The hydrothermal chimneys in Eyjafjörður are a unique natural phenomenon. Hydrothermal chimney formations like these are found nowhere else in the world in such shallow water. They are easily accessible by divers for sport or research, research that would otherwise by extremely costly. It was long suspected that hydrothermal activity did occur in subtidal areas in Eyjafjörður. However, the nature and exact location of these areas was unclear and it proved difficult to prove these rumours.

The location of chimneys was first confirmed by depth sounders on the research vessel Bjarni Sæmundsson in 1990. This was the first time large hydrothermal chimneys were found in such shallow waters.

These submarine hydrothermal chimneys later became known as Ystuvíkurstrýtur (Outermost-bay-chimneys), named after a small bay close by. These chimneys are now protected as natural monuments, the first such marine protected area in Icelandic waters. This means that all use of fishing gear or anchor around them is prohibited. Special license is required to collect scientific samples around them. However, diving around them is allowed as long as the chimneys are not damaged.

The Ystuvíkur chimneys are in fact three, located close to the middle of the inner part of Eyjafjörður fjord. The bottom depth around the chimneys is about 65 m (36 fathoms) and the highest of the chimneys reaches about 45 m (25 fathoms) from the bottom. This is also the only chimney that is still hydrothermally active.The geology and microbiology of the chimneys was studied in 1997 and 1998, this was also the first time they were seen, both from a small submersible and by divers. Although these chimneys look in many ways like chimneys in deep sea vents, they are made of smectite clay (the chemical formula of which is (Ca,Na)0.2Mg6Si7.2Al0.8O20(OH)4*nH2O) while deep sea chimneys are made of anhydrite (which is much simpler: CaSO4).

The chimneys are formed from precipitates that form when hot silicone-dioxide rich geothermal water meets the cold magnesium rich seawater. The water from the chimneys is fresh and has been measured at about 72°C (162 F) and pH 10.0.

Until August 2004, Ystuvíkur chimneys were the only confirmed hydrothermal chimneys in shallow waters. Then strange structures were seen on the echo sounder on the geo-survey vessel Baldur during a survey of Eyjafjörður for Akureyri Municipal Water and Power Company and Iceland Geosurvey (Ísor).

These structures are situated about 500 m (0,27 NM) north of the small peninsula Arnarnes (which translates to Eagle Peninsula) and 4 km (2,2 NM) sailing distance from the harbour of the small hamlet of Hjalteyri. A few days after the discovery, a diver went down to confirm that these were hydrothermally active chimneys. In fact, this is a hydrothermally active zone stretching about 750 m (0,4 NM) from 25 m (14 fathoms) to 50 m (27 fathoms) depth.

The Arnarnes chimneys are in some ways different from the previously known Ystuvíkur chimneys close by. While the chimneys of Ystuvíkur are larger, there are no active fissures there. The hydrothermally active area is much larger at Arnarnes and it features many chimneys of various sizes and venting fissuresas opposed to only three very large chimneys.

The Arnarnes chimneys are also at a much shallower depth. The tops of the chimneys are however at similar depths as in Ystuvíkurstrýtur. This is probably due to wave action which breaks the chimneys when they get close to the surface. The area lies approximately in a straight line on a gently sloping plateau. It is difficult to estimate the age of the chimneys but there are indicators that they can grow quite rapidly (many cm per month).

The ecosystem in Arnarnesstrýtur seems more diverse than at Ystuvíkurstrýtur which is probably because the multitudes of chimneys provide a more diverse environment. Hydrozoans, bryozoans, sponges, sea anemones, blue mussels and red algae cover the bottom around the chimneys. Small mobile invertebrates are also abundant there as well as fish. The only bare areas are directly above the venting fluid where it is too hot.

The fish species noted around the vent sites are Atlantic wolffish and butterfish (rock gunnels) hiding in crevasses, male lumpsuckers apparently guarding their nests, and cod, saithe, haddock and redfish of various age classes (from 0-goup and up). All of these species are however common in the fjord. It is quite unclear if the vents provide some unique benefits for the fish.