Floods swept away cars and debris and forced the evacuation of hundreds of people, including from submerged highways, in the regions of Valencia and Murcia.
Road tunnels in some areas were flooded almost up to the tunnel lighting, and some vehicles were almost fully submerged.
A man died in Almeria on Friday after trying to drive through a flooded tunnel, rescue services said. Two siblings had died on Thursday when torrential rain dragged their car away.
Some affected areas saw record daily rainfall for the month of September.
“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.
Rescue workers were using a helicopter and boats in various areas, he said.
“This man was holding onto a traffic sign… the officer and I jumped to take him out,” one emergency worker told reporters.
Murcia’s airport was closed, while the one in Almeria reopened after being shut for several hours on Friday, Spanish airport operator Aena said.
The torrential rain appeared to be easing but several of the southeastern regions remained on red alert.
Rivers were still at risk of overflowing, including the Segura, which has already flooded the town of Orihuela in Alicante and could flood in the city of Murcia, the local water management authority said.
Acting Prime Minister Pedro Sanchez was due to visit the affected areas on Friday and called on people in a tweet to “reinforce precautions” in case of more flooding.
Authorities have recommended citizens stay at home in the affected areas and avoid using their cars.
Tourists were left stranded in Alicante airport as many flights were delayed or canceled.
“We’ve been in the queue here four or five hours, it’s very difficult to get to the toilet, impossible to get anything to eat,” Haydn Harding, a 78-year old diabetic tourist from Northern Ireland, said at Alicante’s airport.