Services between London Bridge, Charing Cross and Cannon Street were disrupted this morning - as passengers were soaked waiting for trains.
Train operator Southeastern said there was "severe disruption" on routes to and from Charing Cross and Cannon Street after a "complete loss of signalling" at London Bridge.
There were also cancellations between New Cross and London Bridge station.
Southeastern said London Underground, DLR, London Overground and bus services between Lewisham and central London were all accepting tickets.
The delays came ahead of more works at London Bridge Station over the Christmas period, during which Southeastern will not run services from London Bridge, Cannon Street, Charing Cross and Waterloo East.
Commuters using the DLR to travel to Bank also found their journey disrupted by severe delays during rush hour this morning because of a faulty train.
By 9am, TfL was reporting this had eased to minor delays between Bank and Canary Wharf.
Meanwhile, those who took to the roads didn't have much luck, either. Heavy traffic around Elephant & Castle was causing delays. The Metropolitan Police's Southwark branch tweeted it was "doing our best" to reach calls.
The roundabout has been beset by problems since a change to its layout last week. The area was switched from dual roundabouts to a two-way road system for the first time in 50 years - causing a "human busipede".