Torrential rain on Monday night damaged cars, garages, basements, attics, stores, roads and factories and interrupted railway services, the regional government said in a statement.
Video images showed cars floating in water, or piled up in the streets.
The man's body was found in the early morning hours in the town of Ezprogui in the Navarra region, the government statement said.
The mayor of the nearby town of Tafalla, where a river overflowed its banks, said there had been no warning.
"Nature fired water in cannon shots," Jesus Arrizubieta told a news conference.
"If it had been forecast, a situation where we see the river rising, we could have warned locals in the areas adjoining the river to move their cars, and there could have been less damage. But it happened in the blink of the eye."
The Cidacos river surged from a depth of 11 centimeters (4.3 inches) to over four meters (13 feet) in just a few hours in some spots after Navarra received four times as much rain on Monday as had been forecast, according to the government statement.
Six secondary roads remained closed in Navarra on Tuesday because of the damage caused, police said.
In Pamplona, the capital of Navarra, the downpour caused officials to suspend a bullfight on Monday evening that was part of the city's famous San Fermin festival.