Workers placed barricades across roads and railway lines, some of which were set ablaze.
The unions are protesting against government plans to reform employment law.
The protest was called by unions in Spain's northern Basque and Navarre regions on the eve of the first nationwide general strike for eight years - one day ahead of the rest of Spain to emphasise the region's separate identity.
The nationwide action on Thursday is expected to paralyse the country.
It has been called the day before a European Union summit in Seville, to cause maximum embarrassment to Prime Minister Jose Maria Aznar.
Wednesday's strike served as a taster of the national protest.
Many shops were closed, and one bus company was reported to have cancelled services after discovering that vehicles had been vandalised.
In the city of Bilbao, picketing workers confronted police. Some newspapers stopped publishing, and broadcasting on the public television channel EITB was hit.
In San Sebastian, workers threw red and yellow paint at buses.
The unions are angry about plans to cut unemployment benefit for people who refuse three job offers within 30km (20 miles) of their homes. Casual farm labourers could also see their benefits cut.
Thursday's action is expected to cause widespread disruption for travellers, only a day after the chaos caused by an air traffic controllers' strike elsewhere in Europe.
The government has used its powers to insist that a certain number of workers must report for duty in key sectors including transport and broadcasting.
The unions tried to challenge the levels, but the Supreme Court found against them.
National airline Iberia says 80% of its flights on Thursday have been cancelled. All long-distance trains have been cancelled by national rail company RENFE. Commuter services are also being sliced.
Unions were ordered by Supreme Court judges on Wednesday to uphold certain essential essential services during Thursday's general strike.