Business and homes have been hit by the rising waters, while cars have been swept down streets in the town of Elizondo, near Spain's border with France.
Downtown Elizondo on Friday morning.
Other affected locations include Garzarain, Errazu and Arizkun, local daily Diario de Navarra reported.
No one has been injured in the floods but several people were evacuated, according to Spain's Civil Guard police force.
A tweet from the Civil Guard showing the situation in Elizondo.
The floods have been blamed on high rainfall.
They are the latest example of wild weather in Spain in recent times, including an intense hailstorm in Madrid on Thursday.
Feliz navidad!! pic.twitter.com/eNQXJ4f4kf— María Escario (@mariaescariotve) July 3, 2014
On Wednesday evening, a high-speed 'Ave' train also nearly derailed on the line between Alicante and Madrid after intense downpours.
Are you in the area? Let us know what you've seen.