More heavy bursts of rain are expected overnight in the south-east, delaying a clean-up operation following a day of flash floods.
However, forecasters said the rain tonight and tomorrow morning will "not compare" to the deluge that greeted East Anglia, the South East and London throughout the day.
Homes and streets were flooded in East Anglia, the South East and London and commuters tackled disruptive journeys after rail lines were damaged by the storms.
The hail and thunderstorms, described as a "zombie apocalypse" by one rail company, saw more than half a month's worth of rain fall in an hour in some places.
The Environment Agency said that "recovery operations may be affected" but that flooding is not expected during the next three days "despite some heavy bursts of rain possible in Essex, Kent and Sussex overnight tonight".
Parts of western Scotland and Northern Ireland will also see some rain overnight..
While temperatures will remain warm over the next few days, a second spell of wet weather is expected to arrive on Friday night, forecasters warned.
Gareth Harvey, a forecaster for MeteoGroup, said: "The south-east will see further rain overnight but it will not compare to what we saw throughout today.
"It will start to ease in the morning as it spreads into central England but the next few days will return to being clear with above average temperatures of 27C (81F), although still not quite as warm as we have been used to recently.
"There are suggestions that some fairly unsettled weather will arrive Friday night, in to Saturday morning, with some larger spells of rain affecting much of the country."
Today a lightning strike sparked disruption for rail passengers travelling between Worthing and Hove and Brighton during the morning rush hour, while firefighters rescued people from homes and cars hit by floods.
The lightning hit an electricity sub-station near Hove in Sussex, causing power to the coastal rail route to be cut, a Network Rail (NR) spokeswoman said.
London Fire Brigade rescued two drivers and their passengers from their cars in separate incidents after they became stuck in flood water in north-west London.
Twenty houses were also affected by flood water in Bedford Road, Ruislip, while up to 1ft of water flooded a ground floor flat in Northolt Road, Harrow.
Essex Fire and Rescue Service said it had dealt with 20 incidents in Thaxted, Essex, following flash flooding.
Firefighters rescued five people from three neighbouring houses which were flooded, while a road in the town collapsed from the heavy rainfall, it said.
Morning commuters in Brighton and Hove posted descriptions on Twitter of heavy hail and localised flooding caused by the storms.
Laurence Hill wrote: "Used to be roads. Now rivers of hail. Never seen anything like it."
Brighton station tweeted: "At a stand west coastway #Worthing #Brighton Both ways due to zombie apocalypse."
A Southern Water spokeswoman said: "Torrential rain fell across Sussex this morning which has led to parts of our sewer network becoming overwhelmed by the sheer volume of water entering it.
"We are doing all we can to help customers affected by this."
Brighton and Hove City Council's headquarters were forced to close after the basement flooded due to the heavy rain.
The Met Office had issued a "yellow" warning of rain - meaning there was a "moderate risk" - for East Anglia, the South East and London.
It said 43mm (1.7in) of rain - more than half the average monthly total for England in July - fell in an hour in Great Dunmow, Suffolk, between 4am and 5am.
Meanwhile, 37mm (1.5in) of rain was recorded in an hour in Isfield, Sussex, while 35mm (1.4in) fell in Ardingly, Sussex.
In Northolt, north-west London, 43.4mm (1.7in) of rain fell over a three-hour period this morning and in Santon Downham, Suffolk, 51.2mm (2in) of rain was recorded from 3am to 9am.
The AA said it attended 34 flood-related call outs, mostly around west London and West Sussex.
East Sussex Fire and Rescue Service (ESFRS) said nearly 300 calls were received within a few hours this morning.
A further 60 calls had to be passed to colleagues in Cambridgeshire as the storms swept in, causing a surge in 999 calls.
Des Prichard, ESFRS's chief fire officer, praised the "swift and effective response" of his staff during the deluge.
Defra Minister Dan Rogerson, said: "Being flooded is devastating and I have enormous sympathy for all those affected by the adverse weather conditions today.
"Ministers from across Government are working closely with local authorities, emergency services and the Environment Agency. We are responding to any localised surface water flooding to ensure that areas are protected and those who need help get it.
"These thunderstorms are disruptive but, as always, public safety is our priority so please pay close attention to the advice from emergency services and the Environment Agency."