The phenomenon that brought orange skies to Spain, known locally as "calima", formed after a wave of hot air dropped a vast dust cloud from the Sahara desert across parts of Spain.
The country's air quality index qualified as "extremely unfavourable" - its worst rating - the capital and large parts of the southeast coast.
Spain's weather service described the dust storm from the Sahara as "extraordinary and very intense" while adding that it was unclear if it was the worst episode of its kind on record.
The service forecast that the dust will continue to accumulate through Wednesday and could reach northwards as far as the Netherlands and northwestern Germany.
Many Spaniards awoke to find a layer of red dust covering terraces, streets and cars.
The sky in the capital and other cities had a gritty tinge to them.
Visibility in Madrid and cities like Granada and Leon was reduced to 4km, the weather service said.
Emergency authorities have recommended citizens use face masks if they go outside, and avoid outdoor exercise.
The wave of hot air has also affected the air quality in areas north of Madrid, as far west as in Spain's Canary Islands in the Atlantic Ocean, where these events are more frequent, and in the Balearic Islands in the Mediterranean.
The weather service said that the mass of hot air from Africa, which was brought in by a storm that delivered some much needed rain for drought-hit Spain, has also pushed up temperatures in some areas to 20C.
with reporting from EFE
10°C