Three people were trapped in their cars after being submerged in flash floods in south-east London.
Heavy localised rain has also spread further north through England.
London Fire Brigade said it helped one person get out of their car while another two people had managed to escape before firefighters arrived.
Luton Airport warned flash flooding in the local area had hit the power supply to the airport and wider vicinity.
The Environment Agency said 1.4 inches (3.5cm) of rain fell in London in one hour.
The Met Office said the amount was "significant" as it would have normally expected an average of 4.9cm (1.9 inches) of rain to fall across the whole month of June.
Elsewhere, a man and a boy are in a critical condition and a girl is seriously ill after they were struck by lightning in Lisburn, County Antrim, in Northern Ireland.
A spokesman for Luton Airport said the storms had taken out some UK Border Force computer systems.
He added staff were using laptops to process people instead of the usual computers while technicians tried to get the system back online.
The Home Office said that owing to the power interruption, security checks at passport control may take longer than normal but stressed that border security had not been compromised in any way.
Bedfordshire Police said it was currently only able to respond to life-threatening emergencies in Dunstable town centre due to floodwater.
"During this time our routine appointments in Dunstable have been ceased and we are only able to respond to genuine emergencies," the force said.
"We appreciate the public's patience during this time and would like to reassure them that we are working to resolve the issue as soon as possible.
"We are also advising motorists to avoid Dunstable town centre due to a high level of floodwater in both High Street North and South and would ask them to respect any road closure signs that are put in place."
In south London, flash floods hit Mitcham, Croydon and Wallington.
The road near Wallington Station was under two metres (6.5ft) of flood water, the fire brigade said.
Darlington Imoh, one of three drivers rescued, said: "I couldn't open the door because of the force of the water.
"I unwound the window and struggled out and then I was rescued by the fire brigade - that's why I am alive standing here now.
"It is the closest I got to death. Survival was my biggest concern, to survive."
Firefighters were called to London Road in Croydon after lightning struck several buildings.
The brigade said it attended a small fire, however, it was out within 30 minutes.
Trees, billboards and telephone poles were also set on fire by the lightning.
The brigade said the areas were badly affected by the storm between 14:30 and 15:00 BST, when the brigade received about 100 emergency calls.
Between 01:00 and 16:00 on Tuesday, the Met Office recorded 47mm (1.8 inches) of rainfall at Kenley Airfield in Surrey, 29.6mm (1.2inches) in Ravensworth in north Yorkshire and 21.2mm (0.8inches) in Lock Fea in Northern Ireland.
Grahame Madge, forecaster for the Met Office, said the downpours could continue to cause localised flooding, surface water flooding and travel disruption.
"What we have is a situation where we have warm, very moist air coming in from the continent and the heat added to the warm air causes it to rise and sees the development of these showers.
"The intensity of those can be very severe in localised areas - as we have seen in some places like London and Brighton there has been very heavy rainfall."