The four crew members, all Czech, were arrested and remanded to custody after the raid last Thursday on their vessel about 450 nautical miles (830 km) south-west of Spain's Canary Islands.
The raid netted 599 kg in cocaine.
"The cocaine was in a hermetically sealed container hidden inside one of the boat's water reservoirs," a police statement said.
Spanish media said the boat was coming from South America.
The amount of cocaine seized in Spain rose 28.6 percent last year to 27 tonnes, the interior ministry said Monday.
Spain's proximity to north Africa, a major source of hashish, and its close ties with its former colonies in Latin America, a key cocaine producing region, have made it a major gateway into Europe for drug traffickers.