The death toll from Spain’s worst natural disaster this century has risen to at least 158 as rescuers uncover horrors in the mud-smothered aftermath while searching for the missing.

Monstrous flash floods left a trail of destruction as walls of water smashed through villages, with the widespread damage recalling the aftermath of a hurricane or tsunami.

Rushing water turned narrow streets into death traps and spawned rivers that tore through homes and businesses, sweeping away cars, people and everything else in its path in the hardest-hit region of Valencia.

The storms spawned a freak tornado in Valencia and a hail storm that punched holes in cars in Andalusia.

More than 1000 soldiers joined emergency workers in the search for bodies and survivors on Thursday (local time).

“Unfortunately, there are dead people inside some vehicles,” Spain’s Transport Minister Óscar Puente said.

Luís Sánchez, a welder, was one of the lucky ones when the storm turned the V-31 highway south of Valencia city into a floating graveyard strewn with hundreds of vehicles.

“I saw bodies floating past. I called out but nothing,” Sánchez said.

“The firefighters took the elderly first, when they could get in. I am from nearby so I tried to help and rescue people. People were crying all over, they were trapped.”

The cleanup begins, but more rain could be on the way. Photo: AAP

Regional authorities said it seemed no one was left stranded on rooftops or in cars in need of rescue after helicopters had saved some 70 people.

“Our priority is to find the victims and the missing so we can help end the suffering of their families,” Spanish Prime Minister Pedro Sánchez said after meeting regional officials and emergency services in Valencia on Thursday, the first of three official days of mourning.

Spain’s Mediterranean coast is used to autumn storms that can cause flooding, but this was the most powerful flash flood in recent memory.

Scientists link it to climate change, which is also behind increasingly high temperatures and droughts in Spain and the heating up of the Mediterranean Sea.

The greatest pain was concentrated in Paiporta, a community of 25,000 next to Valencia city where mayor Maribel Albalat said on Thursday that 62 people had perished.

“[Paiporta] never has floods, we never have this kind of problem. And we found a lot of elderly people in the town centre,” Albalat told national broadcaster RTVE.

“There were also a lot of people who came to get their cars out of their garages … it was a real trap.’

While the most suffering was inflicted on municipalities near the city of Valencia, the storms unleashed their fury over huge swathes of the south and eastern coast of the Iberian peninsula.

Two fatalities were reported in the neighbouring Castilla La Mancha region and one in southern Andalusia.

The regional president for Castilla La Mancha, Emilion García-Page, said that at least one Guardia Civil police officer was among several missing people in the town of Letur.

Homes were left without water as far south-west as Malaga in Andalusia, where a high-speed train derailed on Tuesday night. None of the nearly 300 passengers were hurt.

Piles of vehicles swept up in the floods. Photo: AAP

Greenhouses and farms across southern Spain, known as Europe’s garden for its exported produce, were also ruined by heavy rains and flooding.

Heavy rain continued on Thursday farther north as the Spanish weather agency issued a red alert for counties in Castellón, in the eastern Valencia region, and for Tarragona in Catalonia. An orange alert was issued for south-west Cadiz.

“This storm front is still with us,” the prime minister said.

“Stay home and heed the official recommendation and you will help save lives.”

-with AAP