Storm Ciara swept across Shropshire on Sunday and high winds lifted a section of the roof above the main pool at the Quarry Pool and Fitness Centre.
Strong winds also blew slates off the roof of Shrewsbury Abbey - leaving a 3ft hole.
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Morning prayers were being said at 8.30am on Sunday when the congregation heard a loud bang as the tiles were torn from the roof and landed in the graveyard.
Reverend Tom Atfield said emergency repairs would be carried out as soon as possible but warned it could take some time.
The Quarry Pool and Fitness Centre was fully shut down today, having been partially closed yesterday when the main pool was shut but the Priory Pool was open.
Contractors were on site today assessing the situation and the entire pool complex was closed to users. Nearby Priory Road was also closed to pedestrians and traffic.
Chris Stanbrook, contract manager for Serco which oversees the operation of the pool, said: "During yesterday’s extremely high winds, damage was caused to the roof of the Quarry Swimming and Fitness Centre.
"In the interests of customer safety, we have closed the centre, while surveyors from Shropshire Council inspect the extent of the damage.
"No customers or members of staff have been injured due to this incident.
"We will keep everyone informed via our website and Facebook page. I would like to take this opportunity to thank Shropshire Council for their prompt assistance on this issue."
A notice on Shropshire Council's website said: "Closed until further notice (parts of roof loose). It's not possible to secure them today due to the weather. Priory Road also cordoned off for public safety as a result."
Dylan Tomlinson from Shrewsbury Canoe Club said: "I am very disappointed that it has taken 12 months since the announcement that the council has got to a state to talk about what's going to happen to the pool. Meanwhile the pool is literally blowing away."
Bernard Wills from the Quarry Pool Forum said: "I have been told that the contractors are not going to be able to do anything until the wind abates.
"They are not prepared to go on the roof until the weather subsides. If the winds get up again there is a possibility that the roof may blow away.
"We are due to be there tomorrow but that is not looking very likely. As I understand it, the pool will be closed for the foreseeable future."
Discussions about the future of the Quarry Pool have been ongoing for a number of years. It was announced last week that Shropshire Council was in favour of two pools in Shrewsbury - one at Sundorne and the other at the current site.
A report concerning the next steps for the pool complex will now be discussed at a meeting of the council's cabinet tomorrow.