The fjord is long and narrow, it measures 60 km from mouth to bottom. Its greatest width is 25 km between Siglunes and Gjogurta at the fjord's mouth but for the greater part of its length it is usually 6-10 km wide. Two smaller fjords branch out of Eyjafjordur's west side, Olafsfjordur and Hedinsfjordur.

The fjord is surrounded by hills and mountains on both sides but the mountains are considerably taller on the west side, in the mountain range of the Trollaskagi peninsula. In the outer part of the fjord there are no lowlands along the coast as the steep hills roll directly into the sea. Further south in the fjord there are strips of lowland along both coasts; these are wider on the west side.