Helicopters were sent to rescue people who had sought refuge on the roofs of their homes in the Toledo area 50km southwest of Madrid, emergency services said.
The sudden downpour on Sunday and early on Monday transformed streets into rivers of mud that swept away cars and trash bins in Madrid, Castile-La Mancha, Catalonia and Valencia regions.
Hail also fell in many areas.
Three people died in the countryside around the central city of Toledo, where the weather service AEMET registered record rainfall of 90 litres per square metre on Sunday.
One of the victims was a young man who was trapped in a lift that filled up with water while another was inside a vehicle when it got flooded, police said.
The third person who died was a 50-year-old man who had been reported as missing.
His body was found in the afternoon floating in a river near his home in the town of Camarena.
"It just kept raining and we were a little scared but we were indoors so we were safe," said Isabella Stewart, a US missionary living in Toledo as she was taking a bus.
Another Toledo resident, Ruben Gonzalez, said: "I live four blocks away and it was very strong. Everything is flooded. This is crazy."
Later on Monday, AEMET said the cut-off low phenomenon - also known as weatherman's woe - that had caused the downpour was starting to move away from the country.
In the Madrid region, emergency services tackled almost 1200 incidents overnight and firefighters and police were searching for one man in the rural area of Aldea del Fresno, southwest of Madrid, the emergency services said.
The man went missing with his son when their car was dragged into the Alberche River after an avalanche caused by a sudden spate.
"The minor was rescued after he had climbed up a tree," the Madrid emergency service said.
Rescuers were also looking for a woman who disappeared under similar circumstances near Toledo and for an 84-year-old man who was dragged away by streams of water and mud in Villamanta, west of Madrid.
Several roads in the Madrid region were closed as half a dozen bridges were torn down by water overflowing the riverbanks.
The defence ministry said it had deployed army engineers to build a so-called Bailey bridge - a type of portable truss bridge - in Aldea del Fresno to connect the banks after the original bridge was swept away.
Several subway lines were closed in central Madrid early on Monday although the service was re-established in most of the city during the morning, subway operator Metro de Madrid said in a statement.
Some high-speed connections between Madrid and the southern region of Andalusia have resumed but trains were operating at lower-than-normal speeds.
