Regional officials said the Guadalquivir and Aguacebas rivers were causing most of the problems, The Local.se reported Wednesday.
The district of Mogon evacuated 180 people while 40 residents of Villafranca de Cordoba were forced to leave their homes.
An emergency plan was put into effect in Ecija in Seville province after several streets in the lower town became impassable.
The Genil River in Palma del Rio flooded farming areas.
Weather forecasters said conditions were expected to improve across Andalusia Wednesday but Cadiz would remain on yellow alert due to strong winds.