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Motorists faced delays of more than an hour and a half after highways teams were forced to carry out emergency work at the Dartford Tunnel, following reports of flooding.
Highways England tweeted water was being "pumped away" from the wider right tunnel, which was closed while contractors worked to fix the issue.
The tunnel has been reopened and delays have cleared.
At its worst, there were 90 minute delays approaching the crossing, with congestion stretching back to junction 4 of the anticlockwise carriageway of the M25.
Many other roads nearby were also disrupted.
It is not yet clear whether the structure has sprung a leak.
The smaller left tunnel remained open to traffic travelling between Kent and Essex during the disruption.
The problem also affected traffic joining the M25 on the London bound carriageway of the A2.
At its worst, congestion stretched back to the Strood turn off.
The A296 near Bluewater and A226 in Greenhithe were also suffering from heavy traffic due to the incident.
A Highways England spokesperson said: "We had to close the east bore of the Dartford Tunnel this afternoon for emergency maintenance.
"We are working hard with our contractors to get the tunnel open again as soon as possible."