Highway tunnels were submerged and cars swept from motorways, as torrents of water led to the closure of roads, railways and airports in the Valencia, Murcia and Andalucia regions.
Hundreds of soldiers, boats and helicopters were deployed to assist the emergency services, as some 3,500 people were evacuated from their homes.
More than 689,000 pupils were affected in Valencia alone as nearly 300 municipalities decided to close schools, AFP reported.
A man who had been missing since leaving his home on foot earlier on Friday was found dead in the village of Redovan in Valencia, and another was found in Granada province after his car was swept off a motorway by a torrent of mud and water.
A third man died in Almeria after trying to drive through a flooded tunnel, unaware that it had been cordoned off. Emergency services were unable to save him but were able to help several others who became trapped in flooded tunnels.
It came after two siblings died on Thursday when their car was swept away by torrential rain.
Spain’s acting interior minister Fernando Grande Marlaska called the floods “a serious tragedy”, and said the railway link between Madrid and Barcelona had been shut. Travellers were stranded as two airports in Murcia and Almeria were closed, as well as Murica’s entire railway service.
“The situation is critical, all the municipality is full of water,” Mario Cervera, mayor of the town of Alcazares, one of the most affected in Murcia, told Spain’s state-run TVE channel.
The record rainfall and gale force winds are part of a slow-moving storm system known locally as a gota fria (cold drop), usually seen in autumn.
This year’s event is being described as the worst since 1987, with the Valencian town Ontinyent experiencing 250mm of rain in 12 hours – 10 times the expected rainfall for September – El Pais reported.
Three small but destructive tornadoes were also triggered by winds of up to 100km per hour in Xábia, Dénia and Guardamar. Spain’s state meteorological agency predicted more tornadoes could follow in Mallorca.
Regions across the country’s southeast remained on red alert on Saturday and local authorities warned people to remain indoors and avoid driving.
The storm is expected to move west towards Portugal, where on Friday the government put the country on alert due to a high risk of wildfires.
Additional reporting by Reuters
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