With an area of 7,900 km², Vatnajükull is the second largest ice cap in Europe by volume (about 3,000 km³) and area (after the still larger Severny Island ice cap of Novaya Zemlya, Russia, which is in the extreme northeast of Europe). On 7 June 2008, it became a part of the Vatnajükull National Park.

The average thickness of the ice is 380 m (1,250 ft), with a maximum thickness of 950 m (3,120 ft). Iceland's highest peak, Hvannadalshnúkur (2,109.6 m (6,921 ft)), as part of the Öræfajökull, is in the southern periphery of Vatnajökull, near Skaftafell.

Under the ice cap, as under many of the glaciers of Iceland, there are several volcanoes. Eruptions from these volcanoes have led to the development of large pockets of water beneath the ice, which may burst the weakened ice and cause a glacial lake outburst flood. During the last ice age, numerous volcanic eruptions occurred under Vatnajükull, creating many subglacial eruptions.

In more modern times, the volcanoes continue to erupt beneath the glaciers, resulting in many documented floods. One jökulhlaup in 1934 caused the release of 15 km³ (3.6 cu mi) of water over the course of several days. The volcanic lake Grímsvötn was the source of a large jökulhlaup in 1996. There was also a considerable but short-lived eruption of the volcano under these lakes at the beginning of November 2004. On 21 May 2011 a volcanic eruption started in Grímsvötn in Vatnajökull National Park at around 7 p.m. The plume reached up to 17 kilometres (11 mi).