Homes were left without power and roads were flooded in parts of the South East, while Lenham in Kent saw 42mm of rain in the space of just one hour.
The Met Office said the deluge in the village, which lies between Maidstone and Ashford, came between 11pm on Tuesday and midnight.
Spectacular lightning was captured in the skies over the region, while Kent Police's Roads Policing Unit tweeted that the lightning was "very active”.
Eastbourne in East Sussex is said to have seen about 1,000 lightning strikes in an hour.
Sussex Roads Policing team described it as a "spectacular electrical storm" over East Sussex but warned about "significant flooding" on the A27 and A259 between Lewes and Hastings, adding: "Power cuts also knowing traffic lights out: please take care.”
Ben Williams, 31, who filmed the storm in Ticehurst, East Sussex, said: "It was full-on, pretty much constant flashes of lightning and thunder at its peak. I've not seen a storm like last nights in the UK before.”
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Susan Pilcher said: "It was possibly the most amazing storm I have ever watched. I had seen lightning in the back garden and decided I had to go to Dungeness to watch it as it is so open there.
"I stayed from about 11pm to 1.30am with sheet lightning and fork lightning chasing across the sky and heavy, heavy rain at times. Very exciting.”
Wendy Howard, from Canterbury, said: "My husband and I were standing at my front porch listening as the rumbles got louder and the flashes got more frequent.
Hi! Thunderstorms in the SE to clear. Further thunderstorms will be a daytime risk in central and eastern England. Occasionally heavy rain over other parts of England and Wales will move eastwards, easing later. Sunshine and showers elsewhere: https://t.co/cQSfu1VDbo ^Jennifer pic.twitter.com/S0hIexr9Cj— Met Office (@metoffice) June 19, 2019
"I don't know anyone affected by flooding, everything is great.”
A yellow weather warning is in place for thunderstorms across much of the south-east of England, including East Anglia, until 9pm on Wednesday.
Forecasters say further rain, hail and lightning could bring potential disruption to travel.
"We've had some heavy, thundery showers overnight," said meteorologist Alex Burkill.
"There has been some flooding near Eastbourne and some power cuts.
"We are going to see some further heavy showers heading towards Kent, and south-east parts of the UK will see some heavy thunderstorms through the morning, while isolated ones could develop this afternoon.”
The flood-hit community of Wainfleet in Lincolnshire is within the Met Office's warning area, but forecasters are optimistic the town will escape the worst of the storms on Wednesday.
"A few showers are possible there, but it doesn't look like it's going to bear the brunt of the heavy downpours," Mr Burkill added.
The town has already seen around 225 Olympic-sized swimming pools' worth of water pumped out to sea following severe flooding last week.
Around 350 tonnes of sand and ballast were dropped in the area by RAF Chinook helicopters over the weekend.
On Tuesday, Lincolnshire Police said almost 600 homes remained evacuated as the clean-up operation continued.
Other parts of the country will see a much brighter day on Wednesday, with sunshine expected in Scotland and Northern Ireland.
The rest of England and Wales could see a damp start, before things brighten up later in the day.
The weekend is also set to bring some respite from the recent downpours, with temperatures rising as high as 23C (73F).