The park consists of three different ecosystems: the southern ranges of the Great Sand Sea including the Silica glass area, the proper Gilf Kebir plateau and the Egyptian portion of the Gabal El Uweinat massif.

The area was settled by a population already at the beginning of the Neolithic area some 9000 years ago during the African humid period, leaving splendid rock paintings and engravings of uncertain age in the wadi Hamra and in the caves of Beasts, Swimmers, Archers and Magharet el Kantara on its southern foothills.

[2] The Gebel Uweinat, situated about 150 km south of the Gilf Kebir and most of which lies in Sudanese and Libyan territories, is another massif important for its abundant rock art.

The presence of humans in the 20th century CE is evidenced by the remains of the Long Range Desert Group WWII-camps such as trucks and an airfield at Eight Bells Hills.

The GKNP contains important desert-adapted flora (trees: Acacia raddiana, shrubs: Zilla spinosa, Fagonia thebaica) and fauna (Barbary Sheep).