The A1(M) was closed for hours while local routes were shut and cars deserted after floodwater made roads impassable.
A stretch of the A1(M) between Newton Aycliffe and Bradbury was closed for most of the day from shortly after 7am when the carriageway became more like a river than a road.
Cars were backed up with delays of more than an hour and some were stuck inside the closed section and not released until after 1.30pm.
Fire crews with pumps helped clear away the rainwater while recovery trucks had to rescue cars from the water.
Motorists reported being stuck in huge queues to pass the area with delays reportedly more than an hour.
It is thought the flooding was caused by the volume of water from nearby fields rather than drainage issues, National Highways said.
The road will be assessed for damage before reopening. In a post on X, formerly Twitter, National Highways said: “Traffic caught within the closures has been released. We’re hoping to be able to re-open the road later this afternoon.”
It caused major disruption for motorists on the main route between Newcastle, Durham, Darlington and the south.
Elsewhere a Mini car was deserted by its driver in deep water on the A68 on the outskirts of Darlington.
Ariel footage showed a huge puddle spanning the road and neighbouring field with cars backed up.
The road was closed near the farmers’ mart with queues of traffic heading west being turned around.Staindrop Road, just after Edgecombe Drive in Darlington, was closed as the beck had burst its banks while Cocker Beck in The Denes was close to overflowing earlier on Wednesday.
A Darlington Council spokesperson said: “We are working closely with the emergency services and other partners to deal with the flooding issue.
“We have closed a number of roads and our Street Scene teams have been out at various locations since the early hours to help reduce the water levels.
“The problems are mainly due to the high levels of rainfall, becks flooding and water running off fields, rather than blocked gullies.”
Motorists were urged to drive with care and plan extra time for journeys.
The Met Office issued a yellow weather warning for rain on Wednesday morning which was in place until 3pm across Darlington, Durham, Teesside and North Yorkshire.
Flood alerts were issued by the Environment Agency for areas including the Tees, River Gaunless and Middlesbrough Becks due to high water levels.
Anthea Smith from Durham County Council said: “Following heavy rain overnight on Tuesday, teams from across the council have been responding to reports of localised flooding on highways and dealing with blocked gullies. We are also responding to requests for sandbags where needed.”
There was disruption to train services between Darlington and Bishop Auckland due to flooding on the line.
In South Shields the A194 was closed for several hours due to flooding between Hobson Way and Tyne Dock. The road reopened shortly before 1.45pm.
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On Tuesday evening, Blyth and Ashington MP Ian Lavery warned parts of Northumberland were experiencing “severe flooding” amid “extreme conditions”.
Mr Lavery said his office had “taken numerous calls about the serious flooding” in his constituency. County Councillor Scott Dickinson said roads had been closed near Blyth and fire and rescue service crews were at the scene. Flooding caused issues on the A189 Spine Road between the Three Horse Shoes roundabout and Bebside on Wednesday morning, while the adjacent Shankhouse to High Pit road in Cramlington was also closed.
Flooding hit in Grangetown in Sunderland where thundery showers turned roads into rivers and locals tried to clear drains blocked with leaves.
The Met Office said it is set to be drier and brighter on Thursday (October 10) with some isolated showers, but rainfall will be less than the last two days.