According to officials, one man and a woman in a auto drowned after a river burst close to Malaga in the south, while two homeless people froze to death in Madrid and Calatayud in the east.
Interior Minister Fernando Grande-Marlaska said the situation on the roads was improving but was still "extraordinary" and many remained closed.
In Madrid, authorities activated a red alert for the first time since the system was adopted four decades ago and called in the military to rescue people from vehicles trapped on everything from small roads to the city's main thoroughfares.
The blizzard dumped over 50 centimeters (20 inches) of snow in some areas and a cold front was turning mounds of fluffy white into sheets of ice and crusted drifts.
"I have been stuck here without water or any other help", she told local television RTVE.
Patricia Manzanares had been trapped in her vehicle on a Madrid motorway since 7pm on Friday.
A few fearless people headed out with their ski gear in the Spanish capital.
People walk through snow at Sol Square in central Madrid
Some 500 people across the Madrid region were forced to spend the night in temporary shelter, including sports centres, after they were trapped by the whiteout. "But we feared running out of certain food that some patients needed", she recounted, adding that the situation in intensive care units with COVID-19 patients was even more hard for her colleagues.
"For security, operations at the Adolfo Suarez Madrid-Barajas Airport have been halted until visibility improves", Spain's airport operator AENA said in a tweet late Friday, adding that workers were frantically trying to clear taking off and landing tracks. "We ask for patience, we will reach you all", he said.
According to the government, traffic remained disrupted on more than 700 routes as of Sunday afternoon as trains to or from Madrid slowly resumed circulation, with the exception of links with the north-eastern quarter, including Barcelona.
Residents of Madrid roll a giant snowball on January 9.
The wintry weather also threatened to interfere with soccer games involving the top teams in La Liga.
Castilla-La Mancha and Madrid's regions, home to 8.6 million people, announced that schools would be closed on Monday and Tuesday.
Snowstorms in Spain left three people dead and caused chaos across much of the country, trapping motorists and shutting down the capital's air and rail links, with more expected. Saturday's match between Spanish league leader Atletico Madrid and Athletic Bilbao was postponed after the plane carrying Bilbao's team on Friday was unable to land in the capital and had to turn around.
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