Police intercepted the 20-metre (65-foot) submarine — thought to be the first of its kind captured in Europe — off the northwestern region of Galicia on Saturday.
Two Ecuadorans were arrested as they tried to escape from the submarine, but the third occupant managed to flee from police.
“A Spanish occupant of the submarine was arrested today,” a police spokesman said Friday.
A fourth person “who provided ground support” was also arrested in the northwestern city of Vigo, according to a source close to the investigation.
While traffickers, especially from Colombia, have been caught using submarines to transport cocaine into Mexico and the United States, police said the seizure was “the first time that this system of transporting drugs has been detected in Europe”.
A total of 240 agents took part in the operation, which was carried out in cooperation with police from Britain, Brazil, Portugal and the United States.
It has been estimated that drug cartels have to date built around 1,000 so-called narco submarines.
Galicia's rugged Atlantic coast with hundreds of hidden coves, inlets and desolate beaches has for years been the gateway for illegal drugs into Spain and Europe.
Spain accounted for the second-highest proportion of cocaine seizures in the European Union last year.