Train operators are attempting to run a normal service from Northampton and Milton Keynes during today's morning rush hour.
An LNR spokesman said the company is running a normal timetable but there could be some disruption until 8am.
The 6.50pm departure from Northampton was cancelled but later services were departing and arriving on time according to National Rail Enquiries.
Some passengers were stranded in the capital after torrential rain closed lines out of Euston.
Commuters were advised not to attempt to travel home with no trains running between London and Milton Keynes.
Passengers who diverted to use East Midlands Railway trains to Wellingborough were also beset with problems as part of the Midland Mainline also flooded at Belsize Tunnel.
Cars were submerged as roads filled with water after two inches of rain fell on London in an hour.