Rescuers located the van in the Bidasoa river in the northern Navarra region on Saturday, a day after the 61-year-old was reported missing after he failed to show up at his job at a factory, a local police spokesman said.
But strong currents and poor visibility prevented them from retrieving his body from the van until Sunday morning, the spokesman added.
A 49-year-old woman died in her car in the Navarra village of Sunbilla on Friday after a landslide that followed two weeks of heavy rains.
The heavy rains which have hit northern Spain were accompanied by the thawing of snow at higher altitudes, which have caused rivers to rise rapidly, engulfing cars and flooding homes.
During a visit to flooded areas on Sunday, the head of the regional government, Maria Chivite, said Navarra needed to improve its flood readiness.
“Navarra will continue to live with floods and we need to be prepared so that when flooding happens, it has the least impact possible,” she told reporters.
Because a warmer atmosphere holds more water, climate change increases the risk and intensity of flooding from extreme rainfall.
Built-up urban areas with poor drainage infrastructure are especially vulnerable to heavy downpours, scientists say.
Spain’s national weather office is forecasting sunshine and warmer weather for Navarra and the rest of northern Spain for the coming days.