Footage from the city showed the runway completely submerged as one plane aborted a landing and the few planes left on the tarmac were forced to sludge through several inches of flood water.
Passengers have been advised to check their flight status, as most upcoming departures are either canceled or delayed by at least an hour. Arrivals have also been heavily impacted.
Spain's national weather agency, AEMET, has described the situation as posing “extreme danger due to torrential rain” and issued a clear warning.
They said: “Do not travel unless strictly necessary.” The agency added that conditions could worsen as the day progresses, and more rainfall is expected throughout the region.
On Monday morning, an alert for “extreme and continued rainfall” was sent to people's phones in Barcelona, urging them to avoid any normally dry gorges or canals.
Spanish Transport Minister Óscar Puente suspended all commuter trains in northeast Catalonia, a region with eight million people, on request from civil protection officials while several motorways were closed due to flooding.
Meanwhile in Valencia, the search for bodies continues with hundreds more feared dead.
Civil and military emergency workers are searching shopping centers, garages and underground car parks for more victims of fatal floods in the Valencia region.
Over the weekend Spain's prime minister ordered the country's largest peacetime military deployment, announcing that another 5,000 troops will be rushed in to deal with the flood's devastating aftermath.
Another 2,500 soldiers were sent to the affected areas yesterday.