At the mouth of the fjord the depth is 150-200 m and beyond that it increases to the north towards Eyjafjarðaráll which is a canyon that is a continuation of Eyjafjörður. Eyjafjarðaráll cuts into the north Icelandic shelf until it opens to the western part of the Iceland Sea west of the Kolbeinsey Ridge and there the depth has reached 500 m. Eyjafjarðaráll is the largest and deepest of the canyons cutting into the Icelandic shelf. West of it lies Haganes Deep and Skagafjörður Deep but in the east is Grímsey Channel between Grímsey and land. The continental shelf north of Iceland is rather wide, frequently over 100 km.

Off Arnarnesnafir there is about 75 m deep threshold in the fjord and inside of it the depth reaches 110 m just south of Hjalteyri in a deep called Baakkaáll. There is also a threshold between Hrísey and Árskógssandur and its depth is about 30 m. This threshold together with Hrísey, Lönguboða and Hrólfssker split the outer part of Eyjafjörður into two parts. The western part can be looked on as a continuation of Svarfaðardalur while the eastern part is a continuation of Eyjafjörður.

Thick layers of sediments on the bottom of the fjord bear witness to a long story of sedimentation and most of the bottom is covered with clay or sand. The sediments are on the average 150-180 m thick. Thus the bottom of the fjord is relatively flat although the depth increases northwards. Generally the sides of the fjord are rather steep down to the sediments but below that the bottom is flat. There are two shallows in the fjord, Hörgárgrunn and Laufásgrunn which is more extensive. They are formed by the sediments brought to the fjord by the Hörgá and Fnjóská rivers respectively. At the head of the fjord Eyfjarðará river has also produced shallow areas but where it ends the fjord is about 40 m deep at its head or in the Pollurinn as the region inside of Oddeyri is commonly called

Steingrímur Jónsson