Hail and rain destroyed hundreds of millions of euros worth of crops. Farmers in Extremadura near the border with Portugal said fruit harvests like early cherries had been ruined. Over 400 people fled their homes in the town of Alcazar de San Juan as a dike came close to bursting in the normally parched province of Ciudad Real, south of Madrid.
Thunderstorms were set to keep pounding the central grain and wine producing region of Castilla La Mancha until the weekend.
A wetter-than-normal spring had helped to alleviate drought conditions in central and southern Spain. However, as much rain has fallen on the central region's rolling plains in the last few days as in the whole of 2005.
Train services, including links between Madrid and major Mediterranean coast cities, were suspended on Thursday as tracks disappeared under water.
"We can't say when they will restart because it's still raining," a spokesman for the state railway operator Renfe said.
Farm union Asaja reported extensive damage.
"Overflowing rivers have dragged away centuries old olive trees and destroyed hillsides," it said on its Web page.
Grain crops had been doing well thanks to a mild, wet spring and harvesting had been set to start next week in the south. If the ground is too wet that will be delayed.
Over 100,000 hectares (250,000 acres) of crops have been damaged in Castilla La Mancha, the Europa Press news agency quoted the deputy president of the regional government saying.
Asaja put damage in the region at up to 160 million euros.
The meteorological institute predicted more heavy rains and storms on Friday, easing gradually over the weekend.