Heathrow Airport cancelled 20% of flights for two hours this afternoon after heavy rain, thunder, lightning and hail was forecast.
The thundery storms came after Britain enjoyed its hottest day of the year on Friday.
A Heathrow spokeswoman said: "During thunderstorms the number of aircraft that can take off and land each hour is reduced."
Sky News weathers forecasters said heavy thundery showers will continue to spread north and west this evening, with eastern Scotland and north-eastern England having a dull damp start to Sunday morning.
Lightning over the Vale of Belvoir in LeicestershireFlights from Dublin, Madrid and Prague were among those cancelled, according to the airport's website.
In a statement, British Airways said: "The forecast of poor weather has meant that we have agreed with Heathrow Airport and other airlines who use the airport to make some proactive flight cancellations on Saturday afternoon.
"If your flight is cancelled please do not travel to the airport."
Manchester Airport also experienced some delays after a thunderstorm caused an electrical surge that stopped some lifts and baggage systems working.
Lightning over Tilbury DocksThe Environment Agency has warned up to 30mm (1.2in) of rain could fall in an hour.
Almost every county in England and Wales is at "medium" risk of flooding, according to the EA, which has issued 59 flood alerts, warning people to be prepared.
The majority of the warnings are in the Midlands, the South East and the South West.
It will be unsettled again on Sunday with sunny spells and showers, and more heavy downpours and thunderstorms.
There is a 60% chance of a heatwave continuing until tomorrow morning, according to the Met Office.