The main facilities are in the Santurtzi and Zierbena municipalities, approximately 15 km (9.3 mi) west of Bilbao.

In 1511 the Consulate of Bilbao privilege was granted, which allowed the port control over the northern European wool export routes.

During the 19th century extensive iron ore deposites were discovered in the nearby hills, which boosted the area's industrial base.

On top of that, vessels have constantly increased their tonnage and large tankers and freighters could not enter the river anymore and the Santurtzi area became too congested.

The port is served by the Renfe railway, but a new rail connection is needed because the current line is shared by commuter traffic and goes through a densely populated metropolitan area.

A high speed connection is being considered, but Spain's current high-speed network does not support freight traffic.