A water main ruptured on Friday morning causing chaos for commuters as services were suspended.
Thames Water eventually fixed the leak on Sunday but water kept flowing from the saturated ground.
Train operator Govia Thameslink Railway has now confirmed that services are back to normal.
Stuart Cheshire, Passenger Service Director for Thameslink, said: “After four days of disruption we’re pleased to confirm that we will be able to operate to our normal timetable tomorrow (Tuesday).
“This has been incredibly frustrating for everyone and I would like to thank our passengers for their patience as well as railway staff for all their hard work.”
Phil Verster, Network Rail’s managing director LNE & EM added on Monday night: “We have had engineers on site since the weekend, working tirelessly and continuously to pump out over 500,000 litres of water from the Clerkenwell tunnels following the failure of Thames’ water main.
“We will continue to work through the night to ensure that a full service can operate as normal on the Thameslink route tomorrow morning. We would like to thank passengers and GTR for their patience whilst we have dealt with this complex recovery programme.”
Thameslink trains ran a quarter of their normal services in the peak as a result of the flooding.