Water was pictured gushing into London Luton Airport in a video posted to Twitter on Friday.
It followed a period of heavy rain and strong winds that caused disruption across the UK.
Weather warnings were in place for much of the country on Friday and continued into Saturday.
The airport attributed the leak to "a period of unprecedented rainfall" in a tweet and said it had "experienced water damage in a number of locations on the terminal”.
The unseasonal weather, which is forecast to continue over the weekend, meant some festivals have been cancelled in the UK.
Thunderstorms have been predicted across Scotland and Northern Ireland on Saturday and torrential showers could cause flooding as well as road closures.
As many as 1,500 residents in the UK's Whaley Bridge had to be evacuated when heavy rain damaged a nearby dam last week.
While residents have now been given the green light to return home, local police said it had been an "unprecedented crisis".
Elsewhere in Europe, a suspected landspout ripped through Amsterdam on Friday, whipping up debris and water, causing severe damage to trees and buildings, according to local media.
A rare tornado also barreled through the southern Luxembourg town of Petange and tore apart a building's roof.
Read more: Watch: Tornadoes and 'whirlwinds' cause havoc in parts of northern Europe