Flash floods transform streets into rivers of mud and force the closure of metro lines and high-speed rail links.
Helicopters were sent to rescue people who had sought refuge on the roofs of their homes in the central city of Toledo, about 50km (31 miles) southwest of Madrid, on Monday.
Three people died in the countryside around Toledo, where the weather service Aemet registered record rainfall of 90 litres per square metre on Sunday.
Spanish media said a man was found dead by police during a rescue attempt on a road near Bargas, while another man died as rescuers tried to reach him in the tow of Casarrubios del Monte. The third person who died was a 50-year-old man who had been reported as missing. His body was found on Monday afternoon floating in a river near his home in the town of Camarena.
According to Aemet, the weekend storm affected almost the whole country, with the heaviest rains recorded on Sunday in the coastal provinces of Cadiz, Tarragona and Castello.
The sudden downpours on Sunday and Monday transformed streets into rivers of mud that swept away cars and rubbish bins in Madrid, Castilla-La Mancha, Catalonia and Valencia regions.
Hail was also reported in many areas.
Several bridges collapsed in Aldea del Fresno, and torrents of water swept away many cars, AFP news agency reported.
“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.”
Rescuers were also looking for a woman who disappeared near Toledo and an 84-year-old man who was dragged off by streams of water and mud in Villamanta, west of Madrid.
Despite being heavy in some places, the rainfall is expected to wane later on Monday. The National Weather Agency lowered the alert level to yellow from orange and red on Sunday.
Several railway lines were closed in central Madrid on Monday. Still, the service was re-established in most of the city during the morning, and only a few stations near the Manzanares River were still closed around noon, the Metro de Madrid subway operator said in a statement.