Coastal areas of Valencia were placed under the highest alert on Wednesday evening, with forecasters warning up to 180mm (7in) of rain could fall there within five hours.
Clean-up efforts in parts of Valencia hardest hit by the October 29 storm are continuing, and there are concerns over what more rain could bring to streets still covered with mud and debris.
In southern Malaga province, streets were flooded while 3,000 people near the Guadalhorce river were moved from their homes as a preventative measure.
Schools across the province were closed, along with many stores. Train services were cancelled between Malaga and Madrid, and between Barcelona and Valencia.
Valencia’s regional government also restricted the use of private vehicles until Thursday in areas hit by the October storm, when tsunami-like floods caused cars to be washed away.
There were no reports of deaths due to the new storms.
Spanish weather forecaster AEMET put Malaga on red alert, saying up to 70mm (3in) of rain had accumulated in an hour. Parts of Tarragona province in the east also faced heavy rain and remained under red alert.
The forecast in Malaga delayed the start of the Billie Jean King Cup tennis finals between Spain and Poland, which was set for Wednesday.
The storm system affecting Spain is caused by warm air that collides with stagnant cold air and forms powerful rain clouds. Experts say that drought and flood cycles are increasing with climate change.
