Lightning struck the East Coast Main Line yesterday, bringing chaos to the region's rail network.
Commuters faced long delays after heavy downpours and the lightning strike on the signalling system just outside York caused morning rush-hour hold-ups.
On the Tyne and Wear Metro, services were suspended for half an hour from 10am, with stations at Tyne Dock, Chichester, South Shields and Bede affected, because of flooding on the track.
Elsewhere in the region, drivers were warned to be careful because of localised flooding on the roads.
A spokeswoman for the Press Association weather centre said: "It has been raining heavily today, with the North-East worst affected out of the whole country, although the rain has travelled up from the South, so everyone has had their fair share."
She said she expected showers in the region today(sat), but no heavy downpours.
"But I would still urge drivers to be careful because there will be a lot of spray on the road and a risk of localised flooding, particularly in city centres, if drainage systems aren't clear," she added.
She said rain would continue until at least Tuesday. Network Rail said the lightening strike at York yesterday had knocked out 12 signaling modules, causing severe disruption from around 7am. Trains resumed running at 9am, but hold-ups continued into the morning because of a backlog of services waiting to get through.
Replacement coaches were laid on between York and Doncaster.
The lightning strike followed storms in the area just before the morning rush-hour. No-one was reported hurt.
A GNER spokesman said: "Our trains were affected by delays, but everything was back to normal by the afternoon."
Many other rail operators also run services through the busy junction, including TransPennine Express, Virgin Cross- Country and Northern Rail.
Northumbria Police said they had received numerous reports of localised flooding on the roads, including at Herrington just off the A19, on Alderley Way in Cramlington, Northumberland, and in Alnwick town centre.
"We've had one car crash we've put down solely to the weather," she added. "A Punto came off the A19 towards Durham during the rush-hour. We believe the driver did not account for the weather conditions and he has hit a barrier, but he wasn't injured.
"We would just urge motorists to be careful."