The city of Almería was particularly badly hit by the wet weather, with over 70 incidents reported on Tuesday.
A father and his 10-year-old son were rescued after becoming trapped in their car by rising flood waters.
The water had reached such a level that the man could not open the car doors and was forced to call the police, who found the car floating under a bridge when they arrived on the scene.
Elsewhere in the region, heavy rain caused 25 incidents along the coast of the province of Granada, closing the N-340 motorway.
In the coastal town of Salobreña, schools were closed and 2,000 students were told by the town hall to stay indoors and not brave the storm.
The town of Motril was also badly hit; several streets were flooded damaging shops and homes.
A major cleanup operation was getting underway across the region on Wednesday morning.
Andalusia's regional government activated its emergency plan because of the high risk of flooding acoss the region.
It has been a rainy week across much of the country: in Madrid, a metro passenger recorded a video of the heavy rain pouring into Nuevos Ministerios station from the roof, while another took a picture of a flooded metro entrance.