Eurostar warned customers traveling from London on Sunday of possible delays after floods forced the cancellation of all Saturday trains.
The first Eurostar train left London St Pancras International just after 8:00 a.m. (08:00 GMT).
Engineers had brought the water in two tunnels in Kent, southern England, under control so that at least one tunnel was usable, it said.
However, Eurostar warned that “some speed restrictions will apply in the morning which may cause delays and stations are expected to be very busy”.
The company operates services from London to Paris, Brussels and Amsterdam.
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It was announced late Saturday that all scheduled trains would run on Sunday after an estimated over 30,000 people were affected by the last-minute cancellations.
Travelers were stuck in mainland Europe while people in St Pancras struggled to find hotel rooms or make alternative travel arrangements.
Some tourists said their New Year holiday plans had been “ruined”.
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A spokesman for HS1, which operates the route between London and the Channel Tunnel, said the flooding was being repaired and “the HS1 line will be operational in the morning”.
“We understand how frustrating this has been for passengers and apologize for the inconvenience caused at such an important time of year.”
The company has not revealed what originally caused the flooding, which began on Friday evening when water filled tunnels near Ebbsfleet International in Kent and blocked the high-speed line.
The spokesman said the cause of the flooding was under investigation, but added that there was no evidence that the cause was caused by a burst pipe feeding the tunnel's fire protection system, as had previously been suggested by a water company.
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Footage taken in the tunnel showed water spraying from a pipe and flooding the tracks.