAA says it is reviewing its response to the deep freeze, which saw 600 flights cancelled Tuesday and another 400 scuttled Wednesday.
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