The Crater Highlands were created from a series of eight volcanoes that dominated the landscape between 3.6 and 2.5 million years ago when the caldera of Ngorongoro itself was formed. To the north-east, Mount Kerimasi developed and, as it died, Mount Lengai was created. Today, after many centuries of weathering, these mountains sit above the Eastern Rift. There are four peaks above 3,000 m, dominated by open moorland habitat at high altitude. The eastern flanks of the highland block are cloaked in montane forest with Croton spp. dominating the lower areas, Acacia lahai and Albiziagummifera the higher ridges and Cassipoureamalosana in the steep valleys.

At lower elevations there are dry acacia woodlands and open grass plains in the rain-shadow of the mountains. Several important wetlands lie within the site, including Lake Makat on the floor of Ngorongoro Crater, at an altitude of 1,700 m. It is shallow and saline and only dries out occasionally.

Over 500 bird species are known from the site. Falco naumanni is a passage migrant and Circus macrourus occurs on passage and in winter. Acacia woodland holds the largest known population of Agapornisfischeri, Parusfringillinus is resident and there have been recent records of Apaliskaramojae from Acacia drepanolobium woodland in the south-west of the site. Prionopspoliolophusmay occur near Maswa Game Reserve. Gallinago media occurs infrequently on passage. Several wetlands hold important numbers of waterbirds, including Lakes Lagaja (also known as Ndutu) and Masek at the western end of Olduvai Gorge and a lake in the Empakai Crater which seasonally holds huge numbers of Phoenicopterus minor.

This lake is also an important site for both Anascapensis and Oxyuramaccoa both of which are now rare in East Africa. Lake Makat is important for Phoenicopterus minor and Phoenicopterusruber, although there have been no regular counts. Gorigor, a freshwater swamp on the eastern side of the crater floor, holds a heronry (at least Threskiornisaethiopicus and Ardeolaralloides) and several uncommon wetland species including Ralluscaerulescens and Chlidoniashybridus, both of which probably breed. During years of exceptional rainfall both the Olbulbul depression and the Malange basin hold temporary wetlands that support large numbers of breeding birds. A roost of 7,000 Bubulcus ibis was located on the edge of the Olbalbal depression.