Officers became suspicious during a routine control of vehicles on Thursday night as they were about to board the ferry headed for Plymouth on the south coast of England, police said in a statement.
They then carried out a "detailed" inspection of the car in question and found a man, an Albanian national, in the trunk of the vehicle, the statement added.
Police detained the female driver of the car, a Spanish national from the northern province of Guipuzcoa, and were checking whether the man hiding in her car was a legal resident of Spain.
The authorities stepped up their controls at the port of Santander after police in March found two Albanian men hidden in the trunk of a car that was trying to board a ferry for Britain.
The port of Santander has regular ferry service to Plymouth and Portsmouth in southern England but, unlike in the northern French port of Calais, has not become a focal point for migrants trying to enter Britain.
Thousands of migrants are holed up in makeshift encampments in Calais, with many trying each night to jump onto trucks or trains, or even walk through the undersea tunnel to Britain. Some have been killed in the attempt.