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Kent commuters are set to get a windfall after the rainfall.
Southeastern has promised to pay double the compensation under its Delay Repay scheme for the troubles suffered by its passengers during the flooding last Thursday.
An announcement today said there had been major flooding, signal failures and a line-side fire on the network.
A statement added: "This closed many of our lines for most of the day, and meant we were unable to offer the level of service we want to provide you and that you rightly expect. For this we are sorry.
"While we cannot change what happened we will be doubling our compensation claimed through our Delay Repay scheme for journeys on June 23."
"We were unable to offer the level of service we want to provide you and that you rightly expect. For this we are sorry" - Southeastern statement
The announcement follows an apology last week for the "significant delays" across the network.
Cannon Street and London Bridge stations were closed for most of the day, but reopened just before 5pm.
A spokesman said on the day: "We would ask passengers to please bear with us. The very heavy torrential rain and thunderstorms have caused a great deal of issues across our network and these have continued throughout the day.
"We would urge people to please leave extra time for their journeys home tonight and check before they travel."
Under the scheme, passengers are entitled to compensation if their journey is delayed by 30 minutes or more.